Differences between cellular integration sites of transcribed and nontranscribed Rous sarcoma proviruses

Sites of retroviral DNA integration: From basic research to clinical applications

One of the most crucial steps in the life cycle of a retrovirus is the integration of the viral DNA (vDNA) copy of the RNA genome into the genome of an infected host cell. Integration provides for efficient viral gene expression as well as for the segregation of viral genomes to daughter cells upon cell division. Some integrated viruses are not well expressed, and cells latently infected with human immunodeficiency virus type 1 (HIV-1) can resist the action of potent antiretroviral drugs and remain dormant for decades. Intensive research has been dedicated to understanding the catalytic mechanism of integration, as well as the viral and cellular determinants that influence integration site distribution throughout the host genome. In this review, we summarize the evolution of techniques that have been used to recover and map retroviral integration sites, from the early days that first indicated that integration could occur in multiple cellular DNA locations, to current technologies that map upwards of millions of unique integration sites from single in vitro integration reactions or cell culture infections. We further review important insights gained from the use of such mapping techniques, including the monitoring of cell clonal expansion in patients treated with retrovirus-based gene therapy vectors, or patients with acquired immune deficiency syndrome (AIDS) on suppressive antiretroviral therapy (ART). These insights span from integrase (IN) enzyme sequence preferences within target DNA (tDNA) at the sites of integration, to the roles of host cellular proteins in mediating global integration distribution, to the potential relationship between genomic location of vDNA integration site and retroviral latency.

Mapping insertions, deletions and SNPs on Venter's chromosomes

BACKGROUND

The very recent availability of fully sequenced individual human genomes is a major revolution in biology which is certainly going to provide new insights into genetic diseases and genomic rearrangements.

RESULTS

We mapped the insertions, deletions and SNPs (single nucleotide polymorphisms) that are present in Craig Venter's genome, more precisely on chromosomes 17 to 22, and compared them with the human reference genome hg17. Our results show that insertions and deletions are almost absent in L1 and generally scarce in L2 isochore families (GC-poor L1+L2 isochores represent slightly over half of the human genome), whereas they increase in GC-rich isochores, largely paralleling the densities of genes, retroviral integrations and Alu sequences. The distributions of insertions/deletions are in striking contrast with those of SNPs which exhibit almost the same density across all isochore families with, however, a trend for lower concentrations in gene-rich regions.

CONCLUSIONS

Our study strongly suggests that the distribution of insertions/deletions is due to the structure of chromatin which is mostly open in gene-rich, GC-rich isochores, and largely closed in gene-poor, GC-poor isochores. The different distributions of insertions/deletions and SNPs are clearly related to the two different responsible mechanisms, namely recombination and point mutations.

A novel, immortal, and multipotent human neural stem cell line generating functional neurons and oligodendrocytes

The discovery and study of neural stem cells have revolutionized our understanding of the neurogenetic process, and their inherent ability to adopt expansive growth behavior in vitro is of paramount importance for the development of novel therapeutics based on neural cell replacement. Recent advances in high-throughput assays for drug development and gene discovery dictate the need for rapid, reproducible, long-term expansion of human neural stem cells (hNSCs). In this view, the complement of wild-type cell lines currently available is insufficient. Here we report the establishment of a stable human neural stem cell line (immortalized human NSCs [IhNSCs]) by v-myc-mediated immortalization of previously derived wild-type hNSCs. These cells demonstrate three- to fourfold faster proliferation than wild-type cells in response to growth factors but retain rather similar properties, including multipotentiality. By molecular biology, biochemistry, immunocytochemistry, fluorescence microscopy, and electrophysiology, we show that upon growth factor removal, IhNSCs completely downregulate v-myc expression, cease proliferation, and differentiate terminally into three major neural lineages: astrocytes, oligodendrocytes, and neurons. The latter are functional, mature cells displaying clear-cut morphological and physiological features of terminally differentiated neurons, encompassing mostly the GABAergic, glutamatergic, and cholinergic phenotypes. Finally, IhNSCs produce bona fide oligodendrocytes in fractions up to 20% of total cell number. This is in contrast to the negligible propensity of hNSCs to generate oligodendroglia reported so far. Thus, we describe an immortalized hNSC line endowed with the properties of normal hNSCs and suitable for developing the novel, reliable assays and reproducible high-throughput gene and drug screening that are essential in both diagnostics and cell therapy studies.

Demethylation of host-cell DNA at the site of avian retrovirus integration

The transcriptional activity of an integrated retroviral copy strongly depends on the adjacent host-cell DNA at the site of integration. Transcribed DNA loci as well as cis-acting sequences like enhancers or CpG islands usually permit expression of nearby integrated proviruses. In contrast, proviruses residing close to cellular silencers tend to transcriptional silencing and CpG methylation. Little is known, however, about the influence of provirus integration on the target sequence in the host genome. Here, we report interesting features of a simplified Rous sarcoma virus integrated into a non-transcribed hypermethylated DNA sequence in the Syrian hamster genome. After integration, CpG methylation of this sequence has been lost almost completely and hypomethylated DNA permits proviral transcription and hamster cell transformation by the proviral v-src oncogene. This, however, is not a stable state, and non-transformed revertants bearing transcriptionally silenced proviruses segregate with a high rate. The provirus silencing is followed by DNA methylation of both provirus regulatory regions and adjacent cellular sequences. This CpG methylation is very dense and resistant to the demethylation effects of 5-aza-2(')-deoxycytidine and/or trichostatin A. Our description exemplifies the capacity of retroviruses/retroviral vectors to overcome, at least transiently, negative position effects of DNA methylation at the site of integration.

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.

Retroviruses in foreign species and the problem of provirus silencing

Retroviruses are known to integrate in the host cell genome as proviruses, and therefore they are prone to cell-mediated control at the transcriptional and posttranscriptional levels. This plays an important role especially after retrovirus heterotransmission to foreign species, but also to differentiated cells. In addition to host cell-mediated blocks in provirus expression, also so far undefined host specificities, deciding upon the pathogenic manifestation of retrovirus heterotransmission, are in play. In this respect, we discuss especially the occurrence of wasting disease and immunodeficiency syndrome, which we established also in avian species using avian leukosis virus subgroup C (ALV-C) inoculated in mid-embryogenesis in duck or chicken embryos. The problem of provirus downregulation in foreign species or in differentiated cells has been in the recent years approached experimentally. From a series of observations it became apparent that provirus downregulation is mediated by its methylation, especially in the region of proviral enhancer-promoter located in long terminal repeats (LTR). Several strategies have been devised in order to protect the provirus from methylation using LTR modification and/or introducing in the LTR sequence motifs acting as antimethylation tags. In such a way the expression of retroviruses and vectors in foreign species, as well as in differentiated cells, has been significantly improved. The complexity of the mechanisms involved in provirus downregulation and further possibilities to modulate it are discussed.

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.

The regional integration of retroviral sequences into the mosaic genomes of mammals

We have reviewed here three sets of data concerning the integration of retroviral sequences in the mammalian genome: (i) our experimental localization of a number of proviruses integrated in isochores characterized by different GC levels; (ii) results from other laboratories on the localization of retroviral sequences in open chromatin regions and/or next to CpG islands; and (iii) our compositional analysis of genes located in the neighborhood of integrated retroviral sequences. The three sets of data have provided a very consistent picture in that a compartmentalized, isopycnic integration of expressed proviruses appears to be the rule ('isopycnic' refers to the compositional match between viral and host sequences around the integration site). The results reviewed here suggest that: (i) integration of proviral sequences is targeted initially towards 'open chromatin regions'; while these exist in both GC-rich and GC-poor isochores, the 'open chromatin regions' of GC-rich isochores are the main targets for integration of retroviral sequences because of their much greater abundance; (ii) isopycnicity is associated with stability of integration; indeed, even non-expressed integrated retroviral sequences tend to show an isopycnic localization in the genome; (iii) transcription of integrated viral sequences (like transcription of host genes) appears to be associated, as a rule, with an isopycnic localization, as indicated by transcribed sequences that show an isopycnic integration and act in trans; (iv) selection plays a role in the choice of specific sites within an isopycnic region; in exceptional cases [such as mouse mammary tumor virus (MMTV) activating GC-rich oncogenes], selection may override isopycnicity.

High-efficiency retrovirus-mediated gene transfer into the livers of mice

Recombinant retroviral vectors represent an attractive means of transferring genes into the liver because they integrate in the host cell genome and result in permanent gene expression. However, efficient gene transfer is limited by the requirement of active cell division for integration. Surgical partial hepatectomy has been the traditional method of inducing hepatocellular proliferation, but this invasive approach would be difficult to justify in clinical gene therapy. As an alternative, we used a recombinant adenovirus expressing a nonsecreted form of urokinase plaminogen activator (Ad.PGKmuPA), which results in liver regeneration over a period of 8 days. When a high-titer retroviral vector was continuously infused into the portal vein of mice during this period of hepatocyte proliferation, 33.5% of hepatocytes were stably transduced. In addition, high-level expression of a secreted transgene reporter was sustained for at least 48 weeks (length of experiment). We investigated the influence of vector titer on the in vivo transduction efficiency in our system, and found that the total number of infectious retroviral particles delivered per target cell is a critical factor. The results presented here demonstrate the ability to obtain a high gene transfer efficiency and long-term gene expression in hepatocytes in vivo without the need for surgical hepatectomy. The two-vector system described here may be of clinical relevance, as the level of hepatic gene transfer achieved has potential to be curative for a large number of genetic liver diseases.

Sp1 binding sites inserted into the rous sarcoma virus long terminal repeat enhance LTR-driven gene expression

Although the Rous sarcoma virus (RSV) long terminal repeat (LTR) is an efficient promoter of transcription, most RSV proviruses are down-regulated upon retroviral integration in non-permissive mammalian cells. Among other mechanisms, DNA methylation has been shown to be involved in proviral silencing. The presence of Sp1 binding sites has been demonstrated to be essential for protection of a CpG island and also non-island DNA regions from de novo methylation. Also, the presence of these sites in the LTRs correlates with the transcriptional activity of certain proviral structures. Using transient and stable transfection assays, we demonstrate that insertion of Sp1 binding sites into the RSV LTR remarkably increases expression of the LTR-driven genes in permissive and non-permissive cells, despite the reported negative effect of insertion of the non-specific DNA into the LTR promoter/enhancer sequences. Particular arrangement of inserted Sp1 sites was effective even in stably transfected reporter gene constructs into non-permissive mammalian cells, where additional factors exert negative effects on expression.

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.

Transcriptional Silencing of Retroviral Vectors

Although retroviral vector systems have been found to efficiently transduce a variety of cell types in vitro, the use of vectors based on murine leukemia virus in preclinical models of somatic gene therapy has led to the identification of transcriptional silencing in vivo as an important problem. Extinction of long-term vector expression has been observed after implantation of transduced hematopoietic cells as well as fibroblasts, myoblasts and hepatocytes. Here we review the influence of vector structure, integration site and cell type on transcriptional silencing. While down-regulation of proviral transcription is known from a number of cellular and animal models, major insight has been gained from studies in the germ line and embryonal cells of the mouse. Key elements for the transfer and expression of retroviral vectors, such as the viral transcriptional enhancer and the binding site for the tRNA primer for reverse transcription may have a major influence on transcriptional silencing. Alterations of these elements of the vector backbone as well as the use of internal promoter elements from housekeeping genes may contribute to reduce transcriptional silencing. The use of cell culture and animal models in the testing and improvement of vector design is discussed. Copyright 1996 S. Karger AG, Basel

The LTR, v-src, LTR provirus in H-19 hamster tumor cell line is integrated adjacent to the negative regulatory region

The tumor hamster cell line H-19 harbors a single copy LTR, v-src, LTR provirus that becomes permanently transcriptionally suppressed in morphological revertants segregating at high rate from this cell line. Our previous data document that the provirus suppression is mediated by epigenetic cell-regulatory mechanisms. In this report, we concentrate on cellular sequences neighboring the integration site. The locus is unique for Syrian hamster and is not detectable in DNA of several animal species. No restriction sites that usually hint at the presence of CpG islands were found in the significantly close vicinity of the provirus. Nevertheless, the chromosomal DNA flanking the provirus is rich in GC content (57.8%). We localized a 0.5-kb region downstream from the provirus that remarkably inhibits transcription in the transient expression assay and is effective both on the homologous RSV LTR promoter/enhancer and heterologous SV40 promoter. We propose that a cellular trans-acting factor is involved in the silencing of the reporter gene. Since this activity is comparable both in transformed and revertant cells, we speculate that this down-regulatory region makes the permissive integration locus prone to provirus silencing initiated by other fluctuating stimuli.

Expression of V-SRC and chromosome analysis of a newly established cell line from rat sarcoma induced by an avian retroviral strain

In the newly established rat sarcoma cell line LSR-SF (SR) expression of pp60v-src was detected. Karyotype analyses revealed various chromosome aberrations during prolonged passaging of the tumor cells in vitro. Polyploidy was found to be a characteristic feature of the line studied. A large metacentric chromosome persistently present in the cells was accepted as a line marker.

Lack of correlation between basal expression levels and susceptibility to transcriptional shutdown among single-gene murine leukemia virus vector proviruses

Integrated retroviruses or retroviral vectors may be transcriptionally inactive although their promoter-enhancer regions are able to direct transcription in the host cell. We have used single-gene retroviral vectors with a long terminal repeat-directed neo marker gene to determine if the level of transcription relates to the susceptibility of a provirus to inactivation. We used two isogenic vectors, carrying long terminal repeats with a strong and a weak transcriptional enhancer derived from SL3-3 and Akv murine leukemia viruses, respectively. Nonselected cell clones of the murine lymphoid cell line L691 with single integrated vector proviruses exhibiting a 20-fold range of initial expression levels were studied. The basal expression level of a given cell clone with a single provirus did not show any pattern of correlation with the long-term stability of expression, as monitored for periods up to 150 days. Our results thus indicate that the inactivation mechanism operates independently of the initial transcriptional activity of the provirus.

Analysis of a viral integration event in a CG-rich region at the 1p36 human chromosomal site

The preinsertion site of an adenovirus-5/simian virus 40 recombinant construct (Ad5/SV40) has been cloned and sequenced. Our data suggest that viral integration has occurred in a genomic region which has been the target of multiple events of Alu element retropositions within a TAA minisatellite. Extensive homologies between the left viral end and the host cellular DNA were also observed. The compositional similarity between Adenoviridae and the region of viral integration is consistent with the observed insertion of exogenous DNA in isochores of similar composition [G. Bernardi, Annu. Rev. Genet. 23 (1989) 637-661].

The isopycnic, compartmentalized integration of Rous sarcoma virus sequences

Rous sarcoma virus (RSV) can cause tumors in hamsters, which harbor complete or partially deleted RSV sequences, in their genomes. Here we have studied the localization of RSV sequences integrated into the genome of cell lines derived from six independent hamster tumors. We have found that integration occurred in the isochores richest in guanine + cytosine, of the host genome, as it had been previously observed for bovine leukemia and hepatitis B viral sequences. The integration of RSV proviral sequences is, therefore, 'isopycnic' (i.e., it takes place in host genome sequences which compositionally match the viral sequences) and compartmentalized (i.e., it occurs in a small compositional compartment of the host genome). The hamster genome compartment hosting RSV sequences precisely corresponds to a compartment of the human genome which is the most active in both transcription and recombination. The notion of a compartmentalized, isopycnic integration of RSV proviral sequences fits, therefore, with the viral integration into transcriptionally active and recombinogenic regions of the host genome observed by other authors, but is broader, in that it includes, in addition, the requirement for a compositional match between host genome sequences and expressed viral sequences.