Human endogenous retroviruses and immune disease

Genomic flexibility of human endogenous retrovirus type K

Human endogenous retrovirus type K (HERV-K) proviruses are scattered throughout the human genome, but as no infectious HERV-K virus has been detected to date, the mechanism by which these viruses replicated and populated the genome remains unresolved. Here, we provide evidence that, in addition to the RNA genomes that canonical retroviruses package, modern HERV-K viruses can contain reverse-transcribed DNA (RT-DNA) genomes. Indeed, reverse transcription of genomic HERV-K RNA into the DNA form is able to occur in three distinct times and locations: (i) in the virus-producing cell prior to viral release, yielding a DNA-containing extracellular virus particle similar to the spumaviruses; (ii) within the extracellular virus particle itself, transitioning from an RNA-containing particle to a DNA-containing particle; and (iii) after entry of the RNA-containing virus into the target cell, similar to canonical retroviruses, such as murine leukemia virus and HIV. Moreover, using a resuscitated HERV-K virus construct, we show that both viruses with RNA genomes and viruses with DNA genomes are capable of infecting target cells. This high level of genomic flexibility historically could have permitted these viruses to replicate in various host cell environments, potentially assisting in their many integration events and resulting in their high prevalence in the human genome. Moreover, the ability of modern HERV-K viruses to proceed through reverse transcription and package RT-DNA genomes suggests a higher level of replication competency than was previously understood, and it may be relevant in HERV-K-associated human diseases.

IMPORTANCE

Retroviral elements comprise at least 8% of the human genome. Of all the endogenous retroviruses, HERV-K viruses are the most intact and biologically active. While a modern infectious HERV-K has yet to be found, HERV-K activation has been associated with cancers, autoimmune diseases, and HIV-1 infection. Thus, determining how this virus family became such a prevalent member of our genome and what it is capable of in its current form are of the utmost importance. Here, we provide evidence that HERV-K viruses currently found in the human genome are able to proceed through reverse transcription and historically utilized a life cycle with a surprising degree of genomic flexibility in which both RNA- and DNA-containing viruses were capable of mediating infection.

Regulation of murine endogenous retroviruses in the thymus after injury1,2

We recently reported the induction of murine endogenous retroviruses (murine AIDS-related) in several distant organs of mice after burn injury. The regulation of endogenous retroviruses in response to burn injury was further investigated in the thymus. Female C57BLKS/J mice were subjected to 18% total body surface area flame burn injury. Thymus tissues collected at several time points (3 h to 7 days) were analyzed for the expression of subgenomic transcripts of murine endogenous retroviruses by RT-PCR. Interestingly, a novel 1.7-Kb subgenomic transcript and a recently described 1.1 Kb subgenomic transcript of murine endogenous retroviruses were transiently down-regulated in the thymus at day 1 after injury. The 1.7 Kb transcript has a coding potential for a truncated form of the envelope protein (total 214 amino acids) with a deletion of 418 amino acids near the C-terminus. The second transcript of 1.1 Kb has an open reading frame for the C-terminal transmembrane domain of the envelope protein including the p2E protein (R peptide). These data suggest the pathophysiologic effects of burn injury on the differential expression of murine endogenous retroviruses in the thymus after injury.

Injury-associated induction of two novel and replication-defective murine retroviral RNAs in the liver of mice

Injury can alter the expression of numerous genes in affected tissues as well as in distant organs. The mouse genome harbors numerous copies of endogenous murine leukemia virus (MuLV)-related retroviral sequences. Mouse liver tissues harvested after burn injury were subjected to RT-PCR analysis to investigate the regulation of MuLV-related sequences using a primer set capable of amplifying the full-length transcript. A doublet of approximately 5-kb was transiently up-regulated at 3 and 6 h after injury. Sequence analyses revealed that these are novel defective endogenous retroviral sequences (MuLV(LI-8) and MuLV(LI-12)), which are predominantly characterized by major deletions in pol and env genes. The MuLV(LI-8) clone is 4.85 kb long and the deduced gag polypeptide sequence was almost identical to a previously reported replication-defective retroviral sequence associated with immunesuppression. In the MuLV(LI-12) clone of 5.06 kb, there were two truncated gag open reading frames (ORFs) and 1 pol ORF fused to the C-terminus of the env p15E. Furthermore, the ORFs for the unique gag p12 presumed to be responsible for the immunesuppression were present in both clones. These novel replication-defective MuLVs may participate in the pathogenesis of distant organs after injury.

Molecular analysis of endogenous retrovirus HRES-1: identification of frameshift mutations in region encoding putative 28-kDa autoantigen

A possible involvement of HTLV-1-related endogenous sequence 1 (HRES-1) in autoimmune diseases has been recently reported. In primate cells, PCRs and RT-PCRs using specific primers reveal the presence and the transcription of gag-related sequences. However antisera generated against selected HRES-1 peptides failed to detect a 28-kDa protein deduced from the translated gag ORF and described previously. Such discordant results led us to perform DNA cloning and sequencing of LTR- and gag-related nucleotidic fragments. Repeated sequence analyses on distinct samples revealed frameshift mutations in the gag and LTR ORFs. Our sequence analyses detected a stop codon in the gag-related ORF, which is inconsistent with the expression of a 28-kDa protein. Instead of the two ORFs previously found, our gag-related region contained three ORFs. One of them demonstrated higher nucleotidic and peptidic homologies with the p19 gag of HTLV-I. However, the molecular analyses of our new sequence did not show evidence of potent translation capacities.

Analysis of the effect of endogenous viral genes in the Smyth line chicken model for autoimmune vitiligo

The Smyth line (SL) chicken, an animal model for autoimmune human vitiligo, is characterized by a spontaneous posthatch pigment loss, determined to be the result of an autoimmune phenomenon. Because endogenous virus (EV) genes have been reported to be associated with a number of autoimmune diseases of human and animal models, we designed this experiment to investigate the role of EV in the SL vitiligo by using the complete sequence of Rous-associated virus-2 as a probe for EV. An F(2) resource population was developed by the matings of SL and parental control (BL) chickens. Linkage disequilibrium between vitiligo and EV was apparent (16.2-kb SacI fragment, P Collapse

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MESH Headings

• Animals
• Autoimmune Diseases/genetics
• Autoimmune Diseases/virology
• Azacitidine/pharmacology
• Blotting, Northern
• Chickens/genetics
• Chickens/virology
• DNA/analysis
• DNA/chemistry
• DNA Fingerprinting
• DNA Methylation
• Deoxyribonuclease HindIII/metabolism
• Deoxyribonucleases, Type II Site-Specific/metabolism
• Disease Models, Animal
• Endogenous Retroviruses/genetics
• Female
• Fibroblasts/drug effects
• Fibroblasts/metabolism
• Genes, Viral
• In Situ Hybridization, Fluorescence
• Male
• Pedigree
• Polymorphism, Restriction Fragment Length
• RNA Viruses
• RNA, Viral/analysis
• Vitiligo/genetics
• Vitiligo/virology

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Grants

• Wellcome Trust

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Affiliation(s)

G P Sreekumar Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, Massachusetts 01003, USA
J R Smyth
S Ambady
F A Ponce de Leon

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Beneficial role of human endogenous retroviruses: facts and hypotheses

Human endogenous retroviruses (HERVs) have recently been suggested as mediators of normal biological processes such as cellular differentiation and regulation of gene expression. Moreover, a direct role for HERVs in pathogenesis and the development of disease is now better appreciated. Elucidation of the mechanisms regulating HERV biology should provide information about fundamental cellular activities and the pathogenesis of multifactorial diseases such as cancer and autoimmune disease. The importance of understanding the roles of HERVs is underscored by the recently obtained insight that activation of endogenous retroviruses poses potential risks following xenotransplantation and in gene therapy using retroviral vectors. Furthermore, HERV-encoded superantigens have recently been implicated as causes of autoimmune disease. This review discusses the established and possible biological roles of HERVs, and proposes hypotheses concerning their involvement as mediators of fundamental cellular responses. We propose that the evolutionary persistence of endogenous retroviruses in the genomes of eukaryotic cells reflects their indispensability in important normal functions in specialized cellular environments. HERVs can also be potentially hazardous through their involvement in the development of disease. In addition, the creation of new retroviruses can occur through recombination, between different HERVs and between HERVs and exogenous retroviruses.

Lupus erythematosus-like features in patients with cutaneous T-cell lymphoma

BACKGROUND

The development of lupus erythematosus-like (LE-like) features in patients with cutaneous T-cell lymphoma (CTCL) has not been reported previously in the literature. Both diseases, however, have been etiologically linked to retroviruses.

OBJECTIVE

Our purpose was to report four cases of patients with CTCL who developed LE-like features during the course of their disease, and to evaluate for evidence of antibodies to retroviruses in the sera of these patients.

PATIENTS

Four patients with biopsy-proven CTCL with clinical or histologic features of systemic lupus erythematosus (SLE) were evaluated for clinical and laboratory criteria for SLE. Only one patient demonstrated four American Rheumatism Association (ARA) criteria sufficient for the diagnosis of SLE. The remaining three patients demonstrated one or two criteria for SLE. In addition, the sera of these patients were examined by Western blot analysis for evidence of human immunodeficiency virus type I (HIV-I), human T-cell lymphotrophic virus type I (HTLV-I), or human intracisternal A-type particle type I (HIAP-I) retroviral proteins. Each patient demonstrated antibodies to some of the retroviral proteins examined. The sera of two patients reacted to proteins for HIAP-I, and the sera of two patients reacted to p24 gag proteins of HIV-I. No patient reacted to HTLV-I proteins.

CONCLUSIONS

Our report identifies four patients with CTCL who developed LE-like features during the course of their disease. Although the etiology of CTCL and SLE has not been well established, each has been linked to retroviruses. Evidence of antibodies to retroviral proteins was identified in each of our patients by Western blot analysis. Although the clinical and laboratory findings in these cases do not resolve the etiologic role of retroviruses in CTCL or SLE, they suggest that retroviruses may have a role in the pathogenesis of the clinical phenomenon reported in these four patients.

Evaluation of PCR and ELISA assays for screening clinical trial subjects for replication-competent retrovirus

Gene delivery via murine-based recombinant retroviral vectors is currently widely used in gene therapy clinical trials. The vectors are engineered to be replication defective by replacing the structural and nonstructural genes of a cloned infectious retrovirus with a therapeutic gene of interest. The retroviral particles are currently generated in packaging cell lines, which supply all retroviral proteins in trans. Recombination between short homologous regions of the retroviral vector and packaging cell line elements can theoretically generate replication-competent retrovirus (RCR) and hence the Food and Drug Administration (FDA) requires the monitoring of clinical trial subjects for the presence of RCR. Sensitive polymerase chain reaction (PCR) assays have been used for the detection of murine leukemia virus (MLV) nucleotide sequences in peripheral blood mononuclear cells (PBMCs). A novel serological enzyme-linked immunosorbent assay (ELISA) for the detection of anti-MLV specific immunoglobulin (Ig) has been developed to be used as an alternative to the PCR assay. Both assays were used to monitor human immunodeficiency virus (HIV)-positive clinical trial subjects who had received multiple injections of HIV-IT (V), a retroviral vector encoding HIV-1 IIIBenv/rev. Western blot analysis and an in vitro vector neutralization assay were used to characterize further a subset of serum samples tested by ELISA. Results show no evidence of RCR infection in clinical trial subjects. PCR and ELISA assays are discussed in terms of their advantages and limitations as routine screening assays for RCR. The PCR assay is our current choice for monitoring clinical trial subjects receiving direct administration of vector, and the ELISA is our choice for those receiving ex vivo treatment regimens.

Human endogenous retrovirus K10 encodes a functional integrase

We cloned a human endogenous retrovirus K1O DNA fragment encoding integrase and expressed it as a fusion protein with Escherichia coli maltose-binding protein. Integrase activities were measured in vitro by using a double-stranded oligonucleotide as a substrate mimicking viral long terminal repeats (LTR). The fusion protein was highly active for both terminal cleavage and strand transfer in the presence of Mn2+ on the K1O LTR substrate. It was also active on both Rous sarcoma virus and human immunodeficiency virus type 1 LTR substrates, whereas Rous sarcoma virus and human immunodeficiency virus type 1 integrases were active only on their corresponding LTR substrates. The results strongly suggest that K1O encodes a functional integrase with relaxed substrate specificity.

Human endogenous retroviruses: nature, occurrence, and clinical implications in human disease

Retroviral diagnostics have become standard in human laboratory medicine. While current emphasis is placed on the human exogenous viruses (human immunodeficiency virus and human T-cell leukemia virus), evidence implicating human endogenous retroviruses (HERVs) in various human disease entities continues to mount. Literature on the occurrence of HERVs in human tissues and cells was analyzed. Substantial evidence documents that retrovirus particles were clearly demonstrable in various tissues and cells in both health and disease and were abundant in the placenta and that their occurrence could be implicated in some of the reproductive diseases. The characteristics of HERVs are summarized, mechanisms of replication and regulation are outlined, and the consistent hormonal responsiveness of HERVs is noted. Clear evidence implicating HERV gene products as participants in glomerulonephritis in some cases of systemic lupus erythematosus is adduced. Data implicating HERVs as etiologic factors in reproductive diseases, in some of the autoimmune diseases, in some forms of rheumatoid arthritis and connective tissue disease, in psoriasis, and in some of the inflammatory neurologic diseases are reviewed. The current major needs are to improve methods for HERV detection, to identify the most appropriate HERV prototypes, and to develop diagnostic reagents so that the putative biologic and pathologic roles of HERVs can be better evaluated.

The Y chromosome: a graveyard for endogenous retroviruses

We have isolated 20 different human endogenous retroviruses (ERV) related to ERV3, Hsrirt and Humer 4-1. Phylogeny and the presence of these ERV among different primates were determined by computer and Southern blot analyses. Preferential localization of ERV to the human, chimpanzee and orangutan Y chromosomes among the low-copy-number ERV is demonstrated. The reason for this accumulation of ERV on the strongly heterochromatic Y chromosome is probably mediated by (i) the absence of recombination of the Y chromosome that makes it more difficult for sequences to be lost, and (ii) integration of retroviruses in heterochromatic regions is less harmful to the organism. If ERV located on the Y chromosome are transcribed and translated to peptides, such peptides could be potential HY-antigens.

Retroviruses, apoptosis and autogenes

Autoimmunity and autoimmune disease are not the same. Autoimmunity is a normal consequence of aging, potentially reversible and possibly physiological. Autoimmune disease is dependent on genetic, viral, hormonal and psychoneuroimmunological factors. Aside from the apparently normal regulation of autoimmune responses by immune response genes, little is known about other genetic factors. Here, Norman Talal and John Mountz propose the term autogene to describe non-MHC genes which directly or indirectly interfere with important immunoregulatory actions. When mutated or otherwise genetically altered (e.g. by retrotransposon insertion), these genes predispose to immune dysregulation, lymphoproliferation and autoimmunity.

Antibodies in human sera recognizing a recombinant outer membrane protein encoded by the envelope gene of the human endogenous retrovirus K

Human endogenous retrovirus (HERV) K is present in about 50 copies in the human genome and transcription of HERV-K has previously been detected in several tumor cell lines as well as in peripheral blood lymphocytes from healthy donors. By means of immunoblotting we investigated the presence of antibodies recognizing recombinant HERV-K-envelope outer membrane constructs in different serum collectives. A total of 12.6% of sera obtained from normal blood donors was found positive. In serum collectives from breast carcinoma patients, HIV-1-positive individuals, and persons with cytomegalovirus infections no significant difference from the normal blood donor serum collective could be observed. Only a group of persons with a repeatedly raised serum neopterin concentration (> 10 nmol/liter) of unknown cause (HIV and hepatitis B and C virus infections were excluded) showed a significant higher percentage of HERV-K-outer membrane envelope-positive sera (21%). Furthermore we could observe a parallel HIV-1/HERV-K seroconversion, which probably is not due to an HIV-1/HERV-K-outer membrane envelope cross-reactivity. Possible implications of these findings are discussed.

Distribution of retroviral p15E-related proteins in neoplastic and non-neoplastic human tissues, and their role in the regulation of the immune response

In patients with head and neck carcinomas and in patients with chronic purulent upper airway infections, low molecular weight retroviral p15E-like factors are found. These factors are responsible for partial defects in the cellular immune response. We studied the distribution of these p15E-related proteins in neoplastic, inflamed and normal human tissues and related these findings with the presence of p15E-like factors in patients' sera. Demonstration of p15E-like proteins in sera of patients with upper airway infections and of patients with head and neck carcinomas correlated exclusively with the presence of p15E in normal and pathologic epithelium of the upper respiratory tract. p15E was not demonstrated in epithelia of other localizations. Our results suggest that chronic stimulation or neoplastic transformation of the epithelia of the upper respiratory tract stimulates the production of p15E-like proteins leading to their reported immunosuppressive actions.

Human T-cell lymphotropic virus (HTLV)-related endogenous sequence, HRES-1, encodes a 28-kDa protein: a possible autoantigen for HTLV-I gag-reactive autoantibodies

The presence of a human T-cell lymphotropic virus (HTLV)-related endogenous sequence, HRES-1, in the human genome has been documented. The HRES-1 genomic locus is transcriptionally active and contains open reading frames. Antibodies 232 and 233, specific for synthetic peptides pep14-24 and pep117-127, corresponding to two nonoverlapping HTLV-related regions in the longer open reading frame of HRES-1, recognize an identical 28-kDa protein in H9 human T cells. Thus, HRES-1 is a human endogenous retroviral sequence capable of protein expression. HRES-1/p28 is localized to the cytoplasm and nuclear bodies. While HTLV-I-specific antibodies react with HRES-1 peptides, antibody 233 cross-reacts with HTLV-I gag p24 protein. Three consecutive highly charged amino acid residues, Arg-Arg-Glu, present in both HRES-1 pep117-127 and HTLV-I gag p24 are likely to be the core of cross-reactive epitopes. The prevalence of antibodies to HRES-1 peptides pep14-24 and pep117-127 was determined in 65 normal blood donors and 146 patients with immunological disorders. Sera of patients with multiple sclerosis (19 out of 65, 29%), progressive systemic sclerosis (4 out of 17, 23%), systemic lupus erythematosus (4 out of 19, 21%), and Sjogren syndrome (2 out of 19, 10%) contained significantly higher HRES-1 peptide binding activity than sera of normal donors. Sera of patients with AIDS showed no specific binding to HRES-1 peptides. Nine of 30 HRES-1-seropositive patients showed immunoreactivity to HTLV-I gag p24. The data indicate that HRES-1/p28 may serve as an autoantigen eliciting autoantibodies cross-reactive with HTLV-I gag antigens.

Are endogenous retroviruses involved in human autoimmune disease?

A role for viruses in the etiopathogenesis of human autoimmune diseases has long been suspected but has not yet been proven. In Sjögren's syndrome (SS), there is continuing experimental support for the possible involvement of Epstein-Barr virus. Since the advent of AIDS, there is also great interest in retroviruses and autoimmune disease. We previously reported that 30% of SS patients and 36% of systemic lupus erythematosus (SLE) patients have serum antibodies to the p24 gag protein of HIV-1. We now report that two mechanisms classic for retroviruses (molecular mimicry and immunosuppression) may be operative in SS and SLE. The p24 gag protein shares a proline-rich epitope with the Sm nucleoprotein to which many SLE patients have antibodies. The impaired lymphocyte activation seen in peripheral blood T cells in SS patients is also seen in a human T cell line infected with an A-type retroviral particle linked to SS. Many studies suggest that endogenous retroviral sequences are important in immunoregulation. We now suggest that endogenous retroviral sequences may also be important in the etiology and pathogenesis of SS and SLE.