Brain and kidney of progressive multifocal leukoencephalopathy patients contain identical rearrangements of the JC virus promoter/enhancer

Characterization of Jc Virus Dna Amplified from Urine of Chronic Progressive Multiple Sclerosis Patients

Thirty-seven chronic progressive multiple sclerosis (MS) patients, 20 of whom were taking cyclosporine, were examined for excretion of JC virus (JCV) in the urine. Polymerase chain reaction (PCR) amplification of DNA in urinary cell extracts detected JCV in 30% of the MS urines. In the cyclosporine treated group four of 20 (20%) excreted JCV, whereas in the untreated group seven of 17 (41%) excreted JCV. Thus, cyclosporine treatment did not enhance urinary excretion of the virus. A control group consisting of an unselected series of 89 patients donating urine in a general medical clinic and 16 healthy volunteers showed 41% with detectable urinary JCV. Thirty-three percent of the control females excreted JCV (18154), as did 49% of the control males (25151). Although the percentage of MS patients excreting detectable virus was not increased compared to the control group, the presence of JCV in the urine provides or convenient source of the virus for further characterization. Genotyping of DNA fragments amplified from the VPI region indicates mainly the presence of JCV Type 1 in these chronic progressive MS patients. This is also the type that predominates in the control group. An apparent recombinant between Type 1 and Type 3 (African) within the VPI region, tentatively designated Type 113 (or Type 4), was found in both the MS group and the controls. A larger series of MS patients that includes relapsing/remitting disease will be required to determine whether the genotype profile of JCV excreted in the urine of MS patients differs significantly from controls.

Polyomaviruses

Over the last 10 years, the number of identified polyomaviruses has grown to more than 35 subtypes, including 13 in humans. The polyomaviruses have similar genetic makeup, including genes that encode viral capsid proteins VP1, 2, and 3 and large and small T region proteins. The T proteins play a role in viral replication and have been implicated in viral chromosomal integration and possible dysregulation of growth factor genes. In humans, the Merkel cell polyomavirus has been shown to be highly associated with integration and the development of Merkel cell cancers. The first two human polyomaviruses discovered, BKPyV and JCPyV, are the causative agents for transplant-related kidney disease, BK commonly and JC rarely. JC has also been strongly associated with the development of progressive multifocal leukoencephalopathy (PML), a rare but serious infection in untreated HIV-1-infected individuals and in other immunosuppressed patients including those treated with monoclonal antibody therapies for autoimmune diseases systemic lupus erythematosus, rheumatoid arthritis, or multiple sclerosis. The trichodysplasia spinulosa-associated polyomavirus (TSAPyV) may be the causative agent of the rare skin disease trichodysplasia spinulosa. The remaining nine polyomaviruses have not been strongly associated with clinical disease to date. Antiviral therapies for these infections are under development. Antibodies specific for each of the 13 human polyomaviruses have been identified in a high percentage of normal individuals, indicating a high rate of exposure to each of the polyomaviruses in the human population. PCR methods are now available for detection of these viruses in a variety of clinical samples.

An Update on Monoclonal Antibody Therapies in Multiple Sclerosis

Multiple sclerosis (MS) is a complex disease that causes a great deal of disability, especially in the young adult population. There have been several immunomodulatory agents that have been approved by the Food and Drug Administration for MS, including glatiramer acetate, interferon-β 1a and -β 1b, mitoxantrone, and corticosteroids. The effectiveness of these therapies has not been optimal, and drugs, such as monoclonal antibodies, that more selectively target the pathogenetic process of MS have been sought. These agents have their own intrinsic limitations such as systemic inflammatory reactions, induction of neutralizing antiantibodies, and even life-threatening infectious processes. The agent that has been in the forefront of the discussion is natalizumab, a monoclonal antibody (mAb) against α 4 integrin, which shows much promise in suppressing MS activity. However, 3 individuals treated with natalizumab developed a life-threatening infection, progressive multifocal leukoencephalopathy. This article reviews the role of mAbs in the treatment of MS, particularly their advantages over other drugs and their limitations, which have to be overcome for these agents to be at the forefront in the treatment of MS.

Polyomaviruses and human diseases

Polyomaviruses are small, nonenveloped DNA viruses, which are widespread in nature. In immunocompetent hosts, the viruses remain latent after primary infection. With few exceptions, illnesses associated with these viruses occur in times of immune compromise, especially in conditions that bring about T cell deficiency. The human polyomaviruses BKV and JCV are known to cause, respectively, hemorrhagic cystitis in recipients of bone marrow transplantation and progressive multifocal leukoencephalopathy in immunocompromised patients, for example, by HIV infection. Recently, transplant nephropathy due to BKV infection has been increasingly recognized as the cause for renal allograft failure. Quantitation of polyomavirus DNA in the blood, cerebrospinal fluid, and urine, identification of virus laden "decoy cells" in urine, and histopathologic demonstration of viral inclusions in the brain parenchyma and renal tubules are the applicable diagnostic methods. Genomic sequences of polyomaviruses have been reported to be associated with various neoplastic disorders and autoimmune conditions. While various antiviral agents have been tried to treat polyomavirus-related illnesses, current management aims at the modification and/or improvement in the hosts' immune status. In this chapter, we provide an overview of polyomaviruses and briefly introduce its association with human diseases, which will be covered extensively in other chapters by experts in the field.

A case of a progressive multifocal leukoencephalopathy patient with four different JC virus transcriptional control region rearrangements in cerebrospinal fluid, blood, serum, and urine

JC virus (JCV) is the etiological agent of progressive multifocal leukoencephalopathy (PML), a fatal demyelinating disease of the central nervous system (CNS). During the acquired immunodeficiency syndrome (AIDS) epidemic, it was the cause of the death in up to 8% of AIDS patients. The genomic organization of JCV and, in particular, the hypervariability of the transcriptional control region (TCR), a regulatory noncoding region, are well known. Given that the TCR plays a central role in the viral replication of JCV, a crucial role in the determination of the neurotropism and in the pathogenic capabilities of the virus is also suspected. Here the authors describe a case of PML that did not respond to highly active antiretroviral therapy (HAART) therapy. There was a simultaneous presence of JCV strains with four different TCR structures in urine, peripheral blood cells, serum, and cerebrospinal fluid (CSF) samples. These data confirmed that the presence of the archetype TCt is restricted to urine, while also suggesting that the degree of the rearrangement varies and increases from the peripheral blood to CSF.

DNA sequencing of viral capsid protein VP-1 region in patients with BK virus interstitial nephritis

BACKGROUND

Mutations in the viral capsid protein VP-1 region are associated with increased pathogenicity of polyomavirus in experimental systems. This study sought to determine whether analogous viral genetic changes occur in human BK virus (BKV) interstitial nephritis (ISN).

METHODS

PCR was used to amplify a 94-bp nucleotide sequence of the viral capsid protein VP-1 region (positions 1740-1833, Dun numbering) in 49 biopsies obtained from 24 patients with BKV-ISN. DNA sequencing was performed by the dideoxy method.

RESULT

The VP-1 region was highly polymorphic and 22 "hot spots" of sequence variability were noted. Genotypes I, II, and IV were assigned to 13, 1, and 5 cases, respectively, but 5 cases could not be unambiguously classified due to sequence heterogeneity at sites used to discriminate between genotypes. Even in cases where genotypes could be assigned, only 5 biopsies showed complete sequence identity with published genotype sequences. Sequential biopsies showed temporal changes in one or more nucleotides in all patients with multiple samples. In one patient, the initial biopsy showed viral genotype 1, although subsequent biopsies showed complex genetic patterns, including a biopsy consistent with viral genotype IV.

CONCLUSIONS

Many viral strains associated with BKV-ISN are difficult to classify and possibly distinct from those described in kidney transplant recipients without BKV-ISN. VP-1 sequences undergo continual modification as patients are followed in time. This genetic instability could conceivably have implications for evasion of host immunity and development of resistance to antiviral drugs.

JC virus infection in allograft kidneys: analysis by polymerase chain reaction and immunohistochemistry

BACKGROUND

Polyoma virus nephropathy after transplantation is believed to be primarily due to the BK virus. We hypothesized that some cases may be associated with the JC polyoma virus (JCV), which is also known to be latent in the kidney.

METHODS

We sought polymerase chain reaction evidence of JCV infection in needle biopsy specimens with and without viral nephropathy. Cases positive by polymerase chain reaction were studied by immunohistochemistry for VP-1 antigen expression.

RESULTS

JCV DNA was found in 7 (36.8%) of 19 allograft kidney biopsy specimens with viral nephropathy and 0 (0%) of 19 native or allograft biopsy specimens without viral nephropathy. Immunohistochemistry localized JCV to the nuclei of tubular epithelial cells in one case.

CONCLUSIONS

JCV is detectable in a subset of renal allograft kidneys with polyoma virus nephropathy. The tubular epithelium is identified as a site capable of supporting JCV viral capsid protein VP-1 expression, and hence viral replication.

Human polyomavirus JC variants in Papua New Guinea and Guam reflect ancient population settlement and viral evolution

The peopling of the Pacific was a complex sequence of events that is best reconstructed by reconciling insights from various disciplines. Here we analyze the human polyomavirus JC (JCV) in Highlanders of Papua New Guinea (PNG), in Austronesian-speaking Tolai people on the island of New Britain, and in nearby non-Austronesian-speaking Baining people. We also characterize JCV from the Chamorro of Guam, a Micronesian population. All JCV strains from PNG and Guam fall within the broad Asian group previously defined in the VP1 gene as Type 2 or Type 7, but the PNG strains were distinct from both genotypes. Among the Chamorro JCV samples, 8 strains (Guam-1) were like the Type 7 strains found in Southeast Asia, while nine strains (Guam-2) were distinct from both the mainland strains and most PNG strains. We identified three JCV variants within Papua New Guinea (PNG-1, PNG-2 and PNG-3), but none of the Southeast Asian (Type 7) strains. PNG-1 strains were present in all three populations (Highlanders and the Baining and Tolai of New Britain), but PNG-2 strains were restricted to the Highlanders. Their relative lack of DNA sequence variation suggests that they arose comparatively recently. The single PNG-3 strain, identified in an Austronesian-speaking Tolai individual, was closely related to the Chamorro variants (Guam-2), consistent with a common Austronesian ancestor. In PNG-2 variants a complex regulatory region mutation inserts a duplication into a nearby deletion, a change reminiscent of those seen in the brains of progressive multifocal leukoencephalopathy patients. This is the first instance of a complex JCV rearrangement circulating in a human population.

Association of simian virus 40 with a central nervous system lesion distinct from progressive multifocal leukoencephalopathy in macaques with AIDS

The primate polyomavirus SV40 is known to cause interstitial nephritis in primary infections and progressive multifocal leukoencephalopathy (PML) upon reactivation of a latent infection in SIV-infected macaques. We now describe a second central nervous system manifestation of SV40: a meningoencephalitis affecting cerebral gray matter, without demyelination, distinct from PML. Meningoencephalitis appears also to be a primary manifestation of SV40 infection and can be seen in conjunction with SV40-induced interstitial nephritis and pneumonitis. The difference in the lesions of meningoencephalitis and PML does not appear to be due to cellular tropism, as both oligodendrocytes and astrocytes are infected in PML and meningoencephalitis, as determined by in situ hybridization or immunohistochemistry for SV40 coupled with immunohistochemistry for cellular determinants. This is further supported by examination of SV40 nucleic acid sequences from the ori-enhancer and large-T-antigen regions, which reveals no tissue-or lesion-specific variation in SV40 sequences.

Tubulointerstitial nephritis due to a mutant polyomavirus BK virus strain, BKV(Cin), causing end-stage renal disease

A renal biopsy from a 36-year-old man with AIDS showed a severe tubulointerstitial nephritis with intranuclear inclusions in epithelial cells. Electron microscopy revealed the characteristic findings of a polyomavirus (PyV) infection, and immunofluorescence indicated the presence of BK virus (BKV) antigen. Inoculation of rhesus monkey kidney cell cultures both with urine and with buffy coat blood cells resulted in a cytopathic response which was subsequently confirmed to be due to BKV. Further characterization of the viral DNA from the kidney by PCR amplification and Southern blot analysis with PyV and strain-specific primers and probes indicated that the virus was closely related to the BK(Dun) strain but different in its apparent sequence arrangement. Subsequent cycle sequencing showed a dinucleotide mutation of TG-->AA which substitutes hydrophilic Gln for hydrophobic Leu in a sequence homologous to an origin DNA-binding domain of simian virus 40 T antigen. It is suggested that the mutation and a coding region rearrangement of this strain of BKV designated BKV(Cin) has the potential to alter viral DNA replication and enhance pathogenicity.

Rearrangements of archetypal regulatory regions in JC virus genomes from urine

The regulatory region of progressive multifocal leukoencephalopathy-type JC virus (JCV) is rearranged in each host by a process of deletion and duplication. Of the more than 40 that have been examined, no two regulatory regions have been rearranged identically in the brain. The substrate for this rearrangement appears to be a highly stable archetypal regulatory region excreted in the urine. Its role as the transmissible form of the virus, although inferred, has never been proven. We have now amplified by PCR and cycle-sequenced the regulatory regions from 48 urinary strains of the virus. We find that the urinary form of the regulatory region is not entirely stable. Short deletions and duplications in the range of 2-16 bp were observed in seven of these strains. One of these, an inverted repeat, is a pattern of rearrangement not yet found in the brain. Two others (#208 and 230) showed a 2-bp deletion at position nos. 221 and 222, and an unusual mutation at position no. 219. These two urines were collected in different states of the USA at different times and analysed months apart. It is very unlikely that these unusual changes represent sample contamination or that they arose independently. This finding indicates that archetypal forms of the JCV regulatory region are infectious, despite their relative inactivity in tissue culture. While changes in the archetypal structure can be found, it is clear that rearrangements in the kidney are rare or rarely infectious.

Detection of archetype and rearranged variants of JC virus in multiple tissues from a pediatric PML patient

JC virus (JCV) establishes persistent infections in its human host, and in some immunocompromised individuals, the virus causes the fatal brain disease progressive multifocal leukoencephalopathy (PML). Two forms of the virus, archetype and rearranged, have been isolated, with the latter being derived from the archetype form by deletion and duplication of sequences within the viral transcriptional control region (TCR). We have used the PCR technique to amplify JCV TCR sequences present within multiple tissues of a pediatric PML patient and have cloned and sequenced the PCR products. Archetype JCV was readily detected in kidney tissue; this form of JCV was also identified for the first time in brain and lymph node tissue by employing archetype-specific PCR primers. In addition, several archetype-like variants containing small deletions within their regulatory regions were isolated from cardiac muscle and lung. Different, but related rearranged forms were detected in most of the tissue examined. Each of the rearranged TCRs lacked portions of a 66 base pair (bp) region found within the archetype promoter-enhancer but retained a 23 bp region that is deleted in the prototype (Mad 1) rearranged form of JCV. Although several rearranged forms of JCV were identified in this patient, the TCRs could be assigned to one of two groups based upon the deletion boundaries generated during the adaptation from archetype to rearranged JCV. This study is the first to characterize multiple JCV variants present in different tissues from a patient likely to have succumbed to PML during a primary infection.

BK virus and a new type of JC virus excreted by HIV-1 positive patients in rural Tanzania

HIV-1 positive patients from Tanzanian villages near Shirati were examined for urinary excretion of the human polyomaviruses JC and BK using the polymerase chain reaction (PCR). BK virus (BKV) was detected in 11 of 23 individuals tested. The BKV DNA sequences were all closely related to prototype Gardner strain and BKV (DUN). In contrast, a new type of JCV, termed Type 3 [or JCV (Shi)], was identified in seven of these same 23 individuals by comparison with Type 1 and Type 2 sequences of the VP1/intergenic/T antigen region of U.S., European and Asian strains. This suggests that JCV and BKV, although closely related, have different evolutionary histories within the African population. The six BKV regulatory regions amplified all showed the archetypal configuration. However, two of the seven JCV regulatory regions showed rearrangements: a small deletion and an inverted repeat. JCV causes a fatal demyelinating disease, progressive multifocal leukoencephalopathy (PML), in about 5% of AIDS patients in Europe and the U.S.A., but only one case has been reported in Africa. Our results suggest that this rarity of PML is not due to the absence of JCV in the African population.