Analysis of the variations in proviral cytosine methylation that accompany transformation and morphological reversion in a line of Rous sarcoma virus-infected Rat-1 cells

Accumulation of long-term transcriptionally active integrated retroviral vectors in active promoters and enhancers

Most retroviruses preferentially integrate into certain genomic locations and, as a result, their genome-wide integration patterns are non-random. We investigate the epigenetic landscape of integrated retroviral vectors and correlate it with the long-term stability of proviral transcription. Retroviral vectors derived from the avian sarcoma/leukosis virus expressing the GFP reporter were used to transduce the human myeloid lymphoblastoma cell line K562. Because of efficient silencing of avian retrovirus in mammalian cells, only ∼3% of established clones displayed stable proviral expression. We analyzed the vector integration sites in non-selected cells and in clones selected for the GFP expression. This selection led to overrepresentation of proviruses integrated in active transcription units, with particular accumulation in promoter-proximal areas. In parallel, we investigated the integration of vectors equipped with an anti-silencing CpG island core sequence. Such modification increased the frequency of stably expressing proviruses by one order. The modified vectors are also overrepresented in active transcription units, but stably expressed in distal parts of transcriptional units further away from promoters with marked accumulation in enhancers. These results suggest that integrated retroviruses subject to gradual epigenetic silencing during long-term cultivation. Among most genomic compartments, however, active promoters and enhancers protect the adjacent retroviruses from transcriptional silencing.

Alpharetroviral vectors: from a cancer-causing agent to a useful tool for human gene therapy

Gene therapy using integrating retroviral vectors has proven its effectiveness in several clinical trials for the treatment of inherited diseases and cancer. However, vector-mediated adverse events related to insertional mutagenesis were also observed, emphasizing the need for safer therapeutic vectors. Paradoxically, alpharetroviruses, originally discovered as cancer-causing agents, have a more random and potentially safer integration pattern compared to gammaretro- and lentiviruses. In this review, we provide a short overview of the history of alpharetroviruses and explain how they can be converted into state-of-the-art gene delivery tools with improved safety features. We discuss development of alpharetroviral vectors in compliance with regulatory requirements for clinical translation, and provide an outlook on possible future gene therapy applications. Taken together, this review is a broad overview of alpharetroviral vectors spanning the bridge from their parental virus discovery to their potential applicability in clinical settings.

Retroviral DNA methylation and epigenetic repression are mediated by the antiviral host protein Daxx

Integrated retroviral DNA is subject to epigenetic transcriptional silencing at different frequencies. This process is mediated by repressive DNA methylation and histone modifications on viral chromatin. However, the detailed mechanisms by which retroviral silencing is initiated and maintained are not well understood. Using a model system in which avian sarcoma virus (ASV) DNA is epigenetically repressed in mammalian cells, we previously found that a cellular scaffolding protein, Daxx, acts as an antiretroviral factor that promotes epigenetic repression through recruitment of histone deacetylases (HDACs). Here we show that human Daxx protein levels are increased in response to retroviral infection and that Daxx acts at the time of infection to initiate epigenetic repression. Consistent with a rapid and active antiviral epigenetic response, we found that repressive histone marks and long terminal repeat (LTR) DNA methylation could be detected within 12 h to 3 days postinfection, respectively. Daxx was also found to be required for long-term ASV silencing maintenance and full viral DNA methylation, and it was physically associated with both viral DNA and DNA methyltransferases (DNMTs). These findings support a model in which incoming retroviral protein-DNA complexes are detected by Daxx, and the integrated provirus is rapidly chromatinized and repressed by DNA methylation and histone modification as part of an antiviral response. These results uncover a possible direct and active antiviral mechanism by which DNMTs can be recruited to retroviral DNA.

Transcriptional provirus silencing as a crosstalk of de novo DNA methylation and epigenomic features at the integration site

The autonomous transcription of integrated retroviruses strongly depends on genetic and epigenetic effects of the chromatin at the site of integration. These effects are mostly suppressive and proviral activity can be finally silenced by mechanisms, such as DNA methylation and histone modifications. To address the role of the integration site at the whole-genome-scale, we performed clonal analysis of provirus silencing with an avian leucosis/sarcoma virus-based reporter vector and correlated the transcriptional silencing with the epigenomic landscape of respective integrations. We demonstrate efficient provirus silencing in human HCT116 cell line, which is strongly but not absolutely dependent on the de novo DNA methyltransferase activity, particularly of Dnmt3b. Proviruses integrated close to the transcription start sites of active genes into the regions enriched in H3K4 trimethylation display long-term stability of expression and are resistant to the transcriptional silencing after over-expression of Dnmt3a or Dnmt3b. In contrast, proviruses in the intergenic regions tend to spontaneous transcriptional silencing even in Dnmt3a(-/-) Dnmt3b(-/-) cells. The silencing of proviruses within genes is accompanied with DNA methylation of long terminal repeats, whereas silencing in intergenic regions is DNA methylation-independent. These findings indicate that the epigenomic features of integration sites are crucial for their permissivity to the proviral expression.

The core element of a CpG island protects avian sarcoma and leukosis virus-derived vectors from transcriptional silencing

Unmethylated CpG islands are known to keep adjacent promoters transcriptionally active. In the CpG island adjacent to the adenosine phosphoribosyltransferase gene, the protection against transcriptional silencing can be attributed to the short CpG-rich core element containing Sp1 binding sites. We report here the insertion of this CpG island core element, IE, into the long terminal repeat of a retroviral vector derived from Rous sarcoma virus, which normally suffers from progressive transcriptional silencing in mammalian cells. IE insertion into a specific position between enhancer and promoter sequences led to efficient protection of the integrated vector from silencing and gradual CpG methylation in rodent and human cells. Individual cell clones with IE-modified reporter vectors display high levels of reporter expression for a sustained period and without substantial variegation in the cell culture. The presence of Sp1 binding sites is important for the protective effect of IE, but at least some part of the entire antisilencing capacity is maintained in IE with mutated Sp1 sites. We suggest that this strategy of antisilencing protection by the CpG island core element may prove generally useful in retroviral vectors.

DNA methylation of Sleeping Beauty with transposition into the mouse genome

The Sleeping Beauty transposon is a recently developed non-viral vector that can mediate insertion of transgenes into the mammalian genome. Foreign DNA elements that are introduced tend to invoke a host-defense mechanism resulting in epigenetic changes, such as DNA methylation, which may induce transcriptional inactivation of mammalian genes. To assess potential epigenetic modifications associated with Sleeping Beauty transposition, we investigated the DNA methylation pattern of transgenes inserted into the mouse genome as well as genomic regions flanking the insertion sites with bisulfite-mediated genomic sequencing. Transgenic mouse lines were created with two different Sleeping Beauty transposons carrying either the Agouti or eGFP transgene. Our results showed that DNA methylation in the keratin-14 promoter and Agouti transgene were negligible. In addition, two different genomic loci flanking the Agouti insertion site exhibited patterns of DNA methylation similar to wild-type mice. In contrast, high levels of DNA methylation were observed in the eGFP transgene and its ROSA26 promoter. These results indicate that transposition via Sleeping Beauty into the mouse genome may result in a significant level of de novo DNA methylation. This may depend on a number of different factors including the cargo DNA sequence, chromosomal context of the insertion site, and/or host genetic background.

CpG island protects Rous sarcoma virus-derived vectors integrated into nonpermissive cells from DNA methylation and transcriptional suppression

CpG islands are important in the protection of adjacent housekeeping genes from de novo DNA methylation and for keeping them in a transcriptionally active state. However, little is known about their capacity to protect heterologous genes and assure position-independent transcription of adjacent transgenes or retroviral vectors. To tackle this question, we have used the mouse aprt CpG island to flank a Rous sarcoma virus (RSV)-derived reporter vector and followed the transcriptional activity of integrated vectors. RSV is an avian retrovirus which does not replicate in mammalian cells because of several blocks at all levels of the replication cycle. Here we show that our RSV-derived reporter proviruses linked to the mouse aprt gene CpG island remain undermethylated and keep their transcriptional activity after stable transfection into both avian and nonpermissive mammalian cells. This effect is most likely caused by the protection from de novo methylation provided by the CpG island and not by enhancement of the promoter strength. Our results are consistent with previous finding of CpG islands in proximity to active but not inactive proviruses and support further investigation of the protection of the gene transfer vectors from DNA methylation.

Inhibition of the rous sarcoma virus long terminal repeat-driven transcription by in vitro methylation: different sensitivity in permissive chicken cells versus mammalian cells

Rous sarcoma virus (RSV) enhancer sequences in the long terminal repeat (LTR) have previously been shown to be sensitive to CpG methylation. We report further that the high density methylation of the RSV LTR-driven chloramphenicol acetyltransferase reporter is needed for full transcriptional inhibition in chicken embryo fibroblasts and for suppression of tumorigenicity of the RSV proviral DNA in chickens. In nonpermissive mammalian cells, however, the low density methylation is sufficient for full inhibition. The time course of inhibition differs strikingly in avian and mammalian cells: although immediately inhibited in mammalian cells, the methylated RSV LTR-driven reporter is fully inhibited with a significant delay after transfection in avian cells. Moreover, transcriptional inhibition can be overridden by transfection with a high dose of the methylated reporter plasmid in chicken cells but not in hamster cells. The LTR, v-src, LTR proviral DNA is easily capable of inducing sarcomas in chickens but not in hamsters. In contrast, Moloney murine leukemia virus LTR-driven v-src induces sarcomas in hamsters with high incidence. Therefore, the repression of integrated RSV proviruses in rodent cells is directed against the LTR.

Molecular biology of cell nonpermissiveness to retroviruses. Has the time come?

The problem of host cell nonpermissiveness to retrovirus infection is characterized and illustrated on several retroviral models, including the role of viral receptors, cell fusion, and endogenous retroviral genomes as modifiers of the outcome of retroviral infection. Special attention is paid to different barriers against the infection of mammalian cells with avian leukosis/sarcoma viruses (ALV/ASV). Even when avian retroviruses become integrated in mammalian cells, several blocks at the level of provirus expression, processing of viral RNAs, and posttranslational modification prevent virus production in such virogenic cells. The significance of these blocks and new strategies making it possible to overcome some of them are discussed in relation to the development of ALV/ASV-based vectors suitable for gene therapy in mammals.

Apoptosis in the central nervous system of developing mouse fetuses from 5-azacytidine-administered dams

To determine the effect of 5-azacytidine (5 Az), a cytidine analogue, on the developing fetus, different strains of mice were injected with various doses of the agent, ip, at 11 days of gestation. Light microscopically, severely pyknotic cell death profiles were observed in different layers of the developing brain and spinal cord (central nervous system) on the day after the injection. Electron microscopy of the pyknotic cells revealed the shrinkage of the cell body, to various degrees margination of the nuclear chromatin, condensation of nuclear materials, fragmentation of the affected cells, and, finally, neat "bite-size" bodies engulfed by surrounding normal neuroepithelial cells and macrophage-like cells. DNA fragmentation was detected in the nuclei of the pyknotic cells by an in situ detection method for fragmented DNA ends. These changes were consistent with the criteria of apoptosis.

Methylation of HSV-1 DNA as a mechanism of viral inhibition: studies of an analogue of methyldeoxycytidine: trifluoromethyldeoxycytidine (F3mdCyd)

Although several hypomethylating agents such as 5-azadeoxycytidine and 5-fluorodeoxycytidine have been shown to activate transcription after incorporation into viral or cellular DNA, agents which selectively affect the methylation status of virus-infected cells have not been described. Studies on the antiviral effect of the methyldeoxycytidine (mdCyd) analogue trifluoromethyldeoxycytidine (F3mdCyd) showed significant antiviral activity against herpes simplex virus type 1 (HSV-1). This analogue of both dCyd and dThd is selectively incorporated into the DNA of herpesvirus infected cells due to the unique specificity of the herpesvirus thymidine kinase (TK) because the HSV-1 TK is both a dCyd and dThd kinase. In contrast, the deoxycytidine kinase of uninfected cells preferentially phosphorylates dCyd and has a poor affinity for F3mdCyd. F3mdCyd hemisubstituted M13 DNA displayed the same properties as mdCyd-substituted M13 DNA with respect to cleavage by restriction enzymes, and acted as an efficient template for eukaryotic DNA methyltransferase (S-adenosyl-L-methionine DNA (cytosine-5) methyltransferase: EC 2.1.1.37). Using the persistently infected CEM cell model system, the extent of DNA methylation was shown to increase in a dose-related manner when HSV-1-infected CEM cells were treated with increasing concentrations of F3mdCyd. Higher levels of methylation correlated with significant decreases in HSV-1 titers. Isoschizomer analyses followed by Southern blotting and hybridization with genomic HSV-1 DNA showed that DNA from HSV-1-infected, analogue-treated Vero cells was resistant to cleavage by restriction enzymes at a time when productive virus was not present in culture. We infer from these results that the methylation-like properties of the incorporated F3mdCyd occur concomitantly with, and appear to be involved in, the mechanisms of the analogue's antiviral effect towards HSV-1.

Epigenetic control of tumor cell morphology

XC cell line derived from a single rat cell transformed by the Prague strain of Rous sarcoma virus produced morphologically different colonies. Among them, two distinct cell types consisting of thick, fusiform cells (L-type), and of flat, polygonal cells (R-type) were apparent. By repeated subclonings, pure cultures, L1 and R1, respectively, were obtained. These clones underwent morphological conversion during prolonged culture; L-type colonies appeared in the R-type clone and vice versa. The kinetic curve suggested that the conversion was multi-stepped. When inoculated into nude mice, L-type cells produced much larger tumors at a higher frequency than R-type cells, and the tumors induced by these two clones were histologically different. The expression of v-src gene was higher in L-type than in R-type cells at both mRNA and protein levels.

Fusion of Rous-sarcoma-virus-transformed rat cells to morphologically normal human or rat cells results in transcriptional suppression of the provirus that depends on its chromosomal integration site

The fusion of a Rous sarcoma virus (RSV)-transformed rat fibroblast clone to at least 2 different human cell types reproducibly produces phenotypically normal hybrids. Analysis of such hybrids reveals that proviral silence is the result of transcriptional down-regulation, presumably by a trans-acting human molecule. Furthermore, this phenomenon seems to be strongly influenced by the proviral chromosomal integration site and its imposition may entail a mechanism that is required only transiently.

DNA methylation and differentiation

The methylation of specific cytosine residues in DNA has been implicated in regulating gene expression and facilitating functional specialization of cellular phenotypes. Generally, the demethylation of certain CpG sites correlates with transcriptional activation of genes. 5-Azacytidine is an inhibitor of DNA methylation and has been widely used as a potent activator of suppressed genetic information. Treatment of cells with 5-azacytidine results in profound phenotypic alterations. The drug-induced hypomethylation of DNA apparently perturbs DNA-protein interactions that may consequently alter transcriptional activity and cell determination. The inhibitory effect of cytosine methylation may be exerted via altered DNA-protein interactions specifically or may be transduced by a change in the conformation of chromatin. Recent studies have demonstrated that cytosine methylation also plays a central role in parental imprinting, which in turn determines the differential expression of maternal and paternal genomes during embryogenesis. In other words, methylation is the mechanism whereby the embryo retains memory of the gametic origin of each component of genetic information. A memory of this type would probably persist during DNA replication and cell division as methylation patterns are stable and heritable.

Shuttle vector system for the analysis of mutational events in mammalian chromosomal DNA

cDNA of the human hprt gene was introduced into the BamHI cloning site of the retroviral shuttle vector pZipNeoSV(X)1. The mouse cell line 2TGOR, a hypoxanthine phosphoribosyltransferase-deficient derivative of Balb/c 3T3, was transformed with the vector and some stably transformed HATrNEOr clones were established. One of the clones, VH-12, contained a single copy of the vector integrated stably into a chromosome in a proviral form. From this clone, we were able to recover efficiently the vector sequence preserving its intact structure by use of COS cell fusion. The relatively small size of the hprt cDNA (657 base pairs for the coding region) allowed quick determination of the entire DNA sequence. It was also notable that use of 6TG NEO double selection for mutant isolation could eliminate the 6TGr derivatives of VH-12 cells which arose from loss of the total vector sequence or from some epigenetic event, because such alterations would lead to inactivation of the neo gene as well as the hprt cDNA. The properties of our shuttle vector system were particularly useful for analysis of the molecular mechanisms of mutational events in chromosomal DNA of mammalian cells.

The methylation state of the proviruses in avian sarcoma virus transformed chick and rat cells

The endogenous viruses in the avian cells are not completely methylated, nor are the Schmidt-Ruppin RSV-D (SRD) proviruses in the infected cells completely unmethylated. Avian sarcoma proviruses integrated in rat transformed cloned cells are heavily methylated. In these cells, a region in the 3' end of the env gene is unmethylated in all the src-containing proviruses but not in the transformed defective (td) proviruses. A possible role for the hypomethylation of the 3' end of the env region is proposed.

Gene reactivation: a tool for the isolation of mammalian DNA methylation mutants

We report the isolation and characterization of a mammalian strain (tsm) that has a temperature-sensitive mutation in DNA methylation. The isolation procedure was based on the observation that treatment of a CHO TK- MT- cell line with demethylating agents introduces up to 46% demethylation, resulting in phenotypic reversion and transcriptional activation of the thymidine kinase (TK) and metallothionein (MT) genes at frequencies ranging from 1% to 59%. Seven thousand individual colonies from an EMS-mutagenized CHO TK- MT- population were screened for spontaneous reversion to TK+ phenotype after treatment at 39 degrees C. Successful isolates were subsequently examined for MT+ reversion. A single clone (tsm) was obtained that showed temperature-dependent reactivation of both TK and MT genes at frequencies of 7.2 X 10(-4) and 6 X 10(-4), respectively. The tsm cells were viable at 39 degrees C and showed no increased mutation frequency. Reactivation correlated with transcriptional activation of the respective genes, whereas backreversion to the TK- phenotype was associated with transcriptional inactivation. TK- backrevertants were reactivable again with demethylating agents. Although demethylation in tsm cells was not detectable by HPLC, Southern blot analysis revealed that reactivants, irrespective of their mode of generation, showed specific demethylation of both TK and MT genes. Also, after about 150 cell generations after treatment, reactivants from both temperature-induced tsm and cells exposed to demethylating agents gained 60% and 23%, respectively, in 5-methylcytosine (5mC). It is proposed that the phenotype of tsm cells is due to a mutation involved in the regulation of DNA methylation. The further characterization of this and other mammalian mutants should help to clarify the physiological role of DNA methylation, as well as its regulation.

Variable stability of a selectable provirus after retroviral vector gene transfer into human cells

Human lymphoblasts deficient in the enzyme hypoxanthine-guanine phosphoribosyltransferase (HPRT) were infected with an amphotropic helper-free retroviral vector expressing human HPRT cDNA. The stability and expression of the HPRT provirus in five cell lines with different proviral integration sites were examined by determining HPRT mutation and reversion frequencies and by blot hybridization studies. Mutation to the HPRT-negative phenotype occurred at frequencies of approximately 4 X 10(-5) to 3 X 10(-6) per generation. Most mutations in each of the five cell lines were associated with partial or complete deletions or rearrangements of the provirus. Several mutants retained a grossly intact HPRT provirus, and in one such mutant HPRT shutdown resulted from a revertible epigenetic mechanism that was not associated with global changes in proviral methylation. Therefore, mutation and shutdown of the HPRT provirus in human lymphoblasts result from mechanisms similar to those reported for several other avian and mammalian replication-competent retroviruses.

Reversion to the nontransformed phenotype of Abelson murine leukemia virus-transformed cells and their subsequent retransformation

Two independent clones of fetal mink lung cells (CCL64) nonproductively transformed by Abelson murine leukemia virus (Ab-MuLV) were used to study spontaneous reversion to the nontransformed phenotype and subsequent retransformation of the revertants. One clone, D62, contained two complete Ab-MuLV proviruses and expressed polyprotein P120. The other clone, K49, contained four proviruses: three of them were complete and one represented a deletion mutant. In addition to P120, a new polyprotein, P60, was expressed in this clone. During the processes of reversion and retransformation proviral DNAs were conserved with respect to size and integration site. In contrast to the transformants, expression of Ab-MuLV P120, and in case of clone K49 also of P60, was blocked in revertant lines as a result of loss of transcription of proviral DNA. In retransformants, expression of Ab-MuLV P120 was found in both clones. However, no expression of P60 was detectable in retransformants of K49-derived revertants. Reversion to the nontransformed phenotype was associated with increased cytosine methylation in proviral DNA sequences, whereas in spontaneous retransformants methylation tended to resume control levels. These findings demonstrate regulation of viral oncogene mediated transformation by cytosine methylation and suggest that transcription of proviral DNA is under both viral and cellular control. They furthermore suggest that processes involved in regulation of proviral expression do not affect all such proviruses simultaneously in the same way.

Variable stability of a selectable provirus after retroviral vector gene transfer into human cells

Human lymphoblasts deficient in the enzyme hypoxanthine-guanine phosphoribosyltransferase (HPRT) were infected with an amphotropic helper-free retroviral vector expressing human HPRT cDNA. The stability and expression of the HPRT provirus in five cell lines with different proviral integration sites were examined by determining HPRT mutation and reversion frequencies and by blot hybridization studies. Mutation to the HPRT-negative phenotype occurred at frequencies of approximately 4 X 10(-5) to 3 X 10(-6) per generation. Most mutations in each of the five cell lines were associated with partial or complete deletions or rearrangements of the provirus. Several mutants retained a grossly intact HPRT provirus, and in one such mutant HPRT shutdown resulted from a revertible epigenetic mechanism that was not associated with global changes in proviral methylation. Therefore, mutation and shutdown of the HPRT provirus in human lymphoblasts result from mechanisms similar to those reported for several other avian and mammalian replication-competent retroviruses.

DNA methylation and transcriptional controls of proviral DNA in avian sarcoma virus-transformed mammalian cells

Restriction mapping has been used to study the integration state of the single provirus present in the DNA of two subclones, RS2/3 and RS2/6, of hamster cells transformed in vitro by Rous sarcoma virus, but differing markedly in their level of proviral transcription which was higher in RS2/3 cells. It was observed that both proviruses are complete and located at the same integration site in each DNA. However, the RS2/6 provirus and its flanking cellular sequences were found to be hypermethylated, although a very short region was hypomethylated at about 1 kb upstream of the src gene. A low level of methylation was observed in RS2/3 cells, in the proviral region. Northern analysis of viral RNA detected only the src mRNA in RS2/6 cells, whereas the two other viral mRNA were found in RS2/3 cells, however their levels were very low compared to that of the src mRNA. These findings suggest a correlation between the methylation state and the transcriptional control of the proviral genes. Sequences responsible for such a control by methylation should lie within both the provirus and its 5' flanking cellular sequences.

Rearrangements of viral and cellular DNA are often associated with expression of Rous sarcoma virus in rat cells

Rous sarcoma virus (RSV) proviruses integrated within the DNA of transformed rat cells frequently display duplications of variable segments of proviral DNA upstream of an intact provirus. The rearrangement in the A11 clone of transformed rat cells consists of a partial duplication of both viral and cellular DNA segments whose origin is a region of approximately 4 kb encompassing the 3' virus-cell junction. Transposition of this DNA appears to have occurred at or after virus integration by a mechanism involving at least two recombination events. In every case examined, including A11, the transcriptional organization of the original provirus has been conserved and viral RNA expression appears to occur normally. The frequency of such rearranged proviruses in the DNA of transformed rat cells suggests that upstream rearrangements may influence provirus expression.

The chromatin structure of Rous sarcoma proviruses is changed by factors that act in trans in cell hybrids

In several lines of Rous sarcoma virus (RSV)-transformed rat cells the proviruses are in a configuration typical of active eukaryotic genes. They are sensitive to pancreatic DNase I, with sites hypersensitive to nuclease near the 5' end of the genome, they are close to the nuclear 'cage' and they show a low level of cytosine methylation in CpG doublets. In contrast, in phenotypically untransformed hybrids between these cells and uninfected rat or mouse cells, RSV inactivity is associated with hypermethylation of the provirus, reduced DNase I sensitivity (in two out of three examples) and, where examined, relative remoteness from the nuclear cage. These changes in proviral configuration, which occur rarely in spontaneous reversion of transformed cells, can thus be induced at high frequency and stability in cell hybrids by trans-acting influences of the uninfected parents.