Induction of thymidine kinase in enzyme-deficient Chinese hamster cells

Weird Animals, Sex, and Genome Evolution

Making my career in Australia exposed me to the tyranny of distance, but it gave me opportunities to study our unique native fauna. Distantly related animal species present genetic variation that we can use to explore the most fundamental biological structures and processes. I have compared chromosomes and genomes of kangaroos and platypus, tiger snakes and emus, devils (Tasmanian) and dragons (lizards). I particularly love the challenges posed by sex chromosomes, which, apart from determining sex, provide stunning examples of epigenetic control and break all the evolutionary rules that we currently understand. Here I describe some of those amazing animals and the insights on genome structure, function, and evolution they have afforded us. I also describe my sometimes-random walk in science and the factors and people who influenced my direction. Being a woman in science is still not easy, and I hope others will find encouragement and empathy in my story.

Weird mammals provide insights into the evolution of mammalian sex chromosomes and dosage compensation

The deep divergence of mammalian groups 166 and 190 million years ago (MYA) provide genetic variation to explore the evolution of DNA sequence, gene arrangement and regulation of gene expression in mammals. With encouragement from the founder of the field, Mary Lyon, techniques in cytogenetics and molecular biology were progressively adapted to characterize the sex chromosomes of kangaroos and other marsupials, platypus and echidna-and weird rodent species. Comparative gene mapping reveals the process of sex chromosome evolution from their inception 190 MYA (they are autosomal in platypus) to their inevitable end (the Y has disappeared in two rodent lineages). Our X and Y are relatively young, getting their start with the evolution of the sex-determining SRY gene, which triggered progressive degradation of the Y chromosome. Even more recently, sex chromosomes of placental mammals fused with an autosomal region which now makes up most of the Y. Exploration of gene activity patterns over four decades showed that dosage compensation via X-chromosome inactivation is unique to therian mammals, and that this whole chromosome control process is different in marsupials and absent in monotremes and reptiles, and birds. These differences can be exploited to deduce how mammalian sex chromosomes and epigenetic silencing evolved.

Can the L5178Y Tk+/- mouse lymphoma assay detect epigenetic silencing?

The mouse lymphoma L5178Y Tk(+/-) assay is broadly used in toxicology to assess genotoxicity because of its known sensitivity to genotoxicants that act through a variety of mechanisms, which may include epigenetic DNA methylation. This brief article highlights the studies that have contributed to this conjecture and suggests an addition to the experimental design that could identify if the test substance is a potential epimutagen acting via hypermethylation.

2'-Deoxyriboguanylurea, the primary breakdown product of 5-aza-2'-deoxyribocytidine, is a mutagen, an epimutagen, an inhibitor of DNA methyltransferases and an inducer of 5-azacytidine-type fragile sites

5-Aza-2′-deoxycytidine (5azaC-dR) has been employed as an inhibitor of DNA methylation, a chemotherapeutic agent, a clastogen, a mutagen, an inducer of fragile sites and a carcinogen. However, its effects are difficult to quantify because it rapidly breaks down in aqueous solution to the stable compound 2′-deoxyriboguanylurea (GuaUre-dR). Here, we used a phosphoramidite that permits the introduction of GuaUre-dR at defined positions in synthetic oligodeoxynucleotides to demonstrate that it is a potent inhibitor of human DNA methyltransferase 1 (hDNMT1) and the bacterial DNA methyltransferase (M.EcoRII) and that it is a mutagen that can form productive base pairs with either Guanine or Cytosine. Pure GuaUre-dR was found to be an effective demethylating agent and was able to induce 5azaC-dR type fragile sites FRA1J and FRA9E in human cells. Moreover, we report that demethylation associated with C:G → G:C transversion and C:G → T:A transition mutations was observed in human cells exposed to pure GuaUre-dR. The data suggest that most of the effects attributed to 5azaC-dR are exhibited by its stable primary breakdown product.

Reverting cholesterol auxotrophy of NS0 cells by altering epigenetic gene silencing

NS0 is a cholesterol-requiring mouse myeloma cell line widely used in the production of recombinant antibodies. We have previously reported that the deficiency of 17beta-hydroxysteroid dehydrogenase type7 (Hsd17b7) is responsible for the cholesterol auxotrophy of NS0 cells. Here we demonstrate DNA methylation to be the mechanism underlying transcriptional suppression of Hsd17b7 in cholesterol dependent NS0 cells. Analysis of the DNA methylation pattern revealed methylation of the CpG-rich region upstream of the Hsd17b7 transcription start site in NS0 cells. This is in contrast to the unmethylated status of this sequence in a naturally isolated cholesterol independent revertant cell population (NS0_r). This transcriptional repression was relieved after treating cells with the demethylating drug, 5-azacytidine. Drug treatment also gave rise to high frequency cholesterol-independent variants. Characterization of revertants revealed substantially elevated transcript level of 17beta-hydroxysteroid dehydrogenase type7 (Hsd17b7) gene along with hypomethylation of the CpG-rich region. These results affirm that deficiency of Hsd17b7 causes cholesterol dependence of NS0 cells. Furthermore, induction of cholesterol independence by altering DNA methylation pattern alludes to the role of epigenetics in the metabolic adaptation of NS0 cells. With the widespread use of NS0 cells, this finding will have a significant impact on the optimization of recombinant antibody production processes.

Metabolic activation of zebularine, a novel DNA methylation inhibitor, in human bladder carcinoma cells

Zebularine (2(1H)-pyrimidinone riboside, Zeb), a synthetic analogue of cytidine that is a potent inhibitor of cytidine deaminase, has been recently identified as a general inhibitor of DNA methylation. This inhibition of DNA methyltransferase (DNMT) is hypothesized to be mechanism-based and result from formation of a covalent complex between the enzyme and zebularine-substituted DNA. Metabolic activation of Zeb thus requires that it be phosphorylated and incorporated into DNA. We have quantitatively assessed the phosphorylation and DNA incorporation of Zeb in T24 cells using 2-[(14)C]-Zeb in conjunction with gradient anion-exchange HPLC and selected enzymatic and spectroscopic analyses. The corresponding 5'-mono-, di- and triphosphates of Zeb were readily formed in a dose- and time-dependent manner. Two additional Zeb-containing metabolites were tentatively identified as diphosphocholine (Zeb-DP-Chol) and diphosphoethanolamine adducts. Intracellular concentrations of Zeb-TP and Zeb-DP-Chol were similar and greatly exceeded those of other metabolites. DNA incorporation occurred but was surpassed by that of RNA by at least seven-fold. Equivalent levels and similar intracellular metabolic patterns were also observed in the Molt-4 (human T-lymphoblasts) and MC38 (murine colon carcinoma) cell lines. For male BALB/c nu/nu mice implanted s.c. with the EJ6 variant of T24 bladder carcinoma and treated i.p. with 500mg/kg 2-[(14)C]-Zeb, the in vivo phosphorylation pattern of Zeb in tumor tissue examined 24h after drug administration was similar to that observed in vitro. The complex metabolism of Zeb and its limited DNA incorporation suggest that these are the reasons why it is less potent than either 5-azacytidine or 5-aza-2'-deoxycytidine and requires higher doses for equivalent inhibition of DNMT.

Continuous zebularine treatment effectively sustains demethylation in human bladder cancer cells

During tumorigenesis, tumor suppressor and cancer-related genes are commonly silenced by aberrant DNA methylation in their promoter regions. Recently, we reported that zebularine [1-(beta-D-ribofuranosyl)-1,2-dihydropyrimidin-2-one] acts as an inhibitor of DNA methylation and exhibits chemical stability and minimal cytotoxicity both in vitro and in vivo. Here we show that continuous application of zebularine to T24 cells induces and maintains p16 gene expression and sustains demethylation of the 5' region for over 40 days, preventing remethylation. In addition, continuous zebularine treatment effectively and globally demethylated various hypermethylated regions, especially CpG-poor regions. The drug caused a complete depletion of extractable DNA methyltransferase 1 (DNMT1) and partial depletion of DNMT3a and DNMT3b3. Last, sequential treatment with 5-aza-2'-deoxycytidine followed by zebularine hindered the remethylation of the p16 5' region and gene resilencing, suggesting the possible combination use of both drugs as a potential anticancer regimen.

Epigenetically mediated loss of UDP-GlcNAc 2-epimerase/ManNAc kinase expression in hyposialylated cell lines

The bifunctional enzyme UDP-GlcNAc 2-epimerase/ManNAc kinase is the key enzyme in sialic acid biosynthesis. Loss of UDP-GlcNAc 2-epimerase activity results in a hyposialylated phenotype as shown for two human hematopoietic cell lines that lack the specific mRNA. We found that treatment with the DNA methylation inhibitor 5'-aza-2'-deoxycytidine (5-aza-dC) restored the UDP-GlcNAc 2-epimerase/ManNAc kinase mRNA, as well as enzyme activity and cell surface sialylation. Increase of UDP-GlcNAc 2-epimerase activity by 5-aza-dC treatment was also found for a rat Morris hepatoma cell line. These results indicate a regulation of UDP-GlcNAc 2-epimerase/ManNAc kinase expression on the transcriptional level by DNA methylation.

Inhibition of DNA methylation and reactivation of silenced genes by zebularine

BACKGROUND

Gene silencing by abnormal methylation of promoter regions of regulatory genes is commonly associated with cancer. Silenced tumor suppressor genes are obvious targets for reactivation by methylation inhibitors such as 5-azacytidine (5-Aza-CR) and 5-aza-2'-deoxycytidine (5-Aza-CdR). However, both compounds are chemically unstable and toxic and neither can be given orally. We characterized a new demethylating agent, zebularine [1-(beta-D-ribofuranosyl)-1,2-dihydropyrimidin-2-one], which is a chemically stable cytidine analog.

METHODS

We tested the ability of zebularine to reactivate a silenced Neurospora crassa gene using a hygromycin gene reactivation assay. We then analyzed the ability of zebularine to inhibit DNA methylation in C3H 10T1/2 Cl8 (10T1/2) mouse embryo cells as assayed by induction of a myogenic phenotype and in T24 human bladder carcinoma cells, using the methylation-sensitive single nucleotide primer extension (Ms-SNuPE) assay. We also evaluated the effects of zebularine (administered orally or intraperitoneally) on growth of EJ6 human bladder carcinoma cells grown in BALB/c nu/nu mice (five mice per group) and the in vivo reactivation of a methylated p16 gene in these cells. All statistical tests were two-sided.

RESULTS

In N. crassa, zebularine inhibited DNA methylation and reactivated a gene previously silenced by methylation. Zebularine induced the myogenic phenotype in 10T1/2 cells, which is a phenomenon unique to DNA methylation inhibitors. Zebularine reactivated a silenced p16 gene and demethylated its promoter region in T24 bladder carcinoma cells in vitro and in tumors grown in mice. Zebularine was only slightly cytotoxic to T24 cells in vitro (1 mM zebularine for 48 hours decreased plating efficiency by 17% [95% confidence interval (CI) = 12.8% to 21.2%]) and to tumor-bearing mice (average maximal weight change in mice treated with 1000 mg/kg zebularine = 11% [95% CI = 4% to 19%]). Compared with those in control mice, tumor volumes were statistically significantly reduced in mice treated with high-dose zebularine administered by intraperitoneal injection (P<.001) or by oral gavage (P<.001).

CONCLUSIONS

Zebularine is a stable DNA demethylating agent and the first drug in its class able to reactivate an epigenetically silenced gene by oral administration.

Parental 5-methylcytosine methylation patterns are stable upon inter-species hybridization of Xiphophorus (Teleostei: Poeciliidae) fish

Cytosine methylation appears to be established as an important DNA base modification involved in regulation of gene expression but is poorly understood from an evolutionary viewpoint. Xiphophorus progeny from inter-species crosses and backcrosses that are utilized in contemporary tumor induction studies were analyzed for cytosine methylation pattern inheritance using Southern blot analyses. Methylation patterns at CCGG sequences of 411 independent chromosomes in three distinct inter-species crosses were analyzed. In every case the non-recurrent parental methylation pattern remained unaltered for each of the genes studied, once introduced into the recurrent parental genetic background. Through F(1) inter-species hybridization and succeeding meiosises leading to first generation (BC(1)) and second generation (BC(2)) backcross hybrid progeny, we demonstrate that parental species methylation patterns are stable.

DNA methylation and epigenetic inheritance

Mammalian cell lines silence genes at low frequency by the methylation of promoter sequences. These silent genes can be reactivated at high frequency by the demethylating agent 5-azacytidine (5-aza-CR). The inactive and active epigenetic states of such genes are stably inherited. A method for silencing genes is now available. It involves treatment of permeabilized cells with 5-methyl deoxycytidine triphosphate (5-methyl dCTP) which is incorporated into DNA. The methylation of promoter sequences has been confirmed using the bisulfite genomic sequencing procedure. Methylated oligonucleotides homologous to promoter sequences might be used to specifically target and silence given genes, but results so far have not been conclusive. Treatments that silence or reactivate genes by changing DNA methylation can be referred to as epimutagens, as distinct from mutagens that act by changing DNA sequences. The epimutagen 5-aza-CR reactivates genes but has little mutagenic activity, whereas standard mutagens (such as ethyl methane sulfonate and ultraviolet light) have little reactivation activity. Nevertheless, much more information is required about the effects of DNA-damaging agents in changing DNA methylation and gene activity and also about the role of epimutations in tumor progression.

Gilbert's conjecture: the search for DNA (cytosine-5) demethylases and the emergence of new functions for eukaryotic DNA (cytosine-5) methyltransferases

In 1985 Walter Gilbert challenged members of the DNA methylation community assembled at a National Institutes of Health meeting organized by Giulio Cantoni and Ahron Razin with the following words: "The most exciting aspect about the methyl groups on DNA is the thought that they might provide a locally inherited change in a DNA structure. However, for that to be interesting, those changes have to be different in different cells. Furthermore, the alterations in methylation have to be freely imposable and have to be maintained. It is not yet clear that all these properties are true. So I don't think one will find that methylation ever is one of the primary, top-level controls on gene expression."In essence, Gilbert's conjecture, that DNA methylation is not one of the top-level controls on gene expression, assumes that evidence in favor of both of its testable propositions will not be obtained. Evidence for the first proposition, that alterations in methylation status associated with gene-expression states have to be maintained, was already available in 1985 and has been strengthened by a number of very recent experiments. However, the extensive effort to obtain evidence for the second proposition, that alterations in methylation status be freely imposable, has not been successful in its original intent. The effort has, on the other hand, resulted in the emergence of new functions for 5-methylcytosine and the cytosine methyltransferases in eukaryotic DNA repair, recombination and chromosome stability.

Modeling the mouse lymphoma forward mutational assay: the Gene-Tox program database

An SAR model of the induction of mutations at the tk(+/-) locus of L5178Y mouse lymphoma cells (MLA, for mouse lymphoma assay) was derived based upon a re-evaluation of experimental results reported by a Gene-Tox (GT) working group [A.D. Mitchell, A.E. Auletta, D. Clive, P.E. Kirby, M.M. Moore, B.C. Myhr, The L5178Y/tk(+/-) mouse lymphoma specific gene and chromosomal mutation assay. A phase III report of the U.S. Environmental Protection Agency Gene-Tox Program, Mutation Res. 394 (1997) 177-303.]. The predictive performance of the GT MLA SAR model was similar to that of a Salmonella mutagenicity model containing the same number of chemicals. However, the structural determinants (biophores) derived from the GT MLA SAR model include both electrophilic as well as non-electrophilic moieties, suggesting that the induction of mutations in the MLA may occur by both direct interaction with DNA and by non-DNA-related mechanisms. This was confirmed by the observation that the set of biophores associated with MLA overlapped significantly with those associated with phenomena related to loss of heterozygosity, chromosomal rearrangements and aneuploidy. The MLA SAR model derived from the GT data evaluation was significantly more predictive than an SAR model previously derived from MLA data reported by the US National Toxicology Program [B. Henry, S.G. Grant, G. Klopman, H.S. Rosenkranz, Induction of forward mutations at the thymidine kinase locus of mouse lymphoma cells: evidence for electrophilic and non-electrophilic mechanisms, Mutation Res. 397 (1998) 331-335.]. Moreover, the latter model appeared to be more complex than the former, suggesting that the GT induction data was both simpler mechanistically and more homogeneous than that of the NTP.

Detection and cloning of the gene encoding a protein produced by nonpathogenic mutants of Fusarium oxysporum

Treatment of Fusarium oxysporum with 5-azacytidine, a potent inhibitor of DNA methylation, induced nonpathogenic mutants. Analysis of the protein expression pattern by two-dimensional gel electrophoresis revealed a protein that is present in yeast-form cells of the mutants but absent in those of the wild-type strain. N-terminal amino acid analysis indicated that this protein is identical to a region of a polypeptide encoded by a cDNA clone, sti35, previously identified as a heat shock gene in F. oxysporum. A genomic clone for sti35 was isolated and sequence analysis revealed an intron and two heat shock elements upstream of sti35. The analysis also revealed the presence of a leader sequence composed of 27 amino acid residues, which shares a common amino acid composition with leader sequences of the proteins located in the mitochondrial matrix. Different expression patterns of sti35 in the mutants and wild-type strain were demonstrated.

DNA methylation represses the expression of the human erythropoietin gene by two different mechanisms

The human erythropoietin gene is expressed predominantly in the kidney and liver in response to hypoxia. Although the signaling cascade for hypoxia is present in many different cell types, the expression of erythropoietin is restricted to only a few tissues. The authors show that the promoter and 5′-untranslated region (5′-UTR) of the erythropoietin gene comprise a CpG island and that methylation of the CpG island correlates inversely with expression. Methylation represses the expression of the erythropoietin gene in 2 ways: high-density methylation of the 5′-UTR recruits a methyl-CpG binding protein to the promoter, and methylation of CpGs in the proximal promoter blocks the association of nuclear proteins. (Blood. 2000;95:111-119)

DNA methylation represses the expression of the human erythropoietin gene by two different mechanisms

The human erythropoietin gene is expressed predominantly in the kidney and liver in response to hypoxia. Although the signaling cascade for hypoxia is present in many different cell types, the expression of erythropoietin is restricted to only a few tissues. The authors show that the promoter and 5′-untranslated region (5′-UTR) of the erythropoietin gene comprise a CpG island and that methylation of the CpG island correlates inversely with expression. Methylation represses the expression of the erythropoietin gene in 2 ways: high-density methylation of the 5′-UTR recruits a methyl-CpG binding protein to the promoter, and methylation of CpGs in the proximal promoter blocks the association of nuclear proteins. (Blood. 2000;95:111-119)

Interaction effects of 5-azacytidine with topoisomerase II inhibitors on CHO cells, as detected by cytogenetic analysis

Different cell treatment protocols with the hypomethylating agent 5 azacytidine (5-aza C) were used in exponentially growing Chinese hamster ovary (CHO) cells in order to test its influence on the induction of chromosomal aberrations (CAs) induced by topoisomerase II inhibitors, ellipticine (EPC) and teniposide (VM-26). Cells pre-treated with 1 microg/ml 5-aza C for 1 h during the S-phase and post-treated in the last 2 h of incubation with 0.6 microg/ml EPC or 0.04 microg/ml VM-26 showed a reduction of 48% and 45%, respectively, in the frequencies of CAs as compared to the sum value of the frequencies obtained for each drug alone. 5-aza C added to the cultures for the last 2 h before cell fixation after a 30-min pulse treatment with EPC or VM-26 caused a 38% and 28% reduction, respectively. Simultaneous treatments with 5-aza C plus EPC, or 5-aza C plus VM-26 during the last 2 h of incubation (G2-phase), showed a significant effect of CA reduction (24%) only for the combination of 5-aza C + EPC. Preliminary assays with 5-aza C alone added to the cultures at different times demonstrated its effectiveness in inducing chromosome damage during the S-phase. Since S-phase-treated CHO cells showed a higher degree of reduction in the frequencies of CAs induced by EPC and VM-26, we suggest that 5-aza C incorporation into DNA may change the topo II cleavage sites, protecting the DNA from the induction of damage, or that the hypomethylation induced by incorporation of 5-aza C into DNA may change the chromatin structure facilitating the access to DNA repair enzymes. An alternative possibility is that 5-azaC can reactivate methylated genes involved in the repair of DNA double-strand breaks induced by topo II inhibitors.

DNA methylation, heterochromatin and epigenetic carcinogens

This paper will explore emerging concepts related to alternative carcinogenic mechanisms of 'non-mutagenic,' and hence epigenetic, carcinogens that may heritably alter DNA methylation without changing the underlying DNA sequence. In this review, we will touch on the basic concepts of DNA methylation, and will elaborate in greater detail on related topics including chromatin condensation, and heterochromatin spreading that is well known to induce gene silencing by position effect variegation in Drosophila and other species. Data from our model transgenic G12 cell system will be presented to support our hypothesis that certain carcinogens, such as nickel, may be carcinogenic not primarily because of their overt mutability, but rather as the result of their ability to promote DNA hypermethylation of important cancer-related genes. We will conclude with a discussion of the broader relevance of our findings and its application to other so-called 'epigenetic' carcinogens.

Evidence that resistance to osmotic stress is mediated by gene amplification

The mechanism for resistance to osmotic stress in V79 Chinese hamster cells is unknown. Previous experiments have provided little or no support for mechanisms based on gene mutation or stable changes in gene expression. An alternative explanation, based on gene amplification is offered in the present study. The evidence comes from experiments with PALA, which is N(Phosphonoacetyl)L-aspartate. Since no other mechanism than gene amplification is known for resistance to PALA, PALA resistance can be used as a reporter for gene amplification in other systems if cross-resistance occurs. Clonal lines resistant to hypertonic NaCl or to hypertonic mannitol were cross-resistant in dose-response tests with graded PALA. PALA resistant lines were also obtained by direct exposure of sensitive stock V79 cells to appropriate levels of PALA. In subsequent tests these lines were found to be refractory to osmotic stress when exposed to hypertonic NaCl or hypertonic mannitol. These results suggest that PALA and osmotic stress act as inductors as well as selective agents. The induction of gene amplification is not confined to the system under selection, but occurs at other points in the genome. It is this more general induction that explains cross-resistance between two otherwise unrelated characteristics.

Carcinogenic nickel silences gene expression by chromatin condensation and DNA methylation: a new model for epigenetic carcinogens

A transgenic gpt+ Chinese hamster cell line (G12) was found to be susceptible to carcinogenic nickel-induced inactivation of gpt expression without mutagenesis or deletion of the transgene. Many nickel-induced 6-thioguanine-resistant variants spontaneously reverted to actively express gpt, as indicated by both reversion assays and direct enzyme measurements. Since reversion was enhanced in many of the nickel-induced variant cell lines following 24-h treatment with the demethylating agent 5-azacytidine, the involvement of DNA methylation in silencing gpt expression was suspected. This was confirmed by demonstrations of increased DNA methylation, as well as by evidence indicating condensed chromatin and heterochromatinization of the gpt integration site in 6-thioguanine-resistant cells. Upon reversion to active gpt expression, DNA methylation and condensation are lost. We propose that DNA condensation and methylation result in heterochromatinization of the gpt sequence with subsequent inheritance of the now silenced gene. This mechanism is supported by direct evidence showing that acute nickel treatment of cultured cells, and of isolated nuclei in vitro, can indeed facilitate gpt sequence-specific chromatin condensation. Epigenetic mechanisms have been implicated in the actions of some nonmutagenic carcinogens, and DNA methylation changes are now known to be important in carcinogenesis. This paper further supports the emerging theory that nickel is a human carcinogen that can alter gene expression by enhanced DNA methylation and compaction, rather than by mutagenic mechanisms.

The effects of 5-azacytidine and 5-azadeoxycytidine on chromosome structure and function: implications for methylation-associated cellular processes

5-Azacytidine (5-aza-C) analogs demonstrate a remarkable ability to induce heritable changes in gene and phenotypic expression. These cellular processes are associated with the demethylation of specific DNA sequences. On the other hand, 5-aza-C analogs have dramatic effects on chromosomes, leading to decondensation of chromatin structure, chromosomal instability and an advance in replication timing. Condensation inhibition of genetically inactive chromatin occurs when the DNA is still hemimethylated or fully methylated. In cell cultures prolonged for several replication cycles, chromosomal rearrangements and instability affect the 5-aza-C-sensitive regions. Moreover, the normally late-replicating inactive chromatin undergoes a transient temporal shift to an earlier DNA replication, characteristic of activatable chromatin. zThe induced alterations of chromosome structure and behavior may trigger the 5-aza-C-dependent process of cellular reprogramming. Apart from their differentiating and gene-modifying effects, 5-aza-C analogs can tumorigenically transform cells and modulate their metastatic potential. High doses of 5-aza-C analogs have cytotoxic and antineoplastic activities.

De novo methylation of an MHC class I transgene following transformation with human adenoviruses is not correlated with its altered expression

The biological importance of class I histocompatibility antigens in a large variety of immune mechanisms is widely recognized, and their role in tumor rejection has been proven in several experimental tumor systems. Reduced expression of class I antigens, which is correlated with enhanced tumorigenicity, was shown in these systems to be mainly the result of transcriptional down-regulation. Mouse embryonal fibroblasts expressing H-2 antigens and the product of a miniature swine class I transgene, transformed by adenovirus 12, exhibit low levels of all class I antigens on the cell surface. Half of the cell lines demonstrate a suppressed level of class I mRNAs. Cell lines derived from transformation with the early region of adenovirus 5 express a high level of class I antigens. DNAs from adenovirus-transformed cells are extensively hypermethylated both in the 5' and the coding regions of the transgene compared to DNAs from immortalized cell lines and primary embryonal fibroblasts. Nevertheless, hypermethylation of these sequences is not correlated with mRNA level or cell-surface expression of the transgene product. Treatment of the transformed cells with high concentration of 5-azacytidine (5 Aza-C) induced merely a minor enhancement in the expression of class I mRNAs and class I antigens. Thus, this system is a perfect example of where viral transformation is associated with induced methylation of a class I gene, but hypermethylation does not affect its expression. The role of de novo methylation of genes in this system might be associated with transformation, or generation of mutations in CpG-rich sequences.

Osmotic stress variants in Chinese hamster cells

Stable variants resistant to hypertonic stress have been obtained from V79 cells by one-step selection in media supplemented with graded concentrations of NaCl. Such variants retain a potential for resistance when isolated and propagated in isotonic media. On replating in graded NaCl, a family of dose-response curves is obtained, rising in level of resistance according to the degree of hypertonicity used to isolate the variants initially. In hybrids between variants and sensitive cells, phenotypic expression of resistance to hypertonic NaCl is recessive. Stable variants can also be isolated by one-step selection in media made hypertonic with D-mannitol. Clonal sublines selected with mannitol, as well as those obtained with NaCl, are resistant to both types of hypertonic media. Fluctuation tests in media supplemented with NaCl show that resistance arises spontaneously and at random, with measured rates of variation that depend on the concentration of NaCl used for selection. Treatment of sensitive cells with 5-azacytidine increases the frequency of resistant variants in assays with high levels of added NaCl but is less effective when selection is performed at lower concentrations. Exposure to ethyl methane sulfonate has little or no effect on variant frequency.

Persistent repression of a functional allele can be responsible for galactosyltransferase deficiency in Tn syndrome

A human hematopoietic disorder designated as Tn syndrome or permanent mixed-field polyagglutinability has been ascribed to a stem cell mutation leading to a specific deficiency of UDP-Gal:GalNAc alpha 1-O-Ser/Thr beta 1-3 galactosyltransferase (beta 3 Gal-T) activity in affected cells. To test for the possibility that an allele of the beta 3Gal-T gene might be repressed instead of mutated, we have investigated whether 5-azacytidine or sodium n-butyrate, both inducers of gene expression, would reactivate expression of beta 3Gal-T in cloned enzyme-deficient T cells derived from a patient affected by the Tn syndrome. Flow cytometry revealed that a single treatment induced de novo expression of the Thomsen-Friedenreich antigen (Gal beta 1-3GalNAc-R), the product of beta 3Gal-T activity. In addition, a sialylated epitope on CD43 (leukosialin), which is present on normal but not on beta 3Gal-T-deficient T cells, was also reexpressed. Although no beta 3Gal-T activity was detectable in untreated Tn syndrome T cells, after exposure to 5-azaC,beta 3Gal-T activity reached nearly normal values. Both agents failed to reactivate beta 3Gal-T in Jurkat T leukemic cells, which also lack beta 3Gal-T activity. These data demonstrate that Tn syndrome T cells contain an intact beta 3Gal-T gene copy and that the enzyme deficiency in this patient is due to a persistent and complete but reversible repression of a functional allele. In contrast, the cause of beta 3Gal-T deficiency appears to be different in Jurkat T cells.

The hypervariable DXS255 locus contains a LINE-1 repetitive element with a CpG island that is extensively methylated only on the active X chromosome

The DXS255 locus at Xp11.22 is highly polymorphic due to a 26-bp variable number of tandem repeats (VNTR) motif. In previous studies, one of the MspI sites flanking the VNTR manifested a correlation between methylation and X chromosome inactivation. Here we show, by DNA sequence analysis, that this MspI site is located within the CpG island at the 5' end of a LINE-1 element, which is 2.5 kb from the VNTR. The methylation status of the CpG island was assessed in Southern blotting experiments using the methylation-sensitive enzymes HpaII, HhaI, and BssHII. All these sites were completely methylated on active X chromosomes, consistent with previously reported findings of full methylation of LINE-1 elements throughout the genome. However, on inactive X chromosomes these sites were predominantly unmethylated, although patterns were found to be heterogeneous. The results suggest that LINE-1 elements on the inactive X chromosome are not suppressed by full methylation of their CpG islands. The differential methylation of the DXS255 CpG island provides the basis for a highly informative X inactivation analysis system.

Is there an association between an increase in c-myc RNA steady state levels and c-myc methylation in HL-60 cells treated with 3-deaza-(+/-)-aristeromycin, an indirect inhibitor of methylation?

Alteration in gene expression of the proto-oncogene c-myc in HL-60 cells is associated with differentiation of these cells. We have studied the steady state levels of c-myc transcripts, the levels of transmethylation metabolites S-adenosylmethionine and S-adenosyl-homocysteine and the methylation pattern of the c-myc gene after treatment of HL-60 cells with the transmethylation inhibitor and granulocytic inducer, 3-deaza-(+/-)-aristeromycin. A transient increase in c-myc RNA levels after 45 min of drug exposure was observed which was accompanied by changes in the ratio of transmethylation metabolites in both whole cells and nuclei. The changes in transmethylation metabolites in whole cells, although compatible with levels frequently associated with hypomethylation of cellular components, caused no changes in methylation of c-myc DNA sequences of the HL-60 cells as detected by HpaII or MspI digestion and Southern blotting.

Differential sensitivity of CG and CCG DNA sequences to ethionine-induced hypomethylation of the Nicotiana tabacum genome

Plant DNA is distinguished from the DNA of all other organisms by its high content of 5-methylcytosine (5mC). 5mC levels may amount to 30% of total cytosines, distributed between the sequences CG and CXG. The results presented here show that the methylation status of CXG sequences could be influenced by culturing tobacco tissues on subtoxic concentrations of ethionine. The hypomethylating effect of ethionine, evaluated as the capability of MspI or HpaII to cleave the DNA, proved to be rather specific for CCG and differed from that of 5-azacytidine which did not discriminate between CG and CXG sequences.

Activation of two new alpha(1,3)fucosyltransferase activities in Chinese hamster ovary cells by 5-azacytidine

Several mammalian alpha(1,3)fucosyltransferases (alpha[1,3]Fuc-T) that synthesize carbohydrates containing alpha(1,3)fucosylated lactosamine units have been identified. Although Chinese hamster ovary (CHO) cells do not express alpha(1,3)Fuc-T activity, the rare mutants LEC11 and LEC12, isolated after mutagenesis or DNA transfection, each express an alpha(1,3)Fuc-T that may be distinguished by several criteria. Two new CHO mutants possessing alpha(1,3)Fuc-T activity (LEC29 and LEC30) have now been isolated after treatment of a CHO cell population with 5-azacytidine (5-AzaC), ethylnitrosourea (ENU), or 5-AzaC followed by N-methyl-N'-nitro-N-nitrosoguanidine (MNNG). Like LEC12, both mutants possess an N-ethylmaleimide-resistant alpha(1,3)Fuc-T activity that can utilize a variety of acceptors and both express the Lewis X (Lex) determinant (Gal beta[1,4](Fuc alpha[1,3])GlcNAc beta 1)) but not the sialyl alpha(2,3)Lex determinant on cell-surface carbohydrates. However, LEC29 and LEC30 may be distinguished from LEC11 and LEC12, as well as from each other, on the basis of their unique patterns of lectin resistance and their abilities to bind the VIM-2 monoclonal antibody that recognizes carbohydrates terminating in NeuNAc alpha(2,3)Gal beta(1,4)GlcNAc beta(1,3)Gal beta(1,4)(Fuc alpha[1,3])GlcNAc beta and also by the different in vitro substrate specificities and kinetic properties of their respective alpha(1,3)Fuc-T activities. The combined data provide good evidence that the LEC29 and LEC30 alpha(1,3)Fuc-Ts are novel transferases encoded by distinct gene products.

DNA methylation and gene expression

A large body of evidence demonstrates that DNA methylation plays a role in gene regulation in animal cells. Not only is there a correlation between gene transcription and undermethylation, but also transfection experiments clearly show that the presence of methyl moieties inhibits gene expression in vivo. Furthermore, gene activation can be induced by treatment of cells with 5-azacytidine, a potent demethylating agent. Methylation appears to influence gene expression by affecting the interactions with DNA of both chromatin proteins and specific transcription factors. Although methylation patterns are very stable in somatic cells, the early embryo is characterized by large alterations in DNA modification. New methodologies are now becoming available for studying methylation at this stage and in the germ line. During development, tissue-specific genes undergo demethylation in their tissue of expression. In tissue culture cells this process is highly specific and appears to involve an active mechanism which takes place in the absence of DNA replication. The X chromosome undergoes inactivation during development; this is accompanied by de novo methylation, which appears necessary to stably maintain its silent state. As opposed to the programmed changes in DNA methylation which occur in vivo, immortalized tissue culture cells demonstrate alterations in DNA modification which take place over a long time scale and which appear to be the result of selective pressures present during the growth of these cells in culture.

Mutations and epimutations in mammalian cells

Early studies on heritable variation in cultured mammalian cells suggested that both mutation and epigenetic events might be involved. The importance of mutations has subsequently been fully documented, but only recently has an alternative form of inheritance been uncovered. This is based on the post-synthetic methylation of cytosine in regulatory regions of genes. The pattern of methylation is heritable, and in almost all cases studied, methylation of a region is associated with lack of gene expression. Such silent genes can be reactivated by the powerful demethylating agent 5-azacytidine (5-aza-CR). Changes in heritable DNA methylation which alter phenotype are referred to as epimutations. It now seems very likely that the well known 'functional hemizygosity' in CHO cells and other near diploid cell lines is due to the existence of one active and one silent gene at many autosomal loci. It is clear that permanent cell lines inactivate genes by de novo methylation, whereas normal diploid cells do not have this activity. This has important implications for our understanding of cellular transformation, tumor progression, and the increase in chromosome number frequently associated with these cellular changes. It is likely that both mutations and epimutations are important in the emergence of fully transformed tumorigenic cells. Agents which increase or reduce DNA methylation in cells can be regarded as epimutagens, although in many cases the mechanisms of inducing hypo- or hyper-methylation are not understood. Two exceptions are 5-aza-CR which inhibits the normal DNA maintenance methylase activity, and 5-methyldeoxycytidine triphosphate which is incorporated into cellular DNA following electroporation and has been shown to silence genes.

Evaluation of the mutagenic effects of SV40 in mouse, hamster, and mouse-human hybrid cells

We have examined the ability of SV40 to induce changes in drug or temperature resistance in mouse, hamster, and mouse-human hybrid cells. SV40 induced a substantial increase of cells resistant to 5-bromodeoxyuridine + trifluorothymidine in Balb/c 3T3 cells and induced an increase of hybrid cells resistant to 6-thioguanine. SV40 was found to be nonmutagenic or weakly mutagenic in other test systems. The 3T3 cells were T-antigen positive, exhibited a marked reduction in TK activity, were heterogeneous for [3H]BrdU incorporation by autoradiography, and exhibited instability of the drug-resistance phenotype, suggesting that SV40 may be inducing resistance by an epigenetic process. SV40-induced 6-thioguanine resistance in the hybrids appears to occur predominantly by chromosome loss.

5-Azacytidine increases the total cellular copper content and basal level metallothionein mRNA accumulation of human Hep G2 cells

In this study we have demonstrated the ability of 5-azacytidine to elevate the basal level expression of the metallothionein (MT)-IF and MT-IG genes and increase the basal level expression of the MT-IIA gene in Hep G2 cells, a cell line which exhibits heavy metal inducible MT gene expression. Atomic absorption analysis of 5-azacytidine treated Hep G2 cells detected a 2-fold increase in the total cellular copper content. Pretreatment of 5-azacytidine exposed cells with hydroxyurea and cycloheximide indicated that the increase in total cellular copper content was a direct response to 5-azacytidine treatment. S1 nuclease analysis illustrated that pretreatment of Hep G2 cells with KCN, a copper specific chelator and uptake inhibitor, suppressed 5-azacytidine- and copper-inducible MT-IG gene expression. Thus, the increase in MT gene expression in response to 5-azacytidine treatment can be correlated to an increase in the total cellular copper content. Possible mechanisms on how 5-azacytidine could alter the influx/efflux of copper in Hep G2 cells are discussed.

Immortalization of primary cells by DNA tumor viruses

Cellular senescence is characterized by a decline in sensitivity to growth factors resulting in cessation of cellular growth. The expression of cellular or viral oncogenes may result in the establishment of cell lines with unlimited proliferative potential ("immortalization"). A variety of viral and cellular oncogenes have been reported to immortalize cells, suggesting that multiple mechanisms may lead to an escape from senescence. Immortalization has been reported to occur as a result of an interaction of viral proteins with cellular suppressor gene products or may result from the elevated expression of "transforming" oncoproteins (such as the polyomavirus middle-t antigen). Here we speculate that a selection for cells with a further decreased probability of cell cycle withdrawal can occur during the growth of cells expressing viral early genes, resulting in a process of tumor progression. Explaining immortalization in terms of mitogenic stimulation due to the expression of viral oncogenes followed by genetic/epigenetic changes may help to explain why lytic DNA viruses have a biological activity which may not be necessary for their life cycle.

High levels of de novo methylation and altered chromatin structure at CpG islands in cell lines

CpG islands are normally methylation free in cells of the animal, even when the associated gene is transcriptionally silent. In mouse NIH 3T3 and L cells, however, over half of the islands are heavily methylated. Near identity of the methylated subset in the two cell lines suggested that methylation is confined to genes that are nonessential in culture. In agreement with this, islands at several tissue-specific genes, but not at housekeeping genes, have become methylated in many human and mouse cell lines. At the chromatin level, methylated islands are Mspl resistant compared with their nonmethylated counterparts. We suggest that mutation-like gene inactivation due to CpG island methylation is widespread in many cell lines and could explain the loss of cell type-specific functions in culture.

The significance of biological heterogeneity

Heterogeneity of expression for a variety of characteristics is found among malignant cells in the organism and in culture. Normal cells are relatively uniform when organized in a tissue, but become heterogeneous for many characteristics when they are dispersed and grown in monolayer culture. The heterogenizing effect of growth in culture indicates that the morphology and behavior of normal cells is ordered by their topological relations in tissues and other homeostatic influences of the organism. Weakening of these ordering relations may contribute to malignant transformation, as it usually does in rodent cell culture. Although phenotypic differences among cells of a given type may be transient, they can be perpetuated by protracted exposure to selective conditions. Examples are cited of selection which leads to an adapted state that is heritable for many cell generations after removal of the selective conditions. Such heritable adaptations are analogous to the Dauermodifikationen, or lingering changes, first described in ciliated protozoa and shown there to be under cytoplasmic control. The concept of progressive state selection is introduced to account for heritable adaptation at the cellular level. It depends on the spontaneous occurrence of transient, variant states and their successive selection to progressively higher levels of adaptation to an altered microenvironment. Although the process is basically epigenetic, it may be stabilized by genetic change. The concept is consistent with our present knowledge of tumor development, including progression to metastasis, and with epigenetic aspects of normal development.

The promoter of the human proliferating cell nuclear antigen (PCNA) gene is bidirectional

The proliferating cell nuclear antigen (PCNA) gene codes for a protein that is necessary for cellular DNA synthesis and cell cycle progression. A functional promoter has been identified in the 5' flanking region of the human PCNA gene. An abbreviated promoter (from the capsite to the PvuII restriction site at -395) was found to be equally efficient in directing transcription from a linked reporter, whether placed in the correct or reverse orientation in respect to the coding sequence. The reporter used was a cDNA of human thymidine kinase (TK), and the bidirectionality of the promoter was demonstrated by its ability to confer the TK+ phenotype to TK- ts 13 cells and by the amount of specific message in RNA blots. The PvuII promoter placed between two coding sequences (the TK cDNA and the bacterial gene for neoresistance) is capable of driving transcription simultaneously in both directions. Finally, in blots of RNA from human cells, two transcripts could be detected that hybridized to a sense riboprobe from the 5' flanking region of the human PCNA gene. We conclude that the locus for the human PCNA gene contains a bidirectional promoter producing diverging transcripts.