Progressive multifocal leucoencephalopathy: analysis of JC virus DNA from brain and kidney tissue

Viral replication centers and the DNA damage response in JC virus-infected cells

JCV is a human polyomavirus (PyV) that establishes a persistent infection in its host. Current immunomodulatory therapies, such as Natalizumab for multiple sclerosis, can result in JCV reactivation, leading to the debilitating brain disease progressive multifocal leukoencephalopathy (PML). JCV is among the viruses that recruit and modulate the host DNA damage response (DDR) to replicate its genome. We have identified host proteins recruited to the nuclear sites of JC viral DNA (vDNA) replication using three cell types susceptible to infection in vitro. Using confocal microscopy, we found that JCV recruited a similar repertoire of host DDR proteins to these replication sites previously observed for other PyVs. Electron tomography of JCV "virus factories" showed structural features like those described for murine PyV. These results confirm and extend previous observations for PyVs to JCV emphasizing a similar replication strategy among members of this virus family.

Progressive multifocal leukoencephalopathy in a heart transplant recipient following rituximab therapy for antibody-mediated rejection

We report the case of a male heart transplant recipient who developed acute antibody-mediated rejection and was treated with 5 weeks of a rituximab-containing regimen. Two months later he presented with progressive motor and cognitive impairments and was diagnosed with progressive multifocal leukoencephalopathy (PML). He was treated with reduction of his immunosuppressive medications, mirtazapine, IVIG and plasmapheresis. He died within weeks. We reviewed the current literature on PML and its association with immunosuppression, highlighting its impact in the setting of solid organ transplantation and considering the potential effect of newer biologic drugs on the incidence of this devastating disease in the transplant population.

Patients with sporadic colorectal cancer or advanced adenomatous polyp have elevated anti-JC virus antibody titer in comparison with healthy controls: a cross-sectional study

OBJECTIVE

JC virus (JCV) is thought to infect approximately 80% of the human population. Antibodies against JCV can be found in the sera of many people with and without colorectal carcinoma (CRC). We hypothesized that JCV antibody titer will be higher in CRC patients than in healthy controls.

AIM

To evaluate this hypothesis in a cohort of patients undergoing colonoscopy. We compared JCV antibody titers in patients with simple adenoma, advanced adenomatous polyp (AAP), CRC, and healthy controls, and evaluated JCV DNA in the tissue.

METHODS

Ninety-seven patients undergoing colonoscopy offered to participate in the study. Normal colonoscopy, simple adenoma, AAP, and CRC were found in 41, 19, 12, and 25 cases, respectively. A blood sample was taken for JCV DNA isolation and serology. In 18 patients with CRC or AAP tissue samples were taken for JCV DNA isolation and T-antigen (T-Ag) detection.

RESULTS

A positive correlation was found between a JCV antibody titer and advanced colonic pathology. The average titer for normal controls, simple polyp, AAP, and CRC was 2.61+/-0.72, 2.95+/-0.77, 3.33+/-0.76, and 3.30+/-0.50 log, respectively (P<0.001). Viral DNA could not be shown in the serum. The presence of neoplastic tissue T-Ag (in 33.3% of the patients) was not associated with a difference in the log titer of serum antibody.

CONCLUSIONS

In this study we showed that patients with advanced neoplasia, compared with patients with normal colonoscopy, harbor a higher JCV antibody titer in the serum. If confirmed, our finding may serve as a marker for CRC or for an earlier stage of AAP.

JC virus T-Antigen DNA in gastrointestinal mucosa of immunosuppressed patients: a prospective, controlled study

BACKGROUND

JC virus (JCV), a polyoma virus, is the etiological agent of progressive multifocal leukoencephalopathy in immunosuppressed patients. JCV T-Ag has proven oncogenic potential and is expressed in colonic polyps and carcinomas. We proposed that the prevalence of JCV T-Ag DNA is higher in the normal gastrointestinal (GI) mucosa of immunosuppressed patients compared with their immunocompetent counterparts.

AIMS

To look for JCV T-Ag DNA in the normal gastrointestinal mucosa of immunosuppressed patients compared with immunocompetent controls.

METHODS

Macroscopically normal samples of upper and lower GI mucosa were obtained from 38 immunosuppressed patients. A control group included samples from 19 immunocompetent inflammatory bowel disease (IBD) and 29 non-IBD cases. DNA was extracted and polymerase chain reaction (PCR) was performed using primers specific for T-Ag.

RESULTS

JCV T-Ag DNA was found in nine of the immunosuppressed patients (23.7%) and in three of the controls (6.3%; P = 0.02). Transplant recipients had a particularly high prevalence of JCV T-Ag DNA (35.3%). Patients with IBD receiving immunosuppressive drugs had a higher prevalence of JCV T-Ag DNA in comparison with IBD patients who did not receive immunosuppression (22.2% versus 10.5%, respectively), but this difference was not statistically significant (P = 0.574).

CONCLUSION

JCV T-Ag DNA is more prevalent in the upper and lower GI mucosa of immunosuppressed patients, possibly indicating that the virus resides in these patients. This may account for the higher prevalence of GI carcinomas in immunosuppressed patients.

Progressive multifocal leukoencephalopathy

Progressive multifocal leukoencephalopathy (PML) was a rare disease until the advent of the HIV/AIDS pandemic. Recent interest in the disorder has been spurred by its appearance in patients treated with the monoclonal antibodies natalizumab and rituximab. Unless the accompanying underlying immune deficit can be reversed, PML typically progresses to death fairly rapidly. Treatment directed against the JC virus has been unhelpful, but an increased understanding of disease pathogenesis may result in effective therapeutic strategies.

Molecular biology and immunoregulation of human neurotropic JC virus in CNS

The human polyomavirus, JC virus (JCV), provides an excellent model system to investigate the reciprocal interaction of the immune and nervous systems. Infection with JCV occurs during childhood and the virus remains in the latent state with no apparent clinical symptoms. However, under immunosuppressed conditions, the virus enters the lytic cycle and upon cytolytic destruction of glial cells, causes the fatal demyelinating disease of the central nervous system (CNS), named progressive multifocal leukoencephalopathy (PML). In this short review, we discuss the molecular pathogenesis of PML by highlighting the role of the immune system in modulating JCV gene activation and replication, and the latency/reactivation of this virus upon immunosuppression. Further, due to the higher incidence of PML among AIDS patients, we further elaborate on the cross-talk between JCV and HIV-1 by direct and indirect pathways that lead to enhanced expression of the JCV genome.

Human cytomegalovirus immediate-early gene 2 expression leads to JCV replication in nonpermissive cells via transcriptional activation of JCV T antigen

Human papovavirus JCV is the causative agent of the demyelinating brain disease progressive multifocal leukoencephalopathy (PML) that typically develops as a complication of impaired immunocompetence. JCV displays a strong tropism for glial cells which is correlated by glial-specific transcriptional regulation of viral gene expression. In a previous report HCMV was shown to overcome the restricted cell specificity of JCV by inducing DNA replication of a PML-derived JCV strain in human fibroblasts which are nonpermissive for the replication of JCV alone. Here we show that productive JCV replication is induced by HCMV in human glioblastoma cells. Both in fibroblasts and in glioblastoma cells, the HCMV immediate-early transactivator 2 (IE2) is sufficient to mediate JCV replication. Furthermore, IE2 induces DNA replication of several structurally different brain- or kidney-derived JCV variants. IE2-induced JCV DNA replication is accompanied by the induction of JCV T antigen expression due to stimulation of the JCV early promoter. Our results indicate that stimulation of JCV early gene expression by HCMV-IE2 is sufficient to overcome the restricted cell specificity of JCV.

Reciprocal interaction between two cellular proteins, Puralpha and YB-1, modulates transcriptional activity of JCVCY in glial cells

Cross communication between regulatory proteins is an important event in the control of eukaryotic gene transcription. Here we have examined the structural and functional interaction between two cellular regulatory proteins, YB-1 and Puralpha, on the 23-bp sequence element derived from the enhancer-promoter of the human polyomavirus JCV. YB-1 and Puralpha are single-stranded DNA binding proteins which recognize C/T- and GC/GA-rich sequences, respectively. Results from band shift studies demonstrated that while both proteins interact directly with their DNA target sequences within the 23-bp motif, each protein can regulate the association of the other one with the DNA. Affinity chromatography and coimmunoprecipitation provide evidence for a direct interaction between Puralpha and YB-1 in the absence of the DNA sequence. Ectopic expression of YB-1 and Puralpha in glial cells synergistically stimulated viral promoter activity via the 23-bp sequence element. Results from mutational studies revealed that residues between amino acids 75 and 203 of YB-1 and between amino acids 85 and 215 of Puralpha are important for the interaction between these two proteins. Functional studies with glial cells indicated that the region within Puralpha which mediates its association with YB-1 and binding to the 23-bp sequence is important for the observed activation of the JCV promoter by the Puralpha and YB-1 proteins. The results of this study suggest that the cooperative interaction between YB-1 and Puralpha mediates the synergistic activation of the human polyomavirus JCV genome by these cellular proteins. The importance of these findings for cellular and viral genes which are regulated by Puralpha and YB-1 is discussed.

Diagnostic criteria and clinical procedures in HIV-1 associated progressive multifocal leukoencephalopathy

The diagnosis of definite progressive multifocal leukoencephalopathy (PML) has been a neuropathological domain. We reviewed all Human Immunodeficiency Virus Type 1 (HIV-1) seropositive patients in our institution between 01.01.1989 and 31.12.1994 and identified 20/823 cases with PML by clinical and imaging criteria. Diagnosis was neuropathologically confirmed in 5 cases. Diagnostic criteria included rapid onset (< 2 weeks) of multifocal neurological signs and symptoms, advanced immunosuppression and asymmetric uni- or multifocal white matter lesions without mass effect, contrast enhancement or cortical atrophy in magnetic resonance imaging (MRI). The overall incidence of PML was stable over the observation period (approximately equal to 2.5%). The mean age at onset (41.7 years) was significantly lower compared to HIV-1 seronegative PML patients (peak in the sixth decade of life), male patients prevailed (100%). Mean survival (3.9 months) was extremely short. Human polyoma virus JC (JCV) polymerase chain reaction (PCR) in the cerebrospinal fluid (CSF) demonstrated a considerable rate of possible cerebral co-infection with HIV-1 and JCV as well as subclinical infection with JCV. Therefore demonstration of JCV deoxyribonucleic acid by PCR in the CSF alone is not sufficient for clinical PML diagnosis. We present diagnostic criteria on the basis of epidemiological, neuroradiological and CSF parameters that allow us to make the clinical diagnosis of PML. Although quick and safe, routine stereotactic brain biopsy is not necessary to confirm the diagnosis.

Transcription of the JC virus archetype late genome: importance of the kappa B and the 23-base-pair motifs in late promoter activity in glial cells

The transcription control region of the archetype strain of the human polyomavirus JC virus (JCV(Cy)), unlike its neurotropic counterpart (JCV(Mad-1)), contains only one copy of the 98-bp enhancer/promoter repeat with the 23-bp and the 66-bp insertion blocks. Early studies by us and others have indicated that the structural organization of JCV(Mad-1) is critical for glial cell-specific transcription of the viral genome. In addition, the kappa B regulatory motif found in the JCV(Mad-1) genome, which also exists in JCV(Cy), confers inducibility to the JCV(Mad-1) early and late promoters in response to extracellular stimuli. In this study, we have investigated the regulatory role of the 23- and the 66-bp blocks and their functional relationship to the kappa B motif in stimulating transcription of the Cy early and late promoters in glial cells. We demonstrate that mutations in the kappa B motif reduce the basal activity of the Cy early promoter and decrease the levels of its induction by phorbol myristate acetate or factors derived from activated T cells. Under similar circumstances, mutation in the kappa B motif completely abrogated the basal and the induced levels of transcription of the viral late promoter. Using deletion and hybrid promoter constructs, we have demonstrated that the 23-bp block of the Cy promoter plays a critical role in the observed inactivation of Cy late promoter transcription in glial cells. Results from DNA binding studies have indicated the formation of a common nucleoprotein complex with the 23-bp sequence, mutant kappa B (kappa B(mut)), and wild-type kappa B (kappa B(wt)). Analysis of this complex by UV cross-linking has identified a 40-kDa protein which binds to the 23-bp sequence and the kappa B motif. The importance of these findings for the activation of JCV(Cy) under various physiological conditions is discussed.

Different genotypes of human polyomaviruses found in patients with autoimmune diseases in Taiwan

We have assayed for the presence of human polyomaviruses in urine of autoimmune disease patients, such as systemic lupus erythematosus (SLE), Sjogren's syndrome (SS), rheumatoid arthritis (RA), or dermatomyositis/polymositis (DM/PM), by PCR. The results indicate that approximately 40% of patients were JCV positive and 15% of the JCV positive patients were also infected by BKV at the same time according to Southern blot and DNA sequencing of the PCR products. Interestingly, the JCV present in autoimmune diseases patients were Taiwan-1, Taiwan-2, and Taiwan-3 strains with pentanucleotide-A (GGGAA) and/or -B (AAAGC) deletions within the regulatory region. In addition, BKV found in the examined samples were Taichung-1 and Taichung-2 strains. Taichung-1 had two nucleotide alterations and Taichung-2 had six nucleotide differences within the regulatory region when compared to WW BKV archetype. Although the examined autoimmune diseases patients included RA, SLE, PM, DM, and SS patients, there appears to be no correlation between disease and virus strains. However, Taiwan-2 strain JCV with two copies of pentanucleotide-A deletion was present in the patient with the longest period of immunosuppressive medication.

Transmission of the human polyomavirus JC virus occurs both within the family and outside the family

JC polyomavirus (JCV) is a ubiquitous symbiote in the human population, infecting children asymptomatically and then persisting in renal tissue. We reevaluated the urinary excretion of JCV in subjects in various age groups using PCR. The detection rate for urinary JCV DNA was 9 to 17% until the age of 20 years; this rate increased dramatically to about 46% at the ages of 20 to 29 years and then increased gradually with age. Therefore, it appears that in most people excretion of JCV begins at the age of 20 to 29 years, which is earlier than suggested previously. Next, we studied the way in which JCV is spread in the human population. We selected eight Japanese families in which both parents and children excreted JCV in their urine. Their JCV subtypes were determined by PCR amplification of a JCV DNA fragment; this was followed by restriction enzyme analysis. JCV species in all JCV-positive family members were classified into either of the two subtypes, subtypes CY and MY, which are prevalent in the Japanese population. The following features of JCV subtype distribution were seen in the families: (i) both subtypes were detected in children of five of the eight families, and (ii) of 21 children who excreted JCV, 14 children excreted the same subtypes excreted by their mothers or fathers, while the remainder (7 children) excreted subtypes different from those excreted by their parents. These features suggest that JCV is transmitted both within the family and outside the family. The data also indicate that vertical transmission is not common in the spread of JCV.

Occurrence of multiple JC virus variants with distinctive regulatory sequences in the brain of a single patient with progressive multifocal leukoencephalopathy

We established 99 JC virus (JCV) DNA clones directly from the brain of a single patient with progressive multifocal leukoencephalopathy (PML). Based upon restriction patterns, the cloned viral DNAs were classified into two major groups (NY-1A and -1B) containing 53 and 35 clones, respectively, and several minor groups containing one or a few clones. The regulatory sequences of representative clones were compared with the archetypal regulatory sequence, which has been detected in JCV DNAs cloned from the urine of healthy and nonimmunosuppressed individuals. The regulatory sequence of NY-1B had the two structural features common to most PML-type regulatory regions, duplication and deletion of specific segments in the archetypal sequence, while that of NY-1A contained a small deletion and an insertion of a 29-bp sequence originating from the early region of the JCV genome. A regulatory region similar to that of NY-1A has never been detected in JCV isolates obtained thus far.

Human cytomegalovirus induces JC virus DNA replication in human fibroblasts

JC virus, a human papovavirus, is the causative agent of the demyelinating brain disease progressive multifocal leucoencephalopathy (PML). PML is a rare but fatal disease which develops as a complication of severe immunosuppression. Latent JC virus is harbored by many asymptomatic carriers and is transiently reactivated from the latent state upon immunosuppression. JC virus has a very restricted host range, with human glial cells being the only tissue in which it can replicate at reasonable efficiency. Evidence that latent human cytomegalovirus is harbored in the kidney similar to latent JC virus led to the speculation that during episodes of impaired immunocompetence, cytomegalovirus might serve as helper virus for JC virus replication in otherwise nonpermissive cells. We show here that cytomegalovirus infection indeed leads to considerable JC virus DNA replication in cultured human fibroblasts that are nonpermissive for the replication of JC virus alone. Cytomegalovirus-mediated JC virus replication is dependent on the JC virus origin of replication and T antigen. Ganciclovir-induced inhibition of cytomegalovirus replication is associated with a concomitant inhibition of JC virus replication. These results suggest that reactivation of cytomegalovirus during episodes of immunosuppression might lead to activation of latent JC virus, which would enhance the probability of subsequent PML development. Ganciclovir-induced repression of both cytomegalovirus and JC virus replication may form the rational basis for the development of an approach toward treatment or prevention of PML.

Origin of JC polyomavirus variants associated with progressive multifocal leukoencephalopathy

JC polyomavirus (JCV) DNAs from the urine of nonimmunocompromised individuals (designated archetypal isolates) regularly contain a regulatory sequence that may have generated various regulatory sequences of JCV isolates derived from the brain of patients with progressive multifocal leukoencephalopathy (PML). In this report, we constructed a phylogenetic tree for 14 isolates (7 archetypes and 7 PML types) from DNA sequence data on the VP1 (major capsid protein) gene. According to the phylogenetic tree, the 14 isolates diverged into types A and B, each of which contained archetypal and PML-type isolates. Each type further diverged into several groups containing archetypal and PML-type isolates. We conclude that PML-type isolates are polyphyletic in their origin and do not constitute a unique lineage. This conclusion suggests that PML-type JCV isolates are generated from archetypal strains during persistence in the hosts. Furthermore, the present phylogenetic analysis indicates that an ancestral JCV carried the archetypal regulatory sequence and that this structure has been conserved in the course of JCV evolution.

Evidence of human polyomavirus BK and JC infection in normal brain tissue

Infection with the polyomaviruses JC and BK is ubiquitous in the human population and JCV is the only virus associated with the central nervous system disease progressive multifocal leukoencephalopathy. In the attempt to analyze the pathogenesis of polyomavirus infections we asked whether human polyomaviruses invade the brain during persistence. Brain autopsy material from 67 individuals with disorders other than PML was examined for the presence of polyomavirus DNA. Southern blot analysis demonstrated JCV-specific full-length virus genomes in healthy brain tissue in about 20% of the patients. Type-specific analysis with polymerase chain reaction and sequencing confirmed these data. Additionally, the presence of BKV DNA sequences covering an early gene fragment and the control region with flanking early and late protein coding sequences was detected. Cloning of the complete BKV genome from two cases supported the assumption that not only full-length JCV DNA was present in those tissue specimens but also BKV genomes. The data obtained demonstrate that dual infection of the brain with the polyomaviruses JCV and BKV is a common event and give strong evidence that both viruses frequently establish a latent CNS infection.

JC virus DNA is present in many human brain samples from patients without progressive multifocal leukoencephalopathy

Sections of normal and diseased brain and kidney tissues were screened for the presence of JC virus (JCV) DNA by using the polymerase chain reaction. As expected, all samples obtained from patients with progressive multifocal leukoencephalopathy (PML) tested positive when multiple JCV-specific primer and probe combinations were used. Unexpectedly, more than 50% of non-PML-affected brains were also found to harbor low levels of JCV DNA. To confirm that the positive signals seen in the tissue sections were not the result of contamination, amplified DNA was cloned and sequenced and in some cases was shown to represent strains of JCV not identified previously. Two predominant regulatory region configurations of JCV have been detected in the human host: archetype JCV, which is excreted in the urine of normal and immunocompromised individuals, and "PML-type" JCV found in diseased brains. This latter group of variants appears to derive from archetype JCV by the deletion and duplication of sequences within the promoter-enhancer region. In the present study, the archetype strain of JCV was identified only in normal kidney samples; JCV DNA found in non-PML-affected brain specimens and in kidney tissue from patients with PML resembled that of strains isolated from PML-affected brain tissue. Our findings indicate that JCV reaches the brain more frequently than previously thought and may persist at this site without causing demyelinating disease. A subsequent episode of prolonged immunodeficiency or a direct interaction with an immunocompromising agent (e.g., human immunodeficiency virus type 1) might activate the latent JCV infection and lead to the development of PML.

Enhancer dependence of polyomavirus persistence in mouse kidneys

We previously showed that alterations in the enhancer sequence of polyomavirus DNA can alter both the level and the organ specificity of viral DNA replication during the acute phase of infection of newborn mice (R. Rochford, B. A. Campbell, and L. P. Villarreal, J. Virol. 64:476-485, 1990). In this study, we examined whether these enhancer sequence alterations can also affect polyomavirus replication during the persistent phase of infection in vivo. After infection of newborn mice with a mixture of three enhancer variants, the individual organs could select for enhancer-specific viral DNA replication during both the acute and the persistent phases of infection. Contrary to expectations, the ability of some variants to establish a high-level acute infection in some organs (e.g., the pancreas) did not necessarily lead to a persistent infection in those organs. Thus, enhancers can affect acute and persistent infections differently. In addition, some enhancer variants tended to establish a high-level persistent infection in the kidneys immediately following an acute infection; however, in all cases considerable histopathology was associated with these elevated long-term infections, and these mice were always runty. A persistent infection in the kidneys thus appears able to exist in two distinguishable states, a high-level pathological state and a low-level nonpathological state, which can be affected by the viral enhancer sequence.

Detection of JC virus DNA in peripheral lymphocytes from patients with and without progressive multifocal leukoencephalopathy

Progressive multifocal leukoencephalopathy (PML) results from lytic infection of oligodendrocytes by JC virus (JCV). Although JCV has been identified in mononuclear cells in bone marrow and hematogenous dissemination of the virus to the central nervous system has been suspected, JCV has never been clearly demonstrated in the peripheral circulation. Using polymerase chain reaction technology, we examined peripheral lymphocytes of 19 patients with brain biopsy-proven PML for the JCV genome. Two non-PML control groups, consisting of 26 patients seopositive for human immunodeficiency virus type 1 (HIV-1) and 30 immunocompetent patients with Parkinson's disease, were also examined for the presence of the JCV genome in lymphocytes. Cerebrospinal fluid from 10 patients with PML was examined for the presence of the JCV genome as well. The JCV genome was detected in the lymphocytes of 89% (17) of the patients with PML, 38% (10) of the HIV-1-seropositive patients without PML, and none of the patients with Parkinson's disease. Sequencing of the JCV regulatory region from the lymphocytes of three patients revealed the prototype MAD-1 strain of JCV in one patient with PML, a MAD-4 strain in a second patient with PML, and a slightly modified MAD-4 strain in an HIV-1-positive patient without PML. Only 3 of 10 patients with PML who had JCV detected in lymphocytes had the JCV genome in their cerebrospinal fluid. These results demonstrate that the JCV genome can be found in circulating lymphocytes from patients with PML and suggest that lymphocytes are an important vector for hematogenous dissemination of JCV to the central nervous system.(ABSTRACT TRUNCATED AT 250 WORDS)

Persistence of archetypal JC virus DNA in normal renal tissue derived from tumor-bearing patients

JC virus DNAs derived from the urine of nonimmunosuppressed individuals generally contain an archetypal regulatory region which may have generated various regulatory regions of JC virus from from the brain with progressive multifocal leukoencephalopathy (PML). In this study, we examined whether JC virus persisting in normal human kidney tissue contains the archetypal regulatory region. Renal medulla, cortex, and tumor from 32 patients bearing renal tumors were screened for JC virus DNA by blot hybridization. Viral DNA was detected in the medulla in 13 cases (41%), in the cortex in 2 cases (6%), but not at all from the tumor. A number of viral DNA-positive specimens (8 from the medulla and 2 from the cortex) were used to amplify and sequence viral regulatory regions by polymerase chain reaction. Structures of the regulatory regions from all the specimens were, with a few nucleotide variations, identical with that of the archetypal region which was previously detected in the JC virus DNA from urine. This finding supports the hypothesis that the JC virus associated with PML evolved from the archetypal JC virus during persistence in human hosts. Furthermore, we present evidence that renal JCV is replicating and that progeny virions are excreted into the urine.

Pathogenesis and molecular biology of progressive multifocal leukoencephalopathy, the JC virus-induced demyelinating disease of the human brain

Studies of the pathogenesis and molecular biology of JC virus infection over the last two decades have significantly changed our understanding of progressive multifocal leukoencephalopathy, which can be described as a subacute viral infection of neuroglial cells that probably follows reactivation of latent infection rather than being the consequence of prolonged JC virus replication in the brain. There is now sufficient evidence to suggest that JC virus latency occurs in kidney and B cells. However, JC virus isolates from brain or kidney differ in the regulatory regions of their viral genomes which are controlled by host cell factors for viral gene expression and replication. DNA sequences of noncoding regions of the viral genome display a certain heterogeneity among isolates from brain and kidney. These data suggest that an archetypal strain of JC virus exists whose sequence is altered during replication in different cell types. The JC virus regulatory region likely plays a significant role in establishing viral latency and must be acted upon for reactivation of the virus. A developing hypothesis is that reactivation takes place from latently infected B lymphocytes that are activated as a result of immune suppression. JC virus enters the brain in the activated B cell. Evidence for this mechanism is the detection of JC virus DNA in peripheral blood lymphocytes and infected B cells in the brains of patients with progressive multifocal leukoencephalopathy. Once virus enters the brain, astrocytes as well as oligodendrocytes support JC virus multiplication. Therefore, JC virus infection of neuroglial cells may impair other neuroglial functions besides the production and maintenance of myelin. Consequently our increased understanding of the pathogenesis of progressive multifocal leukoencephalopathy suggests new ways to intervene in JC virus infection with immunomodulation therapies. Perhaps along with trials of nucleoside analogs or interferon administration, this fatal disease, for which no consensus of antiviral therapy exists, may yield to innovative treatment protocols.

Molecular characterization of a JC virus (Sap-1) clone derived from a cerebellar form of progressive multifocal leukoencephalopathy

Progressive multifocal leukoencephalopathy (PML) is a demyelinating disease caused by polyomavirus JC (JCV). In the majority of cases of PML the cerebrum is mainly affected (cerebral PML) but on rare occasions lesions are restricted to the cerebellum and brain stem (cerebellar PML). We report a rare cerebellar PML case which occurred in a Japanese patient undergoing prolonged hemodialysis treatment. To understand the molecular basis of the viral tissue tropism, we molecularly cloned JCV DNA and compared it with those of cerebral PML. Of ten clones analyzed nine showed identical fragment patterns after digestion with various restriction endonucleases, and we designated these clones Sap-1. It could be shown that the basic structures of the regulatory regions are similar between Sap-1 and isolates from cerebral PML. Restriction endonuclease mapping analysis was used to examine the genetic relationship between Sap-1 and urine-derived isolates containing the archetypal regulatory sequence. We found that Sap-1 was genetically related to an archetypal JCV isolate in Japan.

Typing of human polyomavirus JC virus on the basis of restriction fragment length polymorphisms

JC virus DNA clones from the urine of nonimmunosuppressed Japanese individuals regularly contain an archetypal regulatory sequence which may have generated various regulatory sequences of JC virus isolates from patients with progressive multifocal leukoencephalopathy (PML). In this study, we established 15 new clones from the urine of Dutch, German, and Taiwanese healthy volunteers and patients. Most of these clones contained regulatory sequences essentially identical to the archetypal regulatory sequence. These clones, along with two representative urine-derived clones in Japan and five clones from the brains of PML patients (four established in the United States and one established in Japan), were analyzed with a number of restriction enzymes. We found nine restriction fragment length polymorphisms by which all clones were classified into either of the two types, A and B. Type A contained only clones from the West, while type B contained some from the West and all from eastern Asia. Each type contained both urine-derived and PML-derived clones. Furthermore, there was a close relationship between some urine-derived clones and some PML-derived clones in restriction site mapping analysis. These findings support the adaptation hypothesis which has been postulated to explain the genesis of PML-type JC viruses.

Enhancer/promoter activities of regulatory regions of representative JC virus isolates

The enhancer/promoter activities of JC virus isolates MAD1, MAD8, and MAD11 in HeLa cells and in human glial cells expressing either SV40 or JCV(MAD1) tumor antigens were significantly different from one another in each cell line.

Sequence rearrangement in JC virus DNAs molecularly cloned from immunosuppressed renal transplant patients

From nonimmunocompromised individuals, we have recently identified a possible archetypal JC virus DNA sequence from which various regulatory sequences of JC virus isolates derived from patients with progressive multifocal leukoencephalopathy (PML) could have evolved. In this study, we analyzed the regulatory sequences of JCV DNAs cloned from urine samples of a PML risk group (renal transplant patients on immunosuppressive therapy). A number of JC virus DNAs were molecularly cloned from virions excreted in the urine of eight patients. Furthermore, fragments containing the regulatory region were amplified by the polymerase chain reaction and subsequently molecularly cloned from cell-associated JC virus excreted in the urine of two patients. The regulatory regions in all clones were analyzed with restriction enzymes, and those in representative clones were sequenced. We found that clones with the archetypal regulatory sequence were predominant in all urine samples, but a few clones carried regulatory sequences that diverged from the archetypal sequence by deletion or duplication. The finding that sequence rearrangement in the archetypal regulatory region occurs in the course of infection in immunosuppressed hosts is consistent with the adaptation hypothesis which has been put forward to explain the divergence of the regulatory regions in PML-derived JC virus isolates.

Nucleotide sequence and genome organization of the murine polyomavirus, Kilham strain

The polyomavirus Kilham strain (KV) represents a second murine member of the polyomavirus family. However, in contrast to other polyomaviruses, KV exhibits a stringent host and cell specificity. To determine the relationship of these viruses, the complete DNA sequence of KV consisting of 4754 bp was determined. The predicted organization of K virus was found to be comparable to that of other members of the polyomavirus family with two strands coding in an opposite direction of an intergenic region harboring putative control elements for gene expression. These include consensus elements for the origin of DNA replication as well as predicted promoter protein binding domains. Inferred signal sequences for 3' and 5' end formation of mRNAs and splice/branch site consensus sequences resemble those found among the SV40 group of viruses. From the organization of the genome two nonstructural proteins, large T and small t antigen, are predicted, both of which share the same amino-terminal sequence. Three putative capsid proteins VP1, VP2, and VP3 are encoded by alternative open reading frames. The nucleotide sequence in the proposed origin of DNA replication and the inferred amino acid sequence of the viral proteins suggest an evolutionary relationship placing KV between the murine PyV and the SV40 group of viruses. In the region bearing putative transcriptional control elements less nucleotide similarity to that of other polyomaviruses is found and this may reflect the unique host and cell specificity of KV.

Amplification and sequencing of the control regions of BK and JC virus from human urine by polymerase chain reaction

The various strains of BKV and JCV exhibit a remarkable degree of heterogeneity in the noncoding region near the origin of DNA replication. It is of great interest, therefore, to characterize the naturally occurring variants as a first step towards the attainment of an understanding of the origin and the biological significance of this hypervariability. In this paper we report the use of polymerase chain reaction for amplification and sequencing of the control regions of BKV and JCV DNAs from urines of AIDS patients, bone marrow transplantation recipients, and other patient groups. Our results support the conclusion that BK(WW) and its variants constitute the most prevalent strain in the human population tested so far. A new strain, designated BK(TU), was isolated from some patients from Norway. Urine inocula containing BK(WW) gave BK(TU) after propagation in cell culture, while BK(TU) did not change the sequence of its control region during the same procedure. The JCV isolates were almost identical with several strains molecularly cloned from the urine reported by Y. Yogo, T. Kitamura, C. Sugimoto, T. Ueki, Y. Aso, K. Hara, and F. Taguchi (J. Virol., 1990, 64, 3139-3143). This archetypal strain may represent the JCV circulating in the human population, from which various regulatory sequences of JCV isolates could have evolved by deletions and amplifications.

Isolation of a possible archetypal JC virus DNA sequence from nonimmunocompromised individuals

We molecularly cloned JC polyomavirus DNAs from urine samples of eight nonimmunosuppressed patients and two healthy individuals. The cloned viral DNAs all contained an archetypal regulatory sequence from which various regulatory sequences of JC polyomavirus isolates derived from patients with progressive multifocal leukoencephalopathy could have evolved by deletion and amplification.

Direct isolation and characterization of JC virus from urine samples of renal and bone marrow transplant patients

JC virus DNA was extracted from urine-derived cells of bone marrow and renal transplant patients and cloned directly into the plasmid vector pBR322. These clones represent the first JC virus isolates obtained directly from individuals that did not have progressive multifocal leukoencephalopathy (PML). Three of the clones appeared to be identical to the prototype JC virus Mad 1, and the fourth clone was identical to the type II JC virus variant Mad8-Br. Importantly, the same JC virus strains have been identified both in the urine of non-PML patients and in the brain tissue of PML patients. These results indicate that different organs may be infected with the same JC virus subtype and implies that an adaptation process involving the alteration of viral regulatory signals is not required in the pathogenesis of PML. Furthermore, both a type I and a type II variant were obtained from the same patient, suggesting that an individual may be infected with more than one strain of JC virus at a given time.

Regulatory sequences of SV40 variants isolated from patients with progressive multifocal leukoencephalopathy

Variants of the simian polyomavirus SV40 have been associated in humans with a small number of cases of progressive multifocal leukoencephalopathy (PML). Genomic regulatory regions of two independent isolates, SVPML-1 and -2 [L.P. Weiner et al., N. Engl. J. Med. 286, 385 (1972)], were analyzed to determine if they had acquired any sequences that are present in the genome of the human polyomavirus JC (JCV), the primary causative agent of PML. As compared to SV40 DNA, 83% of SVPML-1 and -2 cloned DNAs contained an apparent deletion of about 30 base pairs in the restriction fragment containing the regulatory region (type alpha); 17% had a deletion of about 60 base pairs (type beta). The regulatory sequences were identical in all four clones representative of SVPML-1 and -2 type alpha grown in human and monkey cells. Thus the primary genomes of two isolates of SV40 from PML are identical in the region that is highly heterogeneous in JCV. The SVPML-alpha-DNAs have a net deletion of 30 base pairs and rearrangements within the transcriptional enhancer. The transcriptional promoter and origin of DNA replication is unaltered from that of SV40. Therefore the human neurotropism of SVPML appears to be a consequence of important rearrangements of SV40 sequences rather than acquisition of JCV-like sequences.

Diagnosis of progressive multifocal leucoencephalopathy by hybridisation techniques

In situ hybridisation with acetyl-aminofluorene (AAF) and 35S-labelled DNA probes for polyomaviruses, was used to detect JC virus DNA in brain necropsy material in a patient with progressive multifocal leucoencephalopathy (PML). In a second patient PML was diagnosed from a brain necropsy specimen using the same technique. The main infected cell type were oligodendrocytes; dot hybridisation was used to estimate the number of viral copies in each infected cell. Southern blot hybridisation for further analysis of the viral genome was also carried out. In situ hybridisation with non-radioactive labelled polyomavirus DNA provides a simple and specific means for studying viral DNA in formaldehyde fixed tissue sections from patients with suspected PML. Even in small biopsy samples hybridisation results can be correlated with standard histopathological, immunocytochemical, and electron microscopic findings.

DNA rearrangements in organ-specific variants of polyomavirus JC strain GS

Variants of JC virus (JCV) strain GS were isolated directly from the central nervous system (variant GS/B) and the kidney (variant GS/K) of a patient with progressive multifocal leukoencephalopathy and were cloned and sequenced. The genomes of the isolates were shown to be nearly identical in the nucleotide sequences of their protein-coding regions, suggesting that both had originated from a single infecting JCV genome. In contrast, the arrangement of the putative elements of transcriptional control revealed considerable differences. The tandemly repeated elements found twice within the enhancer region of JCV GS/B variant were not present in the GS/K variant. The missing elements were replaced by DNA segments containing simian virus 40 and adenovirus E1A core enhancer elements. These differences in the organ-specific GS variants suggest that rearrangements within elements of transcriptional control might be involved in altering the virus-cell interaction in the course of a JCV infection.

Association of polyomaviruses JC, SV40, and BK with human brain tumors

Human brain tumors of 11 different types were analyzed by Southern blot analysis for the presence of JCV, SV40, and BKV. In 21 tumor specimens examined with JCV- and SV40-specific probes no positive hybridizations were obtained. Analysis for BKV DNA, however, revealed the presence of BKV-specific sequences in 11 of 24 tumor specimens. No hybridization was found in DNA from CNS tissues from different areas of 29 individuals without CNS tumors. The BKV DNA sequences were associated with high molecular weight cellular DNA, suggesting a chromosomal location. These data provide evidence for the involvement of BKV in the development of human brain tumors.

Evidence for a shift in 5'-termini of early viral RNA during the lytic cycle of JC virus

We have used primer extension and S1 analysis to localize the 5'-termini of JC virus (JCV) early RNAs in infected primary human fetal glial cells at various times postinfection and in stable JCV-transformed hamster fetal glial cells. At early times postinfection (Days 1-5), two early transcripts are initiated at nucleotides 5122 and 5082. A major shift in 5'-ends at later times results in the synthesis of a new series of early mRNAs beginning upstream at nucleotide 35 and downstream at nucleotides 5047, 5037, and 5012. In the transformed hamster cells, however, only one RNA species was detected, starting at nucleotide 5122. The mechanism underlying the shift in the initiation site of JCV early RNAs during a lytic infection remains unclear but appears analogous to that which occurs in the SV40 lytic cycle. Since the shift occurs during DNA replication, when T-antigen is at maximal levels, it is possible that T-antigen binding to JCV DNA and/or alterations in chromatin structure contribute to this event.

Genetic characterization of JC virus Tokyo-1 strain, a variant oncogenic in rodents

The genome DNA of JC virus Tokyo-1 strain [JCV(Tokyo-1)], a variant oncogenic in rodents, was molecularly cloned directly from the brain of a Japanese patient with progressive multifocal leukoencephalopathy and from tissue culture, and the restriction enzyme cleavage pattern and regulatory sequences were determined. The restriction pattern of the cloned JCV(Tokyo-1) DNA was different from those of JCVs previously reported in the United States and Germany. Also, the arrangement of the regulatory sequence was unique to this strain. Thus JCV(Tokyo-1) can be classified as a new subtype. The relationship between the restriction pattern and the regulatory sequence of JCV(Tokyo-1), and its characteristic oncogenicity, is discussed.

Search for virus nucleic acid sequences in postmortem human brain tissue using in situ hybridization technology with cloned probes: some solutions and results on progressive multifocal leukoencephalopathy and subacute sclerosing panencephalitis tissue

In order to obtain a useful and readily applicable in situ hybridization (ISH) protocol for progressive central nervous system (CNS) diseases of unknown etiology that are possibly due to persistent viral infection, known and well described diseases were studied, namely, progressive multifocal leukoencephalopathy (PML) and subacute sclerosing panencephalitis (SSPE). The procedures described were validated by confirming results obtained by other investigators using histology, immunocytochemistry, electron microscopy, and ISH. A number of frequently encountered problems of tissue preparation are addressed as well as techniques to reduce autoradiography exposure times. A multi-staged specific, sensitive, reliable, and valid procedure for detection of viral genomes, mRNA and proteins is approached. Formalin-fixed and paraffin-embedded (FFPE) brain material from six patients who died with PML and one patient who died from SSPE were studied using ISH with a tritium-labeled cloned JC virus DNA probe and a measles-cloned nucleocapsid (NC) gene cDNA probe, respectively. This report constitutes a methodological framework as well as a detailed neuropathological analysis of identified brain cell populations within which in situ hybridization was detected. In early PML lesions, swollen nuclei or oligodendrocytes were the predominant cells labeled, whereas older lesions revealed increased numbers of reactive and bizarre hypertrophic astrocytes hybridized at the outer periphery of the demyelinated lesions. The hybridization varied greatly in intensity in different cells. Intense hybridization was noted very rarely in microglial cells, including rod cells and rarely in venular pericytes, intravascular mononuclear cells, or in vascular endothelial cells. These results, considered together with previous findings, indicate that in PML the viral infection runs different courses in the various cells: in astrocytes the viral genome persists for a long time inducing pathological changes in some cells. In oligodendrocytes the infection rapidly lyses the cells. There was a good correlation between chromatic changes observable in routinely stained sections and virus presence. In addition, in situ hybridization using a measles-NP-cloned probe in white matter from FFPE SSPE brain is presented confirming earlier results in SSPE cryopreserved brain.

Use of a molecular probe for detecting JCV DNA directly in human brain material

A hybridot assay using a radiolabelled JC virus probe has been used to detect the presence of JCV DNA in brain biopsy and postmortem brain samples from patients with neurological disease and possible progressive multifocal leucoencephalopathy. Sixty-nine brain samples from 45 patients were examined. Eleven samples from eight patients had detectable JCV DNA sequences. In seven of the eight patients this result was confirmed by electron microscopy and/or virus isolation or immunofluorescence.

DNA rearrangement in the control region for early transcription in a human polyomavirus JC host range mutant capable of growing in human embryonic kidney cells

A human polyomavirus JC virus (JCV) host range mutant (JC-HEK) can grow in human embryonic kidney cells, whereas the brain cell-tropic wild-type JCV strain (Mad-1) cannot; JC-HEK contains two complementing defective DNAs, JC-HEK-A and JC-HEK-B. We determined the nucleotide sequence of the putative transcriptional control region of JC-HEK-A DNA that can induce T-antigen synthesis in human embryonic kidney cells and compared it with the sequence of JCV Mad-1 DNA. The JC-HEK-A control region was found to have a complex DNA rearrangement, namely, a partial local duplication of a noncoding region generating two extra replication origins and translocation of segments from the large-T-antigen gene (415 base pairs) and the VP-1 gene (78 base pairs). In the rearranged segment, JC-HEK-A had seven sets of the sequence 5'TGGA(T)A(T)A(T)3', which is found in the simian virus 40 enhancer core, whereas JCV Mad-1 had only one set in its control region. JC-HEK-A also had a 5'TGGAAGTGTAA3' sequence resembling the adenovirus early region 1A enhancer core sequence 5'AGGAAGTGAA3'. Because the viral enhancer is host discriminatory and because another human polyomavirus, BK virus, that grows well in human embryonic kidney cells has these signals in its control region, it is likely that some of the newly acquired signals in JC-HEK play an important role in the altered host range of JCV.