William H. Lewis

A fine-structure deletion map of human chromosome 11p: analysis of J1 series hybrids

Deletion analysis offers a powerful alternative to linkage and karyotypic approaches for human chromosome mapping. A panel of deletion hybrids has been derived by mutagenizing J1, a hamster cell line that stably retains chromosome 11 as its only human DNA, and selecting for loss of MIC1,a surface antigen encoded by a gene in band 11p13. A unique, self-consistent map was constructed by analyzing the pattern of marker segregation in 22 derivative cells lines; these carry overlapping deletions of 11p13, but selectively retain a segment near the 11p telomere. The map orders 35 breakpoints and 36 genetic markers, including 3 antigens, 2 isozymes, 12 cloned genes, and 19 anonymous DNA probes. The deletions span the entire short arm, dividing it into more than 20 segments and define a set of reagents that can be used to rapidly locate any newly identified marker on 11p, with greatest resolution in the region surrounding MIC1.The approach we demonstrate can be applied to map any mammalian chromosome. To test the gene order, we examined somatic cell hybrids from five patients, whose reciprocal translocations bisect band 11p13; these include two translocations associated with familial aniridia and two with acute T-cell leukemia. In each patient, the markers segregate in telomeric and centromeric groups as predicted by the deletion map. These data locate the aniridia gene (AN2)and a recurrent T-cell leukemia breakpoint (TCL2)in the marker sequence, on opposite sides of MIC1.To provide additional support, we have characterized the dosage of DNA markers in a patient with Beckwith-Wiedemann syndrome and an 11p15-11pter duplication. Our findings suggest the following gene order: TEL-(HRAS1, MER2, CTSD, TH/INS/IGF2, H19, D11S32)-(RRM1, D11S1, D11S25, D11S26)-D11S12-(HBBC, D11S30)-D11S20-(PTH, CALC)-(LDHA, SAA, TRPH, D11S18, D11S21)-D11S31-D11S17-HBVS1-(FSHB, D11S16)-AN2-MIC1-TCL2-ΔJ-CAT-MIC4-D11S9-D11S14-ACP2-(D11S33, 14L)-CEN.We have used the deletion map to show the distribution on 11p of two centromeric repetitive elements and the low-order interspersed repeat A36Fc.Finally, we provide evidence for an allelic segregation event in the hamster genome that underlies the stability of chromosome 11 in J1. The deletion map provides a basis to position hereditary disease loci on 11p, to distinguish the pattern of recessive mutations in different forms of cancer and, since many of these genes have been mapped in other mammalian species, to study the evolution of a conserved syntenic group.

Parameters Governing the Transfer of the Genes for Thymidine Kinase and Dihydrofolate Reductase into Mouse Cells Using Metaphase Chromosomes or DNA

The conditions necessary to achieve high frequency transfer of the thymidine kinase and dihydrofolate reductase genes from hamster cells into mouse cells were investigated. Of the parameters examined, the length of adsorption time, input gene dosage, and treatment with dimethylsulfoxide (DMSO) were found to significantly alter the transfer frequency using either metaphase chromosomes or purified DNA as the transfer vehicle. With the mouse cell line as a recipient, the optimal adsorption period for DNA or chromosomes from MtxRIII cells was found to vary from 8 to 16 h in those experiments where the recipient cells were subsequently treated with DMSO. Without DMSO, similar frequencies could be obtained by extending the period of adsorption. Increasing the dosage of DNA or chromosomes resulted in an almost linear increase in the number of transformants. The optimal conditions for transfer did not significantly differ for the two genes studied. On the average, the optimal conditions yielded 1.5×103 transformants per 107 recipient cells with chromosomes; with DNA an average of only 60 transformants were observed. In general, DNA transformants grown in the absence of methotrexate were unstable; whereas, under the same conditions about 20% of the transformants from the chromosome experiments were stable.

Homozygous deletion of a DNA marker from chromosome 11p13 in sporadic Wilms tumor

A random DNA fragment, probe p2.3 (locus D11S87), was cloned from the 11p13 region between a translocation breakpoint associated with familial aniridia and another translocation breakpoint associated with childhood T-cell leukemia. The D11S87 locus maps between the catalase (CAT) locus and the beta subunit of follicle stimulating hormone (FSHB). The D11S87 locus is deleted in a Wilms tumor patient with a constitutional deletion of 11p and in a case of sporadic Wilms tumor (WiT-13) apparently with normal karyotype. In the WiT-13 tumor both maternal and paternal chromosomes 11 are retained; D11S87 is deleted homozygously and FSHB hemizygously. These results suggest two mutational events resulting in homozygous deletion in this patient. The D11S87 homozygous deletion was also demonstrated in WiT-13 nude mouse heterotransplants and in fibroblast-like cell line derived from the primary tumor. The minimum size of the deletion was estimated to be 30 kb as determined by cosmid screening and hybridization. As homozygous deletions in the 11p13 region have not been previously reported for sporadic Wilms tumors, these findings place the D11S87 locus within or approximate to the Wilms tumor gene.

Ribonucleotide reductase M2 subunit sequences mapped to four different chromosomal sites in humans and mice: Functional locus identified by its amplification in hydroxyurea-resistant cell lines

The sites of sequences homologous to a murine cDNA for ribonucleotide reductase (RR) subunit M2 were determined on human and murine chromosomes by Southern blot analysis of interspecies somatic cell hybrid lines and by in situ hybridization. In the human genome, four chromosomal sites carrying RRM2-related sequences were identified at 1p31----p33, 1q21----q23, 2p24----p25, and Xp11----p21. In the mouse, M2 sequences were found on chromosomes 4, 7, 12, and 13 by somatic cell hybrid studies. By Southern analysis of human hydroxyurea-resistant cells that overproduce M2 because of gene amplification, we have identified the amplified restriction fragments as those that map to chromosome 2. To further confirm the site of the functional RRM2 locus, two other cDNA clones, p5-8 and S7 (coding for ornithine decarboxylase; ODC), which are coamplified with RRM2 sequences in human and rodent hydroxyurea-resistant cell lines, were mapped by Southern and in situ hybridization. Their chromosomal map positions coincided with the region of human chromosome 2 (p24----p25) that also contains one of the four RRM2-like sequences. Since this RRM2 sequence and p5-8 and ODC are most likely part of the same amplification unit, the RRM2 structural gene can be assigned to human chromosome 2p24----p25. This region is homologous to a region of mouse chromosome 12 that also carries one of numerous ODC-like sequences. In an RRM2-overproducing mouse cell line, we found amplification of the chromosome 12-specific restriction fragments. Thus, we conclude that mouse chromosome 12 carries the functional locus for RRM2.

Molecular analysis of gene deletion in aniridia-Wilms tumor association

SummaryHybrid clones were produced from the fusion of Chinese hamster cells and human fibroblasts from a patient with the aniridia-Wilms tumor association (AWTA). The DNA from the parental cells and the hybrid clones was screened by Southern blot and DNA hybridization with probes for the human insulin and Ha-ras-1 genes. Two alleles for the Ha-ras-1 gene were shown to exist in the AWTA cells by restriction fragment length polymorphism. One hybrid clone, containing a single allele for Ha-ras-1 was shown to contain a single chromosome 11 with a cytogenetically visible deletion at 11p13. The DNA from this hybrid contained the human genes for insulin, Aγ, Gγ, Ha-ras-1, and calcitonin, but lacked any human sequences homologous to a human catalase cDNA. This clone was also shown to express human lactate dehydrogenase A (LDH A) activity. These data indicate that the deletion of the affected chromosome in this AWTA patient begins distal to LDH A and includes band 11p13, but does not extend to calcitonin or other genes thought to be located in the distal half of chromosome 11p.

Gene for M1 Subunit of Ribonucleotide Reductase Is Amplified in Hydroxyurea-Resistant Hamster Cells

The hydroxyurea-resistant Chinese hamster cell line 600H has been shown to have greatly elevated quantities of ribonucleotide reductase. This increase in enzyme activity is due to an increased level of both the M1 and M2 subunit activities. The M1 subunit has been purified from the 600H cell line and shown to consist of a series of six protein spots with apparent molecular weights of 88,000 daltons, but with varying isoelectric points in the range of pH 6.5–7.0. Western blot analyses with antisera against the M1 and M2 proteins indicated that both subunit proteins are present in elevated quantities in the 600H cell line when compared to the wild-type V79 cell line. Southern blot analyses with genomic DNA from the series of stepwise-selected hydroxyurea-resistant cell lines leading to 600H showed that, in latter steps of selection, genomic sequences homologous to a mouse M1 cDNA have undergone a fivefold amplication. This was accompanied by a four-to eightfold increase in the single M1 homologous mRNA.

Gene order on the short arm of human chromosome 11: regional assignment of the LDH A gene distal to catalase in two translocations.

SummaryLeukemic cells with reciprocal translocations involving 11p13 and 14q13 were obtained from two patients with T-cell acute lymphoblastic leukemia and fused with mouse Ltk- cells. DNA from independent hybrid clones was screened by Southern blot and hybridization to molecular probes for the human catalase and Ha-ras-1 genes. Several clones showed segregation of these two genes, indicating the presence of either the der 11 or der 14 human chromosomes. When DNA from these hybrid clones was examined for the presence of the human genes for calcitonin and γ-globin, both genes were found to segregate with the Ha-ras-1 gene and the der14 chromosome indicating that they lie distal to catalase. When the hybrid clones were examined for the presence of human lactate dehydrogenase A (LDH A) activity, only those clones containing the der14 chromosome expressed activity indicating that the LDH A gene is also distal to catalase on the short arm of chromosome 11.

Establishment of mouse cell lines homozygous for temperature-sensitive mutation in catalase gene

Contact-inhibited and -transformed fibroblast cell lines have been established from the homozygous C3H/Csb mutant mouse. These cell lines have low levels of a temperature-sensitive catalase enzyme activity. When compared to wild-type C3H cells, the catalase-deficient cells are markedly more sensitive to the toxicity of hydrogen peroxide. Furthermore, this cellular sensitivity to external hydrogen peroxide is temperature sensitive. These cell lines will be of use in the study of the role which catalase plays in the intracellular prevention of transformation induced by oxidative stress.

Human Ia molecules carrying MT1 determinants: Purification with a monoclonal antibody

A monoclonal antibody 77.34, reactive with polymorphic HLA class II molecules, was produced. The allotype specificity of this IgG2a antibody was analyzed by cytotoxicity, flow cytometry, and cellular radioimmunoassay. Cytotoxic reactivity on a panel of B cells from 88 unrelated individuals was concordant with the MT1 (DC1) allospecificity (r = 0.83). Immunoanalysis by flow cytometry showed that cells from MT1+ homozygous cell lines were reactive, whereas MT2+ and MT3+ homozygous cells were not. A cellular radioimmunoassay performed under saturating conditions indicated that three MT1+ cell lines bound 14-45 X 10(5) molecules of antibody per cell representing 30-40% of the amount detected with monomorphic anti-DR monoclonal antibody 21w4. The subset of molecules bearing the MT1 allospecificity was purified with a 77.34 IgG immunoadsorbent. The purified molecules were antigenically reactive with several antibodies directed at DQw1 molecules but were devoid of reactivity to monomorphic anti-DR antibodies. Two-dimensional gel electrophoresis showed that the alpha subunit is composed of several acidic spots of Mr 32,000 whereas the beta subunit was seen as a single spot of Mr 25,000, corresponding to DQw1 molecules. DR molecules purified by monoclonal antibody affinity were unreactive with 77.34 antibody. All of the 77.34 reactivity was observed with the fractions depleted of DR molecules. Two-dimensional gel analysis showed marked differences between the purified DR and DQw1 molecules. The presence of the MT1 determinant on Ia molecules referred to as the DQw1 molecules and distinct from those bearing the DR epitopes was confirmed on two DR1, MT1 homozygous cell lines. Thus, DQw1 molecules can be purified away from DR1 molecules by affinity chromatography to 77.34 IgG, specifically reactive with the MT1 (DQw1) allospecificity. The binding of 77.34 IgG to MT1+ cells was not inhibited by all monoclonal antibodies reported to be correlated with the MT1 allospecificity suggesting that the latter might be comprised of more than a single epitope.

Chromosome-mediated gene transfer with the Chinese hamster ovary cell line

Using an improved method of chromosome-mediated gene transfer, we have investigated transfer of the codominantly expressed methotrexate-resistant dihydrofolate reductase (MtxRIIIdhfr) gene into Chinese hamster ovary (CHO) cell recipients. The frequency of dhfr gene transfer with CHO cells varied considerably from clone to clone, ranging from 4 X 10(-7) to 5 X 10(-5). Using appropriate cell recipients we were able to test for linkage of several genetic markers available in the CHO cell line. For example, the mutation resulting in the auxotrophic glyB-CHO cell line has been reported by others to be linked to the dhfr gene. However, we could not demonstrate cotransfer of these two markers when glyB- recipient cells were treated with MtxRIII chromosomes and transformant clones were selected for either methotrexate-resistance (MtxR) or glycine prototrophy. We conclude that these two genes are not closely linked in the hamster genome. However, the genes for thymidine kinase (tk) and galactokinase (gk), which are known to be linked in mammalian genomes, were found to cotransfer into CHO recipients with a frequency of about 50%.