Endogenous Retrovirus Genomes Research Articles

An endogenous lentivirus in the germline of a rodent

Lentiviruses (genus Lentivirus) are complex retroviruses that infect a broad range of mammals, including humans. Unlike many other retrovirus genera, lentiviruses have only rarely been incorporated into the mammalian germline. However, a small number of endogenous retrovirus (ERV) lineages have been identified, and these rare genomic “fossils” can provide crucial insights into the long-term history of lentivirus evolution. Here, we describe a previously unreported endogenous lentivirus lineage in the genome of the South African springhare (Pedetes capensis), demonstrating that the host range of lentiviruses has historically extended to rodents (order Rodentia). Furthermore, through comparative and phylogenetic analysis of lentivirus and ERV genomes, considering the biogeographic and ecological characteristics of host species, we reveal broader insights into the long-term evolutionary history of the genus.

Efficient and Safe Editing of Porcine Endogenous Retrovirus Genomes by Multiple-Site Base-Editing Editor.

Gene-modified miniature pigs serve as alternative tissue and organ donors for xenotransplantation to alleviate the shortage of human allogenic organs. However, the high copy number of porcine endogenous retrovirus (PERV) genomes integrates with the porcine genome, which has a potential risk of cross-species transmission and hinders the clinical practice of xenotransplantation. Recently, CRISPR/Cas9 has been used to inactivate PERVs. However, Cas9 also triggers severe DNA damage at multiple integrated PERV sites in the porcine genome, which induces senescence and apoptosis of porcine cells. In this study, the cytosine base editor (CBE), an efficient and safe editor that does not cause DNA double strand breaks (DSBs), was used for PERV editing to reduce cytotoxic effects. Seven sgRNAs were set to target gag and pol loci of PERVs to induce premature stop codons. We found that approximately 10% of cell clones were completely inactivated for PERVs in pig ST cells, and the plasmid that was used for editing the PERVs did not integrate into host genome and influence the karyotype of the modified cells. Our studies offer a powerful and safe strategy for further generating PERV-knockout pigs using base editors.

Ендогенні ретровіруси PERV А/С у геномах свиней українських порід та їх зв’язок з рівнем осалюваності туш

The article presents the analysis of the PERV retrovirus subtypes A and C frequency in populations of Ukrainian and foreign breed pigs. Different frequencies of the PERV A/C genome presence in animals of the studied breeds were established. The largest relative number was observed in the group of wild pigs (86%), the smallest was in the groups of Poltava meat and Piétrain breeds. Animals free of both virus subtypes were found in all study groups. The article considers the hypothesis of an increase in the frequency of PERV retrovirus in the pigs’ genome during domestication. Its integration caused a gene mutation responsible for fat deposition which led to increased fat amount in carcasses and could be picked up by selection in the process of creating breeds. However, there is no obvious link between the spread of the virus in modern breeds in different areas of productivity. Also, there is no association between carcass fat amount and the presence of PERV in the genome. It is established that the information on the PERV A/C distribution in pig breeds hold in Ukraine is useful in terms of the possibility of using each of them for xenotransplantation. Also, this information can be used to justify the selection of founding breeds in order to create lines of pigs free from the endogenous retrovirus genome.

A Novel Y Chromosome Microdeletion With the Loss of an Endogenous Retrovirus Related, Testis Specific Transcript in AZFb Region

We identified the endogenous retroviruses associated with TTYs (testis specific transcripts linked to the Y) in the AZFb region. We evaluated the relationship between endogenous retroviruses, and TTY expression patterns and function in spermatogenesis. We identified family members of TTYs in the AZFb region using computational screening. After investigating the relationship between the endogenous retrovirus genome and TTY expression patterns we screened genomic polymerase chain reaction products from TTY13 amplified from 790 Japanese men, including 275 with azoospermia, 285 with oligozoospermia and 230 who were fertile. Computational screening revealed that 3 members of the TTY family, TTY9, 10 and 13, were regulated by endogenous retroviruses in the AZFb region. Homologous recombination between long terminal repeat of the TTY13 associated human endogenous retrovirus-K14C resulted in TTY13 deletion events. These deletions were more common in patients with azoospermia and oligozoospermia than in fertile males. Specifically 15.63% of the azoospermia group, 10.88% of the oligozoospermia group and 0% of fertile controls had only the deletion variant, indicating an association between the homologous recombination rate and the severity of spermatogenesis failure that was statistically significant (p <0.05). Because of the finding of what are to our knowledge novel microdeletions due to endogenous retrovirus in the AZFb region, our study raises the possibility that specific variations in genomic structure may contribute to some forms of human idiopathic male infertility.

Mobilization of Endogenous Retroviruses in Mice after Infection with an Exogenous Retrovirus

Mammalian genomes harbor a large number of retroviral elements acquired as germ line insertions during evolution. Although many of the endogenous retroviruses are defective, several contain one or more intact viral genes that are expressed under certain physiological or pathological conditions. This is true of the endogenous polytropic retroviruses that generate recombinant polytropic murine leukemia viruses (MuLVs). In these recombinants the env gene sequences of exogenous ecotropic MuLVs are replaced with env gene sequences from an endogenous polytropic retrovirus. Although replication-competent endogenous polytropic retroviruses have not been observed, the recombinant polytropic viruses are capable of replicating in numerous species. Recombination occurs during reverse transcription of a virion RNA heterodimer comprised of an RNA transcript from an endogenous polytropic virus and an RNA transcript from an exogenous ecotropic MuLV RNA. It is possible that homodimers corresponding to two full-length endogenous RNA genomes are also packaged. Thus, infection by an exogenous virus may result not only in recombination with endogenous sequences, but also in the mobilization of complete endogenous retrovirus genomes via pseudotyping within exogenous retroviral virions. We report that the infection of mice with an ecotropic virus results in pseudotyping of intact endogenous viruses that have not undergone recombination. The endogenous retroviruses infect and are integrated into target cell genomes and subsequently replicate and spread as pseudotyped viruses. The mobilization of endogenous retroviruses upon infection with an exogenous retrovirus may represent a major interaction of exogenous retroviruses with endogenous retroviruses and may have profound effects on the pathogenicity of retroviral infections.

Tissue specific high level expression of a full length human endogenous retrovirus genome transgene, HERV-R, under control of its own promoter in rats.

Human endogenous retrovirus-R (HERV-R) is one of a full length HERV with a long open reading frame in the env region. The env transcripts are expressed in various human tissues. To investigate the biological role of HERV-R in vivo, we established two lines of transgenic rats carrying a full sequence of HERV-R under control of its own long terminal repeat (LTR) promoter. One line with tandem integration of multiple copies of the transgene expressed HERV-R mRNA in various organs with different expression levels and relatively higher in Harderian and submandibular salivary glands. In another line, the transgene was integrated as a single copy in a haploid and the expression was detected only in Harderian and submandibular salivary glands. In the placenta, one of the tissues with high levels of the HERV-R expression in humans, the transcription was evident starting the 12th day after gestation. A rabbit antiserum against synthetic peptides corresponding with the HERV-R env gene sequence led to detection of an 85 kDa product as a glycoprotein in the Harderian glands. While no pathological significance was observed in either line, the transgenic rat may prove to be a suitable model for analyzing the role of HERV-R function in vivo.

Heart valves from pigs and the porcine endogenous retrovirus: Experimental and clinical data to assess the probability of porcine endogenous retrovirus infection in human subjects

Objective: Replacement of heart valves in human subjects has become a routine procedure in cardiac operations. We sought to investigate whether commercially available glutaraldehyde-fixed porcine heart valve prostheses cause porcine endogenous retrovirus infection in human subjects because recent studies revealed that human cells can be infected with porcine endogenous retrovirus. Methods: Blood samples of 18 patients who underwent aortic or mitral valve replacement with porcine heart valves were collected 6 months to 3 years after operation and tested for porcine endogenous retrovirus by means of polymerase chain reaction and reverse transcriptase–polymerase chain reaction. In addition, we tried to trace porcine endogenous retrovirus in 3 commercially available, glutaraldehyde-fixed, porcine heart valves. Results: Porcine endogenous retrovirus can be easily detected in native porcine heart valves and degrades completely within 1 week of fixation in glutaraldehyde. In all 3 commercially available porcine heart valves, no traces of porcine endogenous retrovirus were found. All blood samples showed negative test results for the porcine endogenous retrovirus genome. Conclusion: Our results indicate that glutaraldehyde fixation of porcine heart valves reliably prevents cross-species transmission of porcine endogenous retrovirus. (J Thorac Cardiovasc Surg 2001;121:697-701)

Study of full-length porcine endogenous retrovirus genomes with envelope gene polymorphism in a specific-pathogen-free Large White swine herd.

Specific-pathogen-free (SPF) swine appear to be the most appropriate candidate for pig to human xenotransplantation. Still, the risk of endogenous retrovirus transmission represents a major obstacle, since two human-tropic porcine endogenous retroviruses (PERVs) had been characterized in vitro (P. Le Tissier, J. P. Stoye, Y. Takeuchi, C. Patience, and R. A. Weiss, Nature 389:681-682, 1997). Here we addressed the question of PERV distribution in a French Large White SPF pig herd in vivo. First, PCR screening for previously described PERV envelope genes envA, envB, and envC (D. E. Akiyoshi, M. Denaro, H. Zhu, J. L. Greenstein, P. Banerjee, and J. A. Fishman, J. Virol. 72:4503-4507, 1998; Le Tissier et al., op. cit.). demonstrated ubiquity of envA and envB sequences, whereas envC genes were absent in some animals. On this basis, selective out-breeding of pigs of remote origin might be a means to reduce proviral load in organ donors. Second, we investigated PERV genome carriage in envC negative swine. Eleven distinct full-length PERV transcripts were isolated. The sequence of the complete envelope open reading frame was determined. The deduced amino acid sequences revealed the existence of four clones with functional and five clones with defective PERV PK-15 A- and B-like envelope sequences. The occurrence of easily detectable levels of PERV variants in different pig tissues in vivo heightens the need to assess PERV transmission in xenotransplantation animal models.

The expression of ERV-3 mRNA in a choriocarcinoma model of trophoblastic differentiation

ERV-3 is a human endogenous retrovirus genome that has been isolated and sequenced. The expression of ERV-3 mRNA and its protein in the syncytiotrophoblast of the placenta suggests that ERV-3 proteins may play a role in placental development. The choriocarcinoma cell line BeWo, a model of trophoblast differentiation, is maintained in cell culture in an undifferentiated and non-fused state. Upon addition of forskolin, a cAMP inducing agent, BeWo cells undergo intercellular fusion and differentiation. In untreated BeWo, low level expression of ERV-3 env -specific mRNA was only detected by RT-PCR. Northern blot analysis showed that the expression of 3.5 kb ERV-3 env -specific gene was increased significantly in BeWo cells after 48 hours forskolin treatment and decreased at 96 hours. The up-regulation of ERV-3 env -specific gene was concurrent with the production of human chorionic gonadotropin (β-hCG) mRNA, a trophoblast differentiation marker. In situ hybridization studies revealed that the peak expression of ERV-3 env mRNA occurred at 72 hours after forskolin treatment, when about 80% of cells were fused to form multinuclear syncytia. These results indicate that the expression of ERV-3 env -specific mRNA is up-regulated during forskolin-induced BeWo cell differentiation, suggesting a role for ERV-3 gene products in that process.

Human oocytes express murine retroviral equivalents.

Unfertilized human oocytes expressed a gp70-related epitope as observed when staining section immunocytochemically with a panel of monoclonal antibodies against gp70 of murine leukemia virus. Some oocytes also expressed virus-like particles at the cell membrane. Follicular fluids, corresponding to these oocytes, contained p30- and gp70-related antigens, reverse transcriptase, and an increased titer of interferon. The three- to four-cell human cleavage stages did not contain the gp70-related epitope. It is concluded that human oocytes, but not early cleavage stages, express products that suggest the presence of an active endogenous retrovirus genome.

Human endogenous retroviruses.

AbstractSeveral studies have revealed the presence in human DNA of thousands of endogenous retrovirus genomes, or HERVs. Many HERVs are related to extant retroviruses that infect other vertebrates and some have been present in the germ line of primates for millions of years. Although the HERVs that have been isolated are defective and thus do not encode infectious retroviruses, there may be HERVs that are capable of infection. In addition, because HERVs are so ancient in the human lineage, evolution of the human genome may have included the acquisition of some HERV genes for strictly cellular functions.

Stimulation of expression of the human endogenous retrovirus genome by female steroid hormones in human breast cancer cell line T47D.

Expression of the human endogenous retrovirus genome HERV-K, homologous to mouse mammary tumor virus, was investigated in cultured human tumor cells. In several cell lines, the HERV-K genome was expressed as an 8.8-kilobase poly(A)+ RNA which appeared to be a full-size transcript of this genome. In the human breast cancer cell line T47D, stimulation of HERV-K genome expression by progesterone was observed after estradiol treatment.

Two strains of baboon endogenous virus demonstrate a high degree of genetic conservation

Molecular clones of the baboon endogenous viruses 455K, from Papio anubis, and M 7, from Papio cynocephalus, have been constructed from unintegrated viral DNA. Although two specific restriction sites do distinguish the two, detailed restriction maps are nearly identical and heteroduplex molecules show complete homology. The latter observations indicate that this endogenous retrovirus genome has been strongly conserved among different species of baboon.

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Differential Expression of Two Distinct Endogenous Retrovirus Genomes in Developing Tissues of the Domestic Cat&lt;xref ref-type="fn" rid="FN2"&gt;2&lt;/xref&gt;

Transfection by exogenous and endogenous murine retrovirus DNAs

We have used DNA transfection to study the endogenous retrovirus genomes inherited by uninfected mouse cells. Quantitative assays for infectious DNAs of ecotropic and xenotropic murine leukemia viruses (MuLVs) were developed using donor DNAs of cells that were exogenously infected with ecotropic Moloney, AKR or BALB MuLVs, or with xenotropic AKR, BALB or NZB MuLVs. The DNAs of cells exogenously infected with ecotropic MuLVs had specific infectivities of approximately 0.5 infectious units (IU) per μg DNA in transfection assays on NIH/3T3 cells. The DNAs of cells exogenously infected with xenotropic MuLVs had specific infectivities of approximately 0.2 IU/μg DNA in transfection assays on mink CCL64 cells. In contrast, the DNAs of uninfected NIH/3T3, BALB/3T3 and AKR-2B mouse cells were noninfectious when assayed for infectious endogenous ecotropic MuLV DNAs (<0.001 IU/μg DNA). Similarly, the infectivities of xenotropic MuLV DNAs of uninfected NIH/3T3, BALB/3T3, AKR-2B and NZB-Q mouse cells were more than 100 fold lower than the infectivities of DNAs of xenotropic MuLV-infected cells. Furthermore, the DNAs of BALB/3T3 cells transformed by Kirsten murine sarcoma virus (MSV) or by simian virus 40 (SV40) were noninfectious for either ecotropic or xenotropic MuLV, although these cells contained infectious transforming DNAs of MSV or SV40. The endogenous MuLV genomes of uninfected mouse cells thus appeared to differ from the MuLV proviruses of MuLV-infected cells. These results are consistent with the hypothesis that endogenous MuLV genomes are linked to cellular DNA sequences which result in both inefficient transcription of endogenous MuLV genomes and the reduced infectivity of endogenous MuLV DNAs in transfection assays.