In-gel Renaturation Research Articles

Organization and genesis of dihydrofolate reductase amplicons in the genome of a methotrexate-resistant Chinese hamster ovary cell line.

We have recently isolated overlapping recombinant cosmids that represent the equivalent of two complete dihydrofolate reductase (dhfr) amplicon types from the methotrexate-resistant Chinese hamster ovary (CHO) cell line CHOC 400. In the work described in this report, we used pulse-field gradient gel electrophoresis to analyze large SfiI restriction fragments arising from the amplified dhfr domains. The junction between the 260-kilobase type I amplicons (which are arranged in head-to-tail configurations in the genome) has been localized, allowing the construction of a linear map of the parental dhfr locus. We also show that the 220-kilobase type II amplicons are arranged as inverted repeat structures in the CHOC 400 genome and arose from the type I sequence relatively early in the amplification process. Our data indicate that there are a number of minor amplicon types in the CHOC 400 cell line that were not detected in previous studies; however, the type II amplicons represent ca. 75% of all the amplicons in the CHOC 400 genome. Both the type I and type II amplicons are shown to be composed entirely of sequences that were present in the parental dhfr locus. Studies of less resistant cell lines show that initial amplicons can be larger than those observed in CHOC 400. Once established, a given amplicon type appears to be relatively stable throughout subsequent amplification steps. We also present a modification of an in-gel renaturation method that gives a relatively complete picture of the size and variability of amplicons in the genome.

Organization and genesis of dihydrofolate reductase amplicons in the genome of a methotrexate-resistant Chinese hamster ovary cell line.

We have recently isolated overlapping recombinant cosmids that represent the equivalent of two complete dihydrofolate reductase (dhfr) amplicon types from the methotrexate-resistant Chinese hamster ovary (CHO) cell line CHOC 400. In the work described in this report, we used pulse-field gradient gel electrophoresis to analyze large SfiI restriction fragments arising from the amplified dhfr domains. The junction between the 260-kilobase type I amplicons (which are arranged in head-to-tail configurations in the genome) has been localized, allowing the construction of a linear map of the parental dhfr locus. We also show that the 220-kilobase type II amplicons are arranged as inverted repeat structures in the CHOC 400 genome and arose from the type I sequence relatively early in the amplification process. Our data indicate that there are a number of minor amplicon types in the CHOC 400 cell line that were not detected in previous studies; however, the type II amplicons represent ca. 75% of all the amplicons in the CHOC 400 genome. Both the type I and type II amplicons are shown to be composed entirely of sequences that were present in the parental dhfr locus. Studies of less resistant cell lines show that initial amplicons can be larger than those observed in CHOC 400. Once established, a given amplicon type appears to be relatively stable throughout subsequent amplification steps. We also present a modification of an in-gel renaturation method that gives a relatively complete picture of the size and variability of amplicons in the genome.

Frequent alterations of specific reiterated DNA sequence abundances in human cancer

An in-gel renaturation method allows the visualization, quantitation, and initial characterization of reiterated DNA restriction fragments (RRFs) without prior possession of their probes. Using this method we analyzed EcoRI restricted DNAs from ten human tumors, paired normal tissues from these patients, ten unpaired tumors, and 26 noncancer patients. Frequent qualitative and quantitative differences in the relative radioactive intensities of all or specific RRFs in the DNA from different individuals have been observed. However, we also report frequent two- to ten-fold alterations in the relative radioactive intensities of several specific RRFs in tumor-control analyses of DNA from the same individual. A 0.65-kb alphoid-like DNA RRF was decreased in six tumors and increased in none. Moreover, a new 1.55-kb RRF was observed in two colon cancer DNAs. Several new RRFs, suggestive of gene amplification, were detected in a neuroblastoma, two of which were also seen in a glioma. These data support frequent qualitative and quantitative alterations of specific reiterated DNA sequences in human cancer when compared with paired controls. This approach will allow the future characterization of specific DNA sequences whose patterns of altered reiteration suggest a role in the emergence of specific malignancies.

Detection of amplified sequences in mammalian DNA by in-gel renaturation and SINE hybridization.

The presence of amplified sequences in mammalian DNA can be determined by in-gel renaturation of labeled restriction digests of total genomic DNA, provided that such sequences comprise at least 20-30 copies per haploid human or hamster genome or 40-50 copies per mouse genome. To detect amplified DNA in mouse cells at a lower level of amplification, a new procedure has been developed. This procedure combines in-gel DNA renaturation with Southern hybridization using a cloned probe containing a short interspersed repeated element (SINE). Using mouse cell lines containing amplified dihydrofolate reductase (DHFR) or c-Ki-ras genes as a model system, and the cloned B2 repeated sequence as a SINE probe, we have shown that this technique can detect gene amplification at a level as low as 10-15 copies of amplified DNA per haploid mouse genome. In-gel renaturation-SINE hybridization was used to assay for DNA amplification in different tissues and in different mouse strains. No tissue-specific DNA amplification has been detected, but comparison of B2-containing repeated fragments between three inbred mouse lines revealed strain-specific polymorphism.

Amplification of DNA sequences in human multidrug-resistant KB carcinoma cells.

Four KB carcinoma cell lines selected independently for resistance to either colchicine, adriamycin, or vinblastine were studied. All cell lines showed high levels of resistance to the selecting drug and cross-resistance to the other drugs and to actinomycin D. Double-minute chromosomes could be identified on chromosomal spreads of these multidrug-resistant KB cell lines. Amplification of specific DNA sequences was demonstrated by using the technique of in-gel renaturation. All the cell lines share common amplified sequences. There are also amplified sequences that are specific for each cell line. A revertant cell line that has reacquired drug sensitivity has lost its amplified sequences. Specific probes obtained by cloning amplified sequences from the cell line selected in vinblastine recognize amplified sequences in all the resistant lines. The presence of common amplified sequences in these cell lines is strong evidence for the importance of these regions in multiple drug resistance.

IDENTIFICATION AND CLONING OF GENES RESPONSIBLE FOR MULTIPLE DRUG RESISTANCE

A major obstacle in the successful treatment of malignancies is the emergence of drug resistance. We have chosen a Chinese hamster model system to study the gene(s) responsible for multiple drug resistance and the mechanisms by which they arise. To analyze DNA rearrangements, we used adriamycin(ADR)-resistant subclones of V79 cells, 77A and LZ which are resistant to a 5-fold or 3000-fold concentration respectively of ADR relative to V79, and C5, a colchicine-resistant subline of CHO cells which is cross-resistant to a 150-fold concentration of ADR. DNA from these lines was assayed for the presence of amplified sequences by a novel in-gel renaturation technique (I.B. Roninson, Nuc. Acids Res. 11:5413, 1983). Both LZ and C5 cells contain amplified DNA fragments, a subset of which were commonly amplified in these two independently selected lines, thereby suggesting that they contain the gene(s) responsible for a common mechanism of drug-resistance. We have cloned one of the commonly amplified fragments and shown that the degree of amplification of this fragment correlated with the degree of drug resistance. We have also used this fragment as a probe to isolate several phage clones from a genomic library of LZ DNA. Transcription of these clones is being analyzed. We are currently extending these studies to include an analysis of DNA from newly diagnosed and relapsed patients with leukemia.