Evolution and stability of chromosomal DNA coamplified with the CAD gene

Adenovirus-encoding virus-associated RNAs suppress HDGF gene expression to support efficient viral replication

Non-coding small RNAs are involved in many physiological responses including viral life cycles. Adenovirus-encoding small RNAs, known as virus-associated RNAs (VA RNAs), are transcribed throughout the replication process in the host cells, and their transcript levels depend on the copy numbers of the viral genome. Therefore, VA RNAs are abundant in infected cells after genome replication, i.e. during the late phase of viral infection. Their function during the late phase is the inhibition of interferon-inducible protein kinase R (PKR) activity to prevent antiviral responses; recently, mivaRNAs, the microRNAs processed from VA RNAs, have been reported to inhibit cellular gene expression. Although VA RNA transcription starts during the early phase, little is known about its function. The reason may be because much smaller amount of VA RNAs are transcribed during the early phase than the late phase. In this study, we applied replication-deficient adenovirus vectors (AdVs) and novel AdVs lacking VA RNA genes to analyze the expression changes in cellular genes mediated by VA RNAs using microarray analysis. AdVs are suitable to examine the function of VA RNAs during the early phase, since they constitutively express VA RNAs but do not replicate except in 293 cells. We found that the expression level of hepatoma-derived growth factor (HDGF) significantly decreased in response to the VA RNAs under replication-deficient condition, and this suppression was also observed during the early phase under replication-competent conditions. The suppression was independent of mivaRNA-induced downregulation, suggesting that the function of VA RNAs during the early phase differs from that during the late phase. Notably, overexpression of HDGF inhibited AdV growth. This is the first report to show the function, in part, of VA RNAs during the early phase that may be contribute to efficient viral growth.

Efficient Sequential Gene Regulation via FLP- and Cre-Recombinase Using Adenovirus Vector in Mammalian Cells Including Mouse ES Cells

Site-specific recombinase is widely applied for the regulation of gene expression because its regulatory action is strict and efficient. However, each system can mediate regulation of only one gene at a time. Here, we demonstrate efficient "sequential" gene regulation using Cre-and FLP-expressing recombinant adenovirus (rAd) in two different monitor cell lines, for regulation of one gene (OFF-ON-OFF) and for two genes (ON-OFF and OFF-ON, independently). Generally, serial use of Cre-and FLP-expressing rAd tends to cause significant cytotoxicity, but we here described optimum dose of the rAds for serial regulation. We also established an efficient method of rAd infection to mouse ES cell lines after removing feeder cells, showing that this system is useful for removal of FRT-flanked drug-resistance gene cassette from recombinant ES cells prior to introduction of ES cells into blastocytes for chimeric mice production. Because our sequential gene-regulation system offers efficient purpose-gene regulation and strict OFF-regulation, it is potentially valuable for elucidating not only novel gene functions using cDNA microarray analysis but also for "gene switching" in development and regeneration research.

Efficient production of adenovirus vector lacking genes of virus-associated RNAs that disturb cellular RNAi machinery

First-generation adenovirus vectors (FG AdVs) are widely used in basic studies and gene therapy. However, virus-associated (VA) RNAs that act as small-interference RNAs are indeed transcribed from the vector genome. These VA RNAs can trigger the innate immune response. Moreover, VA RNAs are processed to functional viral miRNAs and disturb the expressions of numerous cellular genes. Therefore, VA-deleted AdVs lacking VA RNA genes would be advantageous for basic studies, both in vitro and in vivo. Here, we describe an efficient method of producing VA-deleted AdVs. First, a VA RNA-substituted “pre-vector” lacking the original VA RNA genes but alternatively possessing an intact VA RNA region flanked by a pair of FRTs was constructed. VA-deleted AdVs were efficiently obtained by infecting 293hde12 cells, which highly express FLP, with the pre-vector. The resulting transduction titers of VA-deleted AdVs were sufficient for practical use. Therefore, VA-deleted AdVs may be substitute for current FG AdV.

Copy number of adenoviral vector genome transduced into target cells can be measured using quantitative PCR: application to vector titration

Both transfection and adenovirus vectors are commonly used in studies measuring gene expression. However, the real DNA copy number that is actually transduced into target cells cannot be measured using quantitative PCR because attached DNA present on the cell surface is difficult to distinguish from successfully transduced DNA. Here, we used Cre/loxP system to show that most of the transfected DNA was in fact attached to the cell surface; in contrast, most of the viral vector DNA used to infect the target cells was present inside the cells after the cells were washed according to the conventional infection protocol. We applied this characteristic to adenoviral vector titration. Current methods of vector titration using the growth of 293 cells are influenced by the effect of the expressed gene product as well as the cell conditions and culture techniques. The titration method proposed here indicates the copy numbers introduced to the target cells using a control vector that is infected in parallel (relative vector titer: rVT). Moreover, the new titration method is simple and reliable and may replace the current titration methods of viral vectors.

Amplicons on chromosome 12q13-21 in glioblastoma recurrences

There is limited knowledge on the in vivo behavior of amplified regions in human tumors. First evidence indicates that amplicon structures are largely maintained in recurrent tumors. Here, we investigated the fate of amplified regions in several independent cases of recurrent glioblastoma and the possible association of 12q13-21 amplifications and survival. We analyzed 12q13-21 amplicon numbers and sizes in glioblastoma and their recurrences by array-CGH. The majority of the 12q13-21 amplicons found in the original tumor are lost in the subsequent recurrence. Likewise, the majority of the amplicons found in the first recurrence are lost in the second recurrence. The remaining amplicons of recurrences often expanded or were maintained in size. Because of re-emergences and de novo appearances of amplicons, however, the overall number of amplicons did not decrease in the recurrences. Understanding genetic changes including gene amplifications in the development of tumor recurrences will contribute to rational therapeutic strategies for an improved patient survival. We recognized a significant longer survival time in glioblastoma patients that lack amplifications of either CDK4, CYP27B1, XRCC6BP1 (KUB3), or MDM2.

A different view on DNA amplifications indicates frequent, highly complex, and stable amplicons on 12q13-21 in glioma

To further understand the biological significance of amplifications for glioma development and recurrencies, we characterized amplicon frequency and size in low-grade glioma and amplicon stability in vivo in recurring glioblastoma. We developed a 12q13-21 amplicon-specific genomic microarray and a bioinformatics amplification prediction tool to analyze amplicon frequency, size, and maintenance in 40 glioma samples including 16 glioblastoma, 10 anaplastic astrocytoma, 7 astrocytoma WHO grade 2, and 7 pilocytic astrocytoma. Whereas previous studies reported two amplified subregions, we found a more complex situation with many amplified subregions. Analyzing 40 glioma, we found that all analyzed glioblastoma and the majority of pilocytic astrocytoma, grade 2 astrocytoma, and anaplastic astrocytoma showed at least one amplified subregion, indicating a much higher amplification frequency than previously suggested. Amplifications in low-grade glioma were smaller in size and displayed clearly different distribution patterns than amplifications in glioblastoma. One glioblastoma and its recurrencies revealed an amplified subregion of 5 Mb that was stable for 6 years. Expression analysis of the amplified region revealed 10 overexpressed genes (i.e., KUB3, CTDSP2, CDK4, OS-9, DCTN2, RAB3IP, FRS2, GAS41, MDM2, and RAP1B) that were consistently overexpressed in all cases that carried this amplification. Our data indicate that amplifications on 12q13-21 (a) are more frequent than previously thought and present in low-grade tumors and (b) are maintained as extended regions over long periods of time.

Different genome organization in two new cell lines established from human gastric carcinoma

Two gastric cancer cell lines, AKG and GK2, were established from a pleural and an ascitic effusion, respectively. GK2 cells have a pseudodiploid karyotype with an add(6)(q27) chromosome in all metaphases examined. The karyotype of AKG cells is highly rearranged: FISH analysis with painting probes has shown that DNA sequences derived from single chromosomes are scattered on several (as many as eight) markers. In this cell line, the C-MYC and the K-RAS oncogenes are amplified. The organization and the copy number of the C-MYC-amplified units are different from the K-RAS units, suggesting that the two oncogenes were amplified independently. The presence of a few marker chromosomes carrying both C-MYC and K-RAS could be due to translocation events that followed the amplification.

GNAI3, GNAT2, AMPD2, GSTM are clustered in 120 kb of Chinese hamster chromosome 1q

We studied a polygenic region located on Chromosome (Chr) 1q in Chinese hamster cells that is coamplified along with the AMPD2 gene. Previous sequence analysis identified both members of the GSTM family and the GNAI3 gene within a cloned 120-kb region surrounding the AMPD2 locus. We show here that the GNAT2 gene, which is inactive in the fibroblastic cells, lies within the 20 kb separating the transcriptionally active GNAI3 and AMPD2 genes. We map most gene ends by sequence comparison with human homologs; one is inferred from the presence of an unmethylated CpG island. This Chinese hamster locus corresponds to a region of conserved linkage between human Chr 1 (locus 1p13) and mouse Chr 3 (position 52.5 cM), where Gnai-3 and Gnat-2 have been mapped. The AMPD2 gene is presently unlocalized in human genome; its proposed position on mouse Chr 3 is at 53.4 cM. Our results, obtained by physical mapping, strongly suggest that the order and possibly the tight linkage of these genes are conserved on all three genomes.

Reversion in Chinese hamster lines amplified at the AMPD2 locus: spontaneous and benzamide-stimulated gradual loss of amplified alleles of marker genes

The HC47 and HC474 cell lines of Chinese hamster fibroblasts resist coformycin through the intrachromosomal amplification of the AMP deaminase 2 (AMPD2) gene. Due to the coamplification of a mu glutathione S-transferase (GST) gene, these mutant lines are more sensitive than GMA32 wild-type parental cells to buthionine sulfoximine (BSO), an inhibitor of glutathione biosynthesis. This property was exploited to select revertants of amplification from HC474 cells. Reversion in that line is frequently a gradual process that does not involve extrachromosomal intermediates. The terminal products of this process are commonly cells with a complete deletion of the amplified allele of marker genes and are therefore haploid for these loci on the homologous chromosome. Exposing HC474 cells to benzamide (BA), an inhibitor of polyADP-ribosylation, increased the recovery of revertants to an extent allowing the detection of reverting cells without BSO selection. This effect of BA was used to isolate revertant cells from the HC47 line that is extremely stable and to demonstrate that the mechanism of gradual reversion also occurs in this line. The gradual deletion of amplified copies within the chromosomes suggests that breakage-fusion-bridge (BFB) cycles drive this process.

Amplification of the murine mdr2 gene and a reconsideration of the structure of the murine mdr gene locus

A common feature of cells selected in vitro for the multidrug resistance (MDR) phenotype is the amplification and concomitant overexpression of the mdr genes. In murine macrophage-like J774.2-derived MDR cell lines, there is a good correlation between levels of amplification and expression for the mdr1b gene, but not for the other two gene family members, mdr1a and mdr2. To understand this phenomenon better, a study of the amplification and expression of the mdr2 gene was undertaken. Southern blotting of genomic DNAs from a series of six MDR cell lines revealed that five of these lines had 5'-end amplification of mdr2, whereas only three contained 3'-end amplification. The analysis also suggested the involvement of a recombination hot-spot in this phenomenon. Despite the observation that the ratio between the number of copies of the 5' and 3' ends of the gene differs among cell lines, the ratio of 5' to 3' end transcription of mdr2 was approximately 1 in all cell lines. An analysis of promoter methylation in MDR cell lines demonstrated that this mechanism may play a role in regulating the transcription of mdr2, but not of mdr1b. Long-range mapping of the mdr locus in parental and amplified cell lines suggested that the three mdr genes are oriented in the same direction, and also revealed the presence of a number of rearrangement events. Models for the murine mdr gene locus in wild-type cells and in a cell line containing a rearrangement are presented.

Rapid conversion of rDNA intergenic spacer of diploid mutants of rice derived from gamma-ray irradiated tetraploids

The organization of tandemly repeated sequences of ribosomal DNA (rDNA) in rice mutants derived from gamma-irradiated tetraploids was analyzed. Southern hybridization analysis of nuclear DNA revealed that most of the intergenic spacers (IGSs) in mutant rDNA are replaced concertedly by new molecular species. The new IGSs are produced by the amplification of a subrepeat of about 250 bp. Results obtained from sequence analyses indicate that various intermediate molecular species of the subrepeat were formed during structuring of the IGS region and that many rearrangements occurred between them. These findings demonstrate the effectiveness of recurrent irradiation of tetraploids for inducing artificial genome rearrangement, and also indicate the extreme plasticity and variability of genome structure in plants.

Patterns of DNA amplification at band q13 of chromosome 11 in human breast cancer

In an attempt to verify the nature of amplification events at band q13 on chromosome 11 we surveyed the amplification status of ten molecular markers specific for this region (GSTP, SEA, D11S97, D11S146, BCLI, PRADI/CCNDI, HST/FGF4, INT2/FGF3, EMSI, and DIIS833E) in a panel of 389 primary breast carcinoma DNA samples. Eighty-eight tumors (23%) showed at least one of these markers amplified, but in a majority of the cases amplification encompassed more than one of the tested loci. Our data confirm that amplicons at 11q13 can cover large portions of DNA and are consistent with the existence of several cores of amplification. One important core seems to be, as previously described, centered around PRADI/CCNDI; 57 tumors (14.7%) showed amplification at PRADI/CCNDI either alone (one tumor) or along with amplification of BCLI or INT2/FGF3. The level of amplification of PRADI/CCNDI sometimes exceeded that of surrounding markers. Three additional amplification events occurring independently of amplification of PRADI/CCNDI were also detected. Centromeric to BCLI, probes to DIIS97, and DIIS146 detected amplification in 60 tumors (15.4%) and were often the only amplified markers. Telomeric to INT2/FGF3, DIIS833E was found amplified alone in ten tumors, and it was the most amplified marker in another six cases. At a shorter distance of INT2/FGF3, EMSI was the only amplified marker in two tumors, with a level of amplification that could exceed that of PRADI/CCNDI and DIIS833E. Our data thus suggest the existence of four independent amplified regions within band 11q13 in breast cancer.

Accumulation of anchorage independent cells showing amplified genes (CAD) during the in vitro propagation of CHEF18 Chinese hamster cells

Anchorage independence and gene amplification have frequently been associated with a transformed or tumorigenic phenotype in cultured mammalian cells. However, it is unknown whether these two traits occur as related events during transformation, or are independent features of the transformed phenotype. To clarify this point, immortalized, untransformed CHEF18 Chinese hamster cells were propagated in culture until they became transformed and tumorigenic. The frequencies with which CHEF18 cells formed colonies either in soft agar, in medium containing N-phosphonacetyl-L-aspartate or in the two selective media simultaneously, were determined. The results indicate that anchorage independence and CAD gene amplification spontaneously arose during the propagation of the cells and that their concurrent emergence was not the consequence of independent events. However, the kinetics of their appearance suggests that anchorage independence is the early event whereas gene amplification might represent one of the numerous events which can be dynamically selected in anchorage-independent cells.

Chromosomes bearing amplified genes are a preferential target of chemicals inducing chromosome breakage and aneuploidy

Micronuclei were induced in V79 Chinese hamster cells and in PALA L and MTX M, two derivative cell lines harboring amplified genes, with 1,3-bis(2-chloroethyl)nitrosourea (BCNU) and vinblastine. Spontaneous and induced micronuclei were analyzed for the presence of centromeres by immunofluorescent CREST staining. Micronuclei formed in PALA L cells were also analyzed for the presence of amplified DNA by in situ hybridization with a CAD gene probe. Both cell lines containing amplified genes showed increased micronucleus induction by BCNU and vinblastine. The marker chromosome of PALA L cells was found to be a preferential target for both the clastogenic and the aneugenic action of the two chemicals. DNA amplification seems therefore to be a destabilizing factor of chromosomal structural integrity and mitotic segregation.

Variation of minisatellites in chemically induced mutagenesis and in gene amplification

A mutation assay in cultured mammalian cells was developed based on direct analysis of minisatellite DNA. Chinese hamster cells (V79) were mutagenized with nitrosoguanidine and independent colonies were isolated and expanded. DNA fingerprints were then obtained after digestion with HinfI or HaeIII and hybridization with 33.15 and 33.6 probes (Jeffreys et al., 1985). 12 colonies from untreated cells were also analyzed. Digestion with HaeIII and hybridization with 33.15 probe detected the highest frequency of induced variants. The results suggest that minisatellite sequences are hypermutable sites that can be used to monitor the mutagenic effect of chemical agents. We have also analyzed the DNA fingerprints of 17 independent Chinese hamster (CHO) cell lines carrying amplification of the CAD gene. The DNA fingerprint analysis showed a variation in minisatellite regions in 3 lines while no variation was observed in independent colonies from the CHO parental cell line. The results suggest that these sequences may be hot spots for recombination during gene amplification.

Gene amplification in a human osteosarcoma cell line results in the persistence of the original chromosome and the formation of translocation chromosomes

Although gene amplification, a process that is markedly enhanced in tumor cells, has been studied in many different cell systems, there is still controversy about the mechanism(s) involved in this process. It is still unclear what happens to the DNA sequences that become amplified, whether they remain present at their original location (conservative gene amplification) or whether gene amplification necessarily results in a deletion at the original location (non-conservative gene amplification). We have studied gene amplification in a human osteosarcoma cell line, starting from a cell clone which contains only one copy of a plasmid integrate. Independent amplificants, originating from this clone and containing elevated plasmid copy numbers, were isolated and analyzed. Based on previous observations, encompassing the persistence of single-copy DNA sequences besides amplified DNA sequences clustered at a different location in the independent amplificants, we proposed an amplification pathway including a local duplication step and transposition of the duplicated DNA to other chromosomal positions. Now we have extended our study to more independent amplificants. We prove that the single-copy plasmid-containing chromosomes in the different amplificants and the single-copy plasmid-containing chromosome in the original parental cell clone are indeed identical, namely a translocation chromosome composed of at least three parts of which two originate from chromosomes 14 and 17. We show that the unit of amplification and the unit of the proposed transposition event are at least 1.5 Mb. We also demonstrate that the amplified DNA sequences, present at genomic locations other than the original single-copy DNA sequences, are preferentially associated with chromosome 16. We find that the amplified DNA sequences are often located at or near a site of chromosome translocation involving chromosome 16. In one cell clone we detect the amplified DNA sequences in most of the cells to be located within a complete chromosome 16 while in a minority of cells the amplified sequences are located at or near a breakpoint on a translocation chromosome 16. This indicates that this amplification region is highly unstable and frequently gives rise to translocation events.

Regularities of karyotypic evolution during stepwise amplification of genes determining drug resistance

Analysis of chromosomal alterations during stepwise development of mdr1, dhfr, or CAD gene amplifications in a large number of independently selected Djungarian hamster DM-15 and murine P388 sublines revealed typical patterns of karyotypic evolution, specific for multiplication of each of these genes in each cell type. Some principal similarities of karyotypic evolution were noted in at least two different systems. They include: (i) appearance at the first selection step of a new chromosomal arm bearing the resident gene copy followed at the next selection steps by the formation in these specific chromosomal arms of amplified DNA tandem arrays; (ii) translocations of amplified DNA from its initial site to other, also non-random, chromosomal sites; and (iii) emergence in the cell variants with high degrees of gene amplification of multiple extra-chromosomal elements. The most prominent distinctions among the systems were as follows: (i) different structures, evidently containing amplified DNAs, appeared at the initial steps of amplification of different genes--additional heterogeneously staining regions in specific chromosomal segments in the case of amplification of dhfr or CAD genes in DM-15 cells, and mini-chromosomes in the case of mdr1 gene amplification in both DM-15 and P380 cells; (ii) distinct patterns of location of the amplified mdr1 gene copies are characteristic of Djungarian hamster DM-15 and murine P388 cell derivatives after subsequent steps of selection--at the site of resident gene localization or in some other, also non-random, chromosomal sites in DM-15 sublines, and predominantly extra-chromosomal in P388 sublines. We propose that different mechanisms are responsible for the initial steps of amplification of dhfr and CAD genes on the one hand and the mdr1 gene on the other: non-equal sister-chromatid exchanges and autonomous replication of the extra-chromosomal elements. It seems, however, that both mechanisms may be involved in further rounds of amplification of each of these three genes.

Distinctive chromosomal structures are formed very early in the amplification of CAD genes in Syrian hamster cells

As visualized by in situ hybridization with fluorescence detection, newly amplified CAD genes in 10(5) cell colonies are contained in multiple copies of very large regions of DNA, each tens of megabases long. The extra DNA is usually linked to the short arm of chromosome B9, which retains CAD at its normal site. The widely spaced genes are often interspersed with new G-negative regions. Individual cells within a clone have highly variable numbers of CAD genes (range 2-15). When resistant clones are examined later, at the 10(15) cell stage, the amplified genes are usually found in much more condensed structures. We propose that, in the initial event of CAD gene amplification, much of the short arm is transferred from one B9 chromosome to another. In subsequent cell cycles this initial duplication expands rapidly through unequal but homologous sister chromatid exchanges. Relatively rare secondary events lead to more condensed structures.

Cytogenetic analysis of amplification and deamplification of UMP synthase genes in Chinese hamster cells

Chinese hamster lung cells selected for resistance to pyrazofurin and 6-azauridine contain amplified UMP synthase genes. With selection in 5-fluorouracil, cells that have lost the amplified gene copies can be isolated. Reselection of deamplified cells in pyrazofurin and 6-azauridine results in reamplification of the UMP synthase genes. We have used chromosomal banding and in situ hybridization techniques to characterize this cyclic process of amplification and deamplification. Homogeneously staining regions (HSRs) were observed in cells containing amplified copies of the UMP synthase gene but not in cells in which the amplified UMP synthase genes had been lost. After reselection in pyrazofurin and 6-azauridine, abnormally banded regions (ABRs) were observed. Both HSRs and ABRs were located at a single site on the distal regions of a small acrocentric autosome, and both were shown to contain the amplified genes. The majority of 5-fluorouracil-selected cells showed residual marker acrocentric chromosomes of various sizes, suggesting excision of portions of the HSR or ABR as the mechanism of deamplification. The acrocentrics carrying the amplified genes resulted from rearrangements involving chromosome 4, site of the endogenous gene. This reversible selection system provides a unique model for investigating gene amplification and deamplification in association with chromosomal rearrangements and the relationship of G-banding to underlying DNA structure.