High prevalence of human polyomavirus JC VP1 gene sequences in pediatric malignancies

The oncogenic potential of human polyomavirus JC (JCV), a ubiquitous virus that establishes infection during early childhood in approximately 70% of the human population, is unclear. As a neurotropic virus, JCV has been implicated in pediatric central nervous system tumors and has been suggested to be a pathogenic agent in pediatric acute lymphoblastic leukemia. Recent studies have demonstrated JCV gene sequences in pediatric medulloblastomas and among patients with colorectal cancer. JCV early protein T-antigen (TAg) can form complexes with cellular regulatory proteins and thus may play a role in tumorigenesis. Since JCV is detected in B-lymphocytes, a retrospective analysis of pediatric B-cell and non-B-cell malignancies as well as other HIV-associated pediatric malignancies was conducted for the presence of JCV gene sequences. DNA was extracted from 49 pediatric malignancies, including Hodgkin disease, non-Hodgkin lymphoma, large cell lymphoma and sarcoma. Polymerase chain reaction (PCR) was conducted using JCV specific nested primer sets for the transcriptional control region (TCR), TAg, and viral capsid protein 1 (VP1) genes. Southern blot analysis and DNA sequencing were used to confirm specificity of the amplicons. A 215-bp region of the JCV VP1 gene was amplified from 26 (53%) pediatric tumor tissues. The JCV TCR and two JCV gene regions were amplified from a leiomyosarcoma specimen from an HIV-infected patient. The leiomyosarcoma specimen from the cecum harbored the archetype strain of JCV. Including the leiomyosarcoma specimen, three of five specimens sequenced were typed as JCV genotype 2. The failure to amplify JCV TCR, and TAg gene sequences in the presence of JCV VP1 gene sequence is surprising. Even though JCV TAg gene, which is similar to the SV40 TAg gene, is oncogenic in animal models, the presence of JCV gene sequences in pediatric malignancies does not prove causality. In light of the available data on the presence of JCV in normal and cancerous colon epithelial tissue and our data on amplification of JCV from the cecum of an HIV-infected pediatric patient, further studies are warranted on the role of colon epithelium in the pathogenesis of JCV infection.

JC virus T' proteins encoded by alternatively spliced early mRNAs enhance T antigen-mediated viral DNA replication in human cells

Alternative splicing of the JC Virus (JCV) precursor early mRNA yields five transcripts that encode proteins that regulate the life cycle of this human polyomavirus. Large T protein (TAg) mediates viral DNA replication and oncogenic activities, and small t protein influences these functions under certain conditions. Recently, three new early proteins, T'(135), T'(136), and T'(165), were discovered that contain sequences overlapping amino-terminal TAg functional domains. Initial studies with the T' proteins suggested they contribute to viral DNA replication and transformation. Mutation of a donor splice site utilized by all three T' mRNAs creates a mutant that exhibits a 10-fold decrease in viral DNA replication compared to wild type JCV. To assess the influence that individual T' proteins have on the replication process, a set of T' acceptor site mutants was created in which the unique second acceptor splice site of each T' mRNA was altered to eliminate production of one, two or all three T' mRNAs. The patterns of early mRNA and protein expression in these seven mutants were examined, and it was found that mutation of the T'(135) acceptor site resulted in the utilization of cryptic splice sites and the generation of new T' species. Additional mutations were made to prevent these aberrant splicing reactions prior to measuring DNA replication potential of the mutants. DpnI assays revealed that each T' protein contributes to TAg-mediated DNA replication activity. The three single mutants that express two T' proteins and the double mutant that only produces T'(136), exhibited levels of replication equivalent to that of wild type virus, whereas the two double mutants that fail to express T'(136) replicated about twofold less efficiently than wild-type JCV. Replication activity of the triple acceptor site mutant, like that of the T' donor site mutant from an earlier study, was impaired significantly.

Purified JC virus T and T' proteins differentially interact with the retinoblastoma family of tumor suppressor proteins

The amino termini of polyomavirus T antigens contain LXCXE and J domains, which are necessary for binding and inactivating the retinoblastoma family of tumor suppressors. Both of these motifs are found in the JC virus (JCV) early proteins T'(135), T'(136), and T'(165), leading to the suggestion that these recently discovered proteins complement the cell-cycle-deregulating function of the JCV large T antigen (TAg). To investigate this hypothesis, the three JCV T' proteins were produced in a baculovirus expression system and purified by immunoaffinity chromatography. To facilitate purification, hybridomas that secrete antibodies recognizing amino-terminal epitopes of JCV early proteins were produced. Potential interactions between the early viral proteins and the cellular proteins pRB, p107, and p130 were investigated by incubating purified JCV TAg and T' proteins with extracts of MOLT-4 cells, a human T cell line. The four viral proteins preferentially bound hypophosphorylated species of the cellular proteins and exhibited the highest binding affinity to p107 and the lowest affinity to pRB. TAg and T'(165) bound more pRB and less p107 than did T'(135) and T'(136); T'(165) also bound less p130 than the other three early proteins. Results of these in vitro interactions were compared to those obtained in vivo using POJ cells, a transformed human glial cell line that expresses JCV early proteins, relatively high levels of pRB and p107, and low levels of p130. Most of the pRB in POJ cells is hyperphosphorylated, and only a fraction of the hypophosphorylated form(s) of pRB is bound by the viral proteins. In contrast, only hypophosphorylated p130 is detected in the transformed cells, and most of this protein was found in complex with the viral proteins. Finally, nearly all of the p107 in POJ cells is bound by the JCV proteins.

Identification of archetype and rearranged forms of BK virus in leukocytes from healthy individuals

BK virus (BKV) establishes a persistent, asymptomatic infection in more than 80% of the human population, and in immunocompromised individuals BKV causes acute urinary tract infections. Two forms of BKV, archetype and rearranged, have been recovered previously from urine samples. The rearranged form is believed to have emerged from the archetype form by the deletion and duplication of sequences within the transcriptional control region (TCR). We have PCR-amplified unique rearranged forms of the BKV TCR from peripheral blood leukocytes (PBLs) of healthy donors. By employing archetype-specific PCR primers, the archetype BKV TCR was also detected in PBLs. These findings are consistent with the hypotheses that PBLs transport BKV to different sites within the body and play a role in the TCR rearrangement process. BKV sequences were detected in 21 of 38 BKV-seropositive and 1 of 2 BKV-seronegative individuals. Because of recent suggestions that SV40 may circulate in the human population, the donors' sera were also examined for the presence of specific anti-SV40 antibodies. A high antibody titer to SV40 was detected in only 1 of the 40 donor specimens. This study is the first to characterize multiple BKV TCR variants in PBLs from healthy people and to correlate PCR and serological methods used to detect BKV infections.

Identification of JC virus variants in multiple tissues of pediatric and adult PML patients

The transcriptional control region (TCR) of JC virus (JCV), the causative agent of progressive multifocal leukoencephalopathy (PML), undergoes rearrangement during replication of the virus in its human host. The mechanism by which viral promoter/enhancer sequences are deleted and duplicated within the TCR of the archetype form of JCV is not understood, but it is hypothesized that the generation of JCV variants with rearranged TCRs contributes to the virus's pathogenic potential. In a recent study of a pediatric PML patient, we detected extensive rearrangement of the JCV TCR in multiple tissues, and the archetype TCR was amplified from sites other than the kidney. These findings differed from those of previous studies that had examined tissues from adult PML patients. Since exposure to JCV usually occurs early in life, it is likely that some pediatric cases of PML arise as the result of a primary infection, whereas adult cases of PML are thought to result from the reactivation of an infection suffered as an immunocompetent child. To investigate further whether rearrangement of the JCV TCR is affected by the host's age and immune status at the time of exposure, a second pediatric patient and two adult PML patients were examined. As in our first study, multiple tissues were found to contain JCV DNA; however, fewer rearranged variants were detected. In one adult patient, related rearranged variants were detected in the brain, while archetype JCV was found in the other tissues. Based on differences in their VP1 sequences, these two forms represented different JCV genotypes, indicating that this patient had suffered a dual infection. The relevance of these findings to the rearrangement process that alters the JCV TCR is discussed.

Rearranged and chimaeric primate polyomavirus genomes

Recombination between different primate polyomavirus genomes (SV40, JCV, BKV) or within the genome of the same species (e.g. archetype to rearranged type virus) might contribute to the establishment of SV40-like viruses within the human population. Alternatively, it is possible that these polyomaviruses might, upon co-infection of human cells, complement each other's growth through direct virus-virus interactions or by indirect effects on host cell permissiveness. Our laboratory has investigated the activity of JCV-BKV-SV40 chimaeras constructed in vitro, and some of them exhibit altered lytic, host range, and oncogenic behaviour. Our work has also included the PCR analysis of human tissue specimens for the presence of polyomaviral sequences. Archetype and rearranged variants of JC virus have been detected in normal and diseased tissues, but evidence for naturally arising JCV-BKV or JCV-SV40 recombinant genomes has not been obtained.

Identification of SV40 in brain, kidney and urine of healthy and SIV-infected rhesus monkeys

Recent reports of simian virus 40 (SV40) sequences in human tumors have prompted investigations into the poorly understood association of this polyomavirus with its primate host, the rhesus monkey (Macaca mulatta). In the present study we have used PCR to analyze tissues from 20 monkeys for the presence of SV40. Five of the animals, which were infected with simian immunodeficiency virus (SIV), were found to exhibit SV40-induced lesions and to have SV40 sequences present in their kidney and brain. Lesions associated with SV40 were not observed in 15 SIV monkeys, and SV40 DNA was detected in kidney and urine of only one of these animals. Three regions of SV40 DNA were examined in each tissue: the non-coding transcriptional control region (TCR), the sequences encoding the host range domain (HRD) within the carboxy-terminus of T antigen (TAg), and a portion of the VP1 gene. Each region contained nucleotide alterations compared to the SV40 reference strain 776. In all six animals, the TCR had an archetype structure containing a single 72 bp enhancer element. In addition, the TCR amplified from two animals lacked one of three copies of a GC-rich 21 bp repeat which is part of the promoter in strain 776. Multiple clones of unique HRD sequences were derived from different animals, and in some instances from the same animal. No correlation was found between a particular HRD sequence and its presence in a specific tissue type. Nucleotide changes identified within the VP1 gene indicate that this region, as with the closely-related human polyomavirus JCV, may permit the typing of the virus into individual strains. This study is the first to characterize SV40 sequences present in both healthy and SIV-infected animals and supports the suggestion that strain 776 is not the predominant type of SV40 circulating in its natural host.

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.

Replication activity of JC virus large T antigen phosphorylation and zinc finger domain mutants

The replication potential of the human polyomavirus JC virus (JCV) relative to that of the related monkey virus SV40 is limited, in part, by differences in the multifunctional T antigen (T Ag). Earlier genetic analyses of the SV40 T protein indicated that specific phosphorylation sites and a zinc finger motif are involved in the regulation of viral replication. The JCV and SV40 T Ags differ with respect to sequences encoding these functional domains, and in the present study mutational analysis of the JCV protein was conducted to assess the role that unconserved residues might play in the restricted lytic behavior of JCV. Amino acids Asn316 and His317 in the zinc finger domain and Thr664 and Glu666 in the carboxy-terminal phosphorylation domain were mutated to either an SV40-like residue or an alanine. Each of the mutant JCV genomes replicated with wild type efficiency suggesting that, unlike the case for SV40 T Ag, these amino acids are not critical to the regulation of viral replication. On the other hand, mutation of amino acid Thr125 within the amino-terminal phosphorylation domain abolished JCV DNA replication and viability. This site is conserved in the SV40 T Ag, and previous results have revealed that phosphorylation of this residue (Thr124) is required for T Ag replication function.

Purified JC virus T antigen derived from insect cells preferentially interacts with binding site II of the viral core origin under replication conditions

The human polyomavirus JC virus (JCV) establishes persistent, asymptomatic infections in most individuals, but in severely immunocompromised hosts it may cause the fatal demyelinating brain disease progressive multifocal leukoencephalopathy. In cell culture JCV multiplies inefficiently and exhibits a narrow host range. This restricted behavior occurs, in part, at the level of DNA replication, which is regulated by JCV's multifunctional large tumor protein (TAg). To prepare purified JCV TAg (JCT) for biochemical analyses, the recombinant baculovirus B-JCT was generated by cotransfection of insect cells with wild-type baculovirus and the vector pVL-JCT(Int-) containing the JCT-coding sequence downstream of the efficient polyhedrin promoter. JCT expressed in infected cells was immunoaffinity purified using the anti-JCT monoclonal antibody PAb 2000. Characterization of the viral oncoprotein indicated that it exists in solution as a mixture of monomeric and oligomeric species. With the addition of ATP, the population of monomers decreased and that of hexamers and double hexamers increased. A DNA mobility shift assay indicated that origin binding occurred primarily with the double-hexamer form. A comparison of the specific DNA-binding activities of JCT and SV40 TAg (SVT) revealed that JCT generally exhibited greater affinity for binding site II relative to binding site I (B.S. I) of both viral origin regions, whereas SVT preferentially bound B.S. I. Furthermore, JCT bound nonviral DNA more efficiently than did SVT. These functional differences between the two TAgs may contribute to the reduced DNA replication potential of JCV in vitro, and to the virus' ability to establish persistent infections in vivo.

Sequences within the early and late promoters of archetype JC virus restrict viral DNA replication and infectivity

Two forms of JC virus (JCV) have been isolated from its human host, an archetype found in kidney tissue and urine of nonimmunocompromised individuals and a rearranged type detected in lymphocytes and brain tissue of patients with and without progressive multifocal leukoencephalopathy. To investigate the hypothesis that alterations to the archetype transcriptional control region yield rearranged forms of the virus exhibiting new tissue tropic and pathogenic potentials, attempts were made to propagate archetype JCV in human renal and glial cell cultures. Although rearranged forms of JCV multiplied in these cells, archetype JCV failed to do so. Through the use of chimeric and mutant viral genomes, and a cell line that constitutively expresses viral T protein, we demonstrated that archetype's inactivity relative to that of rearranged forms was due to differences in the promoter-enhancer and not in the protein coding regions or origin of DNA replication. Additional analyses revealed that the absence of a large tandem duplication and the presence of a 23- and a 66-base pair sequence in the archetype transcriptional control region were responsible for this restricted lytic behavior. We discuss the possibility that deletion and duplication events within the archetype promoter-enhancer might yield more active viral variants via the loss of a negative, or the creation of a positive, transcriptional control signal(s).

Biochemical characterization and localization of JC virus large T antigen phosphorylation domains

Large T antigen (T Ag), the major regulatory protein produced by the primate polyomaviruses, is a multifunctional phosphoprotein expressed early in the viral life cycle. T Ag performs many functions essential to viral DNA replication, and studies with SV40 T Ag indicate that the regulation of these functions is modulated, in part, by the phosphorylation status of this oncoprotein. In this study, we demonstrate that JC virus (JCV) T Ag obtained from lytically infected and transformed cells is phosphorylated at serine and threonine residues. Analysis of JCV T Ag via two-dimensional tryptic peptide mapping generates 14 phosphopeptides. Additional mapping studies of intact, hybrid, mutant, and truncated forms of JCV T Ag have aided the localization of phosphorylation sites to the N- or C-terminal region of the protein; both serine and threonine residues are modified at each terminus. The data indicate that, unlike the corresponding regulatory phosphorylation site Ser677 in SV40, Thr664 is not phosphorylated in JCV T Ag. The phosphorylation sites utilized for JCV T Ag, and the regulatory role of these sites, are predicted to contribute to the unique biology of this human virus.

Identification of three new JC virus proteins generated by alternative splicing of the early viral mRNA

The genome of the human polyomavirus JC Virus (JCV) encodes two regulatory proteins, large and small T antigen which are expressed early in a lytic infection, and three structural proteins, VP1, VP2, VP3, which are produced late in an infection. A fourth late protein, agnoprotein, may contribute to the assembly of the virion. In this study, we demonstrate the presence of three additional early proteins, T'135, T'136, and T'165, which are expressed in lytically-infected cells; T'135 is also readily detected in JCV transformants. The three species of T' are phosphoproteins generated via an alternative splicing mechanism. This mechanism involves the excision of a second intron from the large T mRNA using a common donor splice site at JCV nucleotide 4274 and three unique acceptor splice sites at nucleotides 2918, 2777 and 2704 for T'135, T'136 and T'165, respectively. The mutant JCV delta T' was created by converting the G at nucleotide 4274 to an A, thereby disrupting the consensus sequence of the shared donor splice site without altering the amino acid sequence of any early JCV protein. Upon transfection of permissive human brain cells, JCV delta T' replicated its DNA 10-fold less efficiently than did wild type JCV. Passage of extracts of the infected cells on to fresh human brain cells revealed that the expression of T antigen was greatly reduced and the presence of T' proteins was undetectable in the mutant versus wild type JCV-infected cells.

Immortalization of human cells by mutant and chimeric primate polyomavirus T-antigen genes

Human fibroblasts were morphologically transformed with wild type and mutant SV40 T-antigens (T-Ags) and with SV40/JCV and SV40/BKV chimeric T-Ags. The transformants were then assayed for the attainment of immortal cell growth. Several observations relating T-Ag and T-Ag domains to immortalization were made. Approximately 10% of SV40-transformants became immortal. Transformants generated by transfection or infection of cells with C-terminal T-Ag deletion mutants of SV40 did not immortalize. SV40/JCV and SV40/BKV chimeric T-Ags, containing C-terminal sequences from JCV or BKV, immortalized cells more efficiently than did the intact SV40 T-Ag, suggesting that the C-termini of the JCV and BKV T-Ags contain an enhanced immortalization function. However, chimeras in which the N-terminal or proximal-central portions of T-Ag were composed of JCV sequences failed to immortalize but did induce transformation. Constructs in which the JCV T-Ag Rb binding domain was replaced with SV40 sequences transformed human cells, but again the cells failed to immortalize. Transformants and immortalized cell lines produced by some SV40/JCV chimeras, contained p53 which was unbound by T-Ag. This occurred under conditions where p53 from SV40 and SV40/BKV transformants was bound to T-Ag. This may reflect the reduced stability of the SV40/JCV T-Ags.

Cooperative action of cellular proteins YB-1 and Pur alpha with the tumor antigen of the human JC polyomavirus determines their interaction with the viral lytic control element

Human JC polyomavirus (JCV) is the etiologic agent of the neurodegenerative disease progressive mulifocal leukoencephalopathy. By using JCV as a model, we investigated the role of the viral early protein tumor antigen (TAg) in the binding of two cellular proteins, Pura alpha and YB-1, to JCV regulatory sequences. Results from band-shift assays with purified YB-1, Pur alpha, and TAg indicated that efficient binding of Pur alpha, a strong activator of early gene transcription, to a single-stranded target sequence corresponding to the viral lytic control element, is diminished in the presence of the late gene activator YB-1, which recognizes the opposite strand of the Pur alpha binding site. Of particular interest was the ability of Pur alpha and TAg to enhance binding of YB-1 to DNA molecules without being associated with this complex. Binding studies using a mutant peptide encompassing the N terminus of YB-1 indicated that the C terminus of YB-1 is important for its DNA binding activity. The ability of Pur alpha and TAg to increase binding of YB-1 to DNA is independent of the YB-1 C terminus. Similarly, results from band-shift assays using Pur alpha variants indicated that two distinct regions of this protein contribute either to its ability to bind DNA or to its ability to enhance YB-1 DNA binding activity. Based on the interaction of Pur alpha, YB-1, and TAg, and their binding to DNA, a model is proposed for the role of these proteins in transcription of viral early and late genes during the lytic cycle.

DNA replication of chimeric JC virus-simian virus 40 genomes

The ubiquitous virus JCV is the etiologic agent of the human brain disease progressive multifocal leukoencephalopathy. Although infection usually occurs early in life and the virus can remain latent in human tissues, including brain, little information is available regarding its replication. It is known that DNA replication of primate polyomaviruses is dependent upon the synthesis of T antigen and the subsequent interactions of this protein with cellular factors and the viral origin of replication. We constructed chimeric genomes between JCV and SV40, two genetically similar viruses with distinct biologies, in which segments of the T antigen coding region and the replication origin were exchanged. Because the engineering of these genomes created a defect in the structural protein VP1, their DNA replicating activities could be compared without the complication of secondary infection of adjacent cells and amplification of the replication signal. The ability of the JCV-SV40 hybrid T antigens to initiate replication from the two viral origins in primate cells was investigated. A region of the JCV T antigen that includes the DNA binding and zinc finger domains was found to be responsible for the failure of JCV T antigen to interact productively with the SV40 origin. In addition, the ability to replicate in monkey cells was limited to constructs expressing T antigens which contained the carboxy-terminal host range domain of SV40.

Converting the JCV T antigen Rb binding domain to that of SV40 does not alter JCV's limited transforming activity but does eliminate viral viability

Two sets of mutations were introduced into a region of the JC virus (JCV) large tumor (T) antigen involved in binding the retinoblastoma susceptibility gene product (Rb). The first set converted the JCV sequences to those found in the corresponding region of the simian virus 40 (SV40) T antigen. The second set contained sequence changes predicted to abolish Rb binding. Each of these mutations was also inserted into a chimeric T antigen (MSTn) composed of JCV and SV40 sequences at its amino- and carboxy termini, respectively. The JCV T antigen is less efficient than its SV40 counterpart at transforming Rat2 cells and at binding Rb and viral DNA. These activities were altered in the two sets of mutants generated in this study. A JCV T antigen mutant having an SV40-like Rb-binding domain exhibited increased DNA binding activity while, unexpectedly, displaying decreased Rb binding and wild-type transforming behavior. A mutant T antigen that was unable to bind Rb exhibited decreased DNA binding and failed to transform Rat2 cells. Both mutants were defective for DNA replication and did not produce infectious virions. Additional phenotypic changes were observed when each mutation was introduced into the chimeric MSTn T antigen. As the oligomerization state of SV40 T antigen is known to influence several of its activities, including Rb binding, the quaternary structure of the T proteins used in this study was assessed by sucrose gradient sedimentation. The SV40 and chimeric MSTn T antigen sedimented as a mixture of monomers/dimers and higher oligomers, whereas the JCV T antigen sedimented predominantly as monomers/dimers; neither mutation in the T antigen Rb-binding motif affected the sedimentation profiles of the parental T proteins. Restricted biochemical activity of the JCV T protein relative to that of SV40 supports the suggestion that this regulatory protein contributes to the attenuation of the JCV lytic cycle.

Analysis of G418-selected Rat2 cells containing prototype, variant, mutant, and chimeric JC virus and SV40 genomes

The human polyomavirus JC virus (JCV) is highly tumorigenic in rodents, but transforms cells in culture inefficiently. To explore the basis for JCV's restricted transforming behavior, nonpermissive Rat2 cells were contransfected with pSV2-neo (encodes G418 resistance) and viral DNAs including prototype, variant, and mutant JCV genomes and two JCV-SV40 chimeras. By selecting cells displaying G418 resistance, lines were established that contain viral DNA and exhibit a wide range of transformed phenotypes. The G418-resistant lines were tested for their ability to grow under anchorage-independent conditions, to overgrow a monolayer of untransformed cells, and to form dense colonies on plastic. Expression of the viral T and t proteins and interaction of T protein with the cellular anti-oncoprotein p53 were measured. Also determined was the number of intact viral early coding regions integrated within the cellular DNA. The results of these studies suggested that most of the G418-resistant lines failed to express JCV T protein above a minimum threshold level required for their conversion to a fully transformed phenotype. In anchorage-independent growth assays, higher levels of a 17-kDa T-related peptide in JCV transformants appeared to compensate for decreased T antigen levels. Comparison of the T to p53 ratios in the cell lysates suggested that the quaternary structure of the JCV protein differed from that of its SV40 counterpart in the T-p53 complex. The presence of multiple vs single integrated copies of the viral genome in the cells did not correlate with elevated T antigen expression or an enhanced transformation status.

Expression of viral T-antigen in pathological tissues from transgenic mice carrying JC-SV40 chimeric DNAs

Immunostaining methods were used to detect viral T-antigen and the cellular protein p53 in pathological tissues obtained from transgenic mice carrying JC-SV40 hybrid viral DNAs. A transgenic mouse carrying the SV40 regulatory region and JC virus (JCV) T-antigen-coding sequences exhibited an SV40-characteristic choroid plexus papilloma that expressed JCV T-antigen and p53. JCV-associated pathology was observed in two other mice in which the JCV regulatory signals directed SV40 T-antigen-induced adrenal neuroblastomas and brain neoplastic cells. However, these mice also exhibited an SV40-characteristic osteosarcoma and abdominal lymphoma that contained SV40 T-antigen and p53-positive cells. Contrasting thymic pathology was observed in the two types of mice where the SV40 regulatory region directed a JCV T-antigen-induced thymoma in one mouse, and the JCV regulatory region directed SV40 T-antigen-induced thymic hypoplasia in two other mice.

Transcription initiation sites of prototype and variant JC virus early and late messenger RNAs

The locations of the authentic viral transcription initiation sites utilized during the course of a JCV(Mad1) infection of primary human fetal glial (PHFG) cells have been identified using the S1 nuclease and primer extension techniques. Early viral mRNA start sites were located 20 to 30 nucleotides (positions 89-92 and 5115-5125) downstream from the two TATA elements present within the promoter-enhancer region of the JCV(Mad1) strain. Absence of the distal TATA element, as seen in the JCV(Mad4) promoter-enhancer, resulted in the alteration of the position and intensity of these sites. Several start sites were observed for late viral mRNAs; two sites were located 25 and 35 nucleotides (positions 191-192 and 200-203) downstream from a potential surrogate TATA signal. To determine whether the presence of constitutively expressed JCV large T protein would alter the pattern of transcription initiation, RNA isolated from JCV(Mad1)-infected POJ cells was analyzed. Although the positions of the early and late viral mRNA start sites were similar to those observed in JCV(Mad1)-infected PHFG cells, they were detected earlier in the course of the 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.

PAb 2000 specifically recognizes the large T and small t proteins of JC virus

A monoclonal antibody, PAb 2000, has been derived which recognizes the large T protein of JC virus (JCV), but not the corresponding proteins of the related polyomaviruses BK virus (BKV) and SV40. The epitope bound by PAb 2000 was localized to the amino-terminal 81 amino acids of this multifunctional protein. As observed previously with several monoclonal antibodies that bind a similar region of SV40 large T antigen, PAb 2000 was found to interact with the small t antigen and the denatured form of large T antigen. This monoclonal antibody recognized a subpopulation of T protein, the abundance of which varied in different species of cells transformed by JCV. The availability of PAb 2000, the first JCV T antigen-specific monoclonal antibody, will facilitate the purification and biochemical characterization of the JCV oncoproteins.

Altered DNA binding and replication activities of JC virus T-antigen mutants

Ten mutations were introduced into the JC virus (JCV) T antigen within a region corresponding to the SV40 T-antigen DNA binding domain (SV40 amino acids 131 to 220); nine of these increased homology between the two proteins in sequences critical for SV40 T antigen DNA binding. All mutant JCV T antigens bound to JCV and SV40 origins of DNA replication. Binding efficiency relative to the of wild-type JCV T antigen ranged from 83 to 301% for the JCV binding sites and from 44 to 240% for the SV40 binding sites. Nine mutant proteins promoted viral DNA replication in primary human fetal glial (PHFG) and CV-1 cells. In PHFG cells, promotion of DNA replication ranged from 26 to 220% relative to that of wild-type T antigen; in CV-1 cells it ranged from 14 to 522%. Coding sequences for five mutant proteins were transferred into the hybrid virus M1 (SV40) [M1(SV40) contains coding sequences from JCV and regulatory sequences from SV40]. Wild-type T antigen promoted replication weakly from the SV40 origin in these hybrid viruses in CV-1 cells (2% that from the JCV origin); replication driven by the mutant proteins ranged from 110 to 412% of that induced by the wild-type protein. Efficient specific DNA binding by a mutant T antigen was not a reliable indicator of that mutant protein's ability to promote DNA replication.

Localization of common cytotoxic T lymphocyte recognition epitopes on simian papovavirus SV40 and human papovavirus JC virus T antigens

Human papovavirus JC virus (JCV) and Simian virus 40 (SV40) tumor or T antigens demonstrate considerable sequence homology which is reflected by antibody cross-reactivity. This similarity raised the possibility that JCV and SV40 T antigen also might contain common cytotoxic T lymphocyte (CTL) recognition epitopes. In this study we identified and mapped such sites on the JCV T antigen. C57Bl/6 cell lines transformed by JCV/SV40 T antigen chimeras were generated and tested for susceptibility to lysis by five H-2b restricted SV40-specific CTL clones: Y-1, Y-2, Y-3, Y-4, and Y-5. These CTL clones recognize specific epitopes within amino acids 205-219 (site I), 220-233 (sites II and III), 369-511 (site IV), and 489-503 (site V) on SV40 T Ag, respectively. The results show that sites I, II, III, and IV (recognized by CTL clones Y-1, Y-2, Y-3, and Y-4, respectively) represent common epitopes on SV40 and JCV T antigens. CTL clone Y-5 failed to recognize JCV T antigen indicating that CTL can discriminate between the two antigenically related T antigens.

Factors contributing to the restricted DNA replicating activity of JC virus

The basis for the restricted host range behavior of JC virus (JCV) in vitro was investigated by focusing on its DNA replicating activity and comparing it to that of simian virus 40 (SV40). Prototype, mutant, and hybrid JCV and SV40 DNAs were tested for their replicating activity in cells permissive for one or both of the viruses. Results from these experiments indicated that, relative to its SV40 counterpart, the JCV T antigen functioned less efficiently and was more specific in its interactions with polyomavirus DNA replication origins. The JCV T antigen exhibited a lower specific DNA binding activity than did the SV40 T antigen, which might contribute to this virus' reduced DNA replicating activity. However, the JCV protein did bind to both the JCV and SV40 replication origins with similar efficiency, indicating that the ability of the JCV T antigen to discriminate between the JCV and SV40 origins involved a step subsequent to specific DNA binding. The results also suggested that the failure of JCV to replicate to detectable levels in monkey kidney cells was due to the inefficient interactions of its T protein with the viral origin and the host replication machinery. The inability of the JCV T antigen to carry out one or more of these DNA replication functions efficiently contributes to the restricted lytic behavior of this virus.

Identification of critical elements within the JC virus DNA replication origin

The T antigen of JC virus (JCV) does not interact productively with the simian virus 40 (SV40) origin of replication. In contrast, the SV40 T antigen does drive replication from the JCV origin as well as from its own. The basis for this restricted interaction was investigated by analyzing the structure of the JCV replication origin. The replication activities of JCV-SV40 hybrid origin plasmids were tested in cells constitutively producing either the JCV or SV40 T antigen. Results indicated that a region of the JCV origin critical for interaction with the JCV T antigen was positioned to the late side of the central palindrome of the putative core origin. A mutational analysis of this region indicated that the sequence of the A + T-rich tract was primarily responsible for determining the efficiency with which JCV can initiate replication from its origin. The tandemly repeated pentameric sequence AGGGA located proximal to the A + T-rich tract in the JCV enhancer element was found to stimulate JCV, but not SV40, T antigen-mediated replication. The effect on replication of other elements within the JCV enhancer was also dependent on the T antigen employed for initiation. A plasmid containing the replication origin of prototype BK virus was unable to replicate in cells containing JCV T antigen, again indicating the inflexibility of the JCV T antigen in interacting with heterologous origins.

Antigenic and transforming properties of the DB strain of the human polyomavirus BK virus

The analysis of the antigenic and transforming properties of the DB strain of the human polyomavirus BK Virus [BKV(DB)] is presented. Two genomes were molecularly cloned from a single virus preparation and were shown to represent viable virus; one clone [pBKV(DB)dl82] contained an 82 nucleotide deletion in the regulatory region relative to the second clone [pBKV(DB)]; pBKV(DB)dl82 demonstrated enhanced lytic and transforming activities relative to pBKV(DB). BKV(DB) is antigenically distinct from the prototype Gardner strain of BK Virus, and 50 to 60% of the population display serological evidence of BKV(DB) infection. Implications of the existence of antigenic variants on estimation of BK virus prevalence in the population are discussed.

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.

JC virus-simian virus 40 genomes containing heterologous regulatory signals and chimeric early regions: identification of regions restricting transformation by JC virus

The papovavirus JC virus (JCV) is highly oncogenic in experimental animals but, unlike simian virus 40 (SV40), is severely restricted in its ability to transform cells in culture. We exploited the close genetic relatedness of these two viruses to delimit region(s) of the T protein which can restrict transforming activity. Novel chimeric genomes were produced by exchanging various segments of the JCV and SV40 T-protein-coding regions. These DNA constructs specified early proteins with in-frame substitutions of analogous amino acid sequences. A second set of genomes was prepared which, in addition to chimeric early proteins, contained substituted regulatory regions. The transformation efficiencies of these chimeric genomes were intermediate between those of SV40 and JCV, with the source of T protein exerting a greater effect than that of the regulatory region. The ability of certain constructs to induce efficient transformation required the presence of an SV40 regulatory region or specific sequences within the SV40 early coding region. Cloned cell lines prepared from representative transformants were characterized; the ability to form colonies in soft agarose was investigated, and the presence of viral T and cellular p53 proteins was determined. The various T proteins differed in amount, stability, and the ability to form stable complexes with p53.

Nucleotide sequence of the human polyomavirus AS virus, an antigenic variant of BK virus

The complete DNA sequence of the human polyomavirus AS virus (ASV) is presented. Although ASV can be differentiated antigenically from the other human polyomaviruses (BK and JC viruses), it shares 94.9% homology at the nucleotide level with the Dunlop strain of BK virus. Differences found in ASV relative to BK virus include the absence of tandem repeats in its regulatory region, the deletion of 32 nucleotides in the late mRNA leader region (altering the initiation codon for the agnoprotein), the presence of a cluster of base pair substitutions within the coding region of the major capsid protein, VP1, and the absence of 4 amino acids in the carboxy-terminal region of the early protein, T antigen. The 43 nucleotides deleted in the Dunlop strain of BK virus relative to the Gardner prototype strain of BK virus are present in ASV. Possible reasons for the distinct antigenicity of the ASV capsid, given the high degree of nucleotide homology with BK virus, are discussed. To reflect the high degree of sequence homology between ASV and BK virus, we suggest ASV be renamed BKV(AS).

Hybrid genomes of the polyomaviruses JC virus, BK virus, and simian virus 40: identification of sequences important for efficient transformation

Hybrid viral genomes were used to investigate the influence of specific polyomavirus sequences on the transforming behavior of JC virus (JCV). One set of chimeric DNAs was made by exchanging the regulatory regions between JCV and simian virus 40 (SV40) or JCV and BK virus (BKV). A second set of constructs was produced that expressed hybrid JCV-BKV T proteins under the control of either JCV or BKV regulatory signals. Transformation of Rat 2 cells with the parental and chimeric DNAs indicated that both the JCV regulatory signals and the sequence encoding the amino terminus of T protein contributed to the restricted transforming behavior of this virus. Analysis of the viral proteins in the transformed rat cells indicated that the large T antigens of JCV and BKV were less stable than their SV40 counterpart, that small t protein was produced in JCV transformants, and that the subpopulation of T antigen that forms a stable complex with cellular p53 protein was smaller in JCV-transformed cells than in SV40- or BKV-transformed cells.

Extinction of JC virus tumor-antigen expression in glial cell--fibroblast hybrids

JC virus (JCV) is a ubiquitous human papovavirus that shares sequence and structural homology with simian virus 40 (SV40). In contrast to SV40, expression of JCV is restricted to a small number of cell types, including human fetal glial cells, uroepithelial cells, amnion cells, and some endothelial cells. To study the control of JCV early region expression, we made heterokaryons and stable hybrids between JCV-transformed hamster glial cells and mouse fibroblasts. Binucleate heterokaryons exhibited extinction of large tumor antigen expression in the hamster nuclei as assayed by indirect immunofluorescence. This extinction was both time and dose dependent: extinction reached maximal levels at 24-36 hr after fusion and was dependent on the ratio of glial cell to fibroblast nuclei in multinucleated heterokaryons. Extinction also was observed in stable hybrids between the glial cells and mouse Ltk- cells. Southern blot analysis showed that the extinguished hybrids contained viral sequences. Reexpression of large tumor antigen was observed in several subclones, suggesting that extinction was correlated with the loss of murine fibroblast chromosomes from these hybrids. The cis-acting region that mediates extinction resides within the viral regulatory region, which contains two 98-base-pair repeats that have enhancer activity. These data demonstrate that cellular factors that negatively regulate viral gene expression contribute to the restricted cell-type specificity of this virus.

Derivation and characterization of POJ cells, transformed human fetal glial cells that retain their permissivity for JC virus

The study of the medically important polyomavirus JC virus is limited to only a few laboratories, primarily because the permissive cell system most often used, primary human fetal glial cells, is difficult to obtain and propagate. We have introduced mutations at the origin of DNA replication of JC virus and transformed glial cells with the replication-defective genomes. Although normal glial cell cultures rapidly lose their permissivity for the virus after subculture, the transformed cells (designated POJ) had a greatly expanded life span and remained permissive for JC virus even after 30 passages in vitro. POJ cells constitutively express a functional T protein that complements the replication defect of lethal early-region mutations in JC virus. We expect that these cells will greatly facilitate the study of this human virus.

Construction and characterization of hybrid polyomavirus genomes

Several studies have suggested that certain unique features of the JC virus (JCV) regulatory region are responsible for the restricted lytic and transforming activities of this virus in vitro. To pursue this possibility, we have constructed hybrid polyomavirus genomes by exchanging the regulatory sequences of JCV, BK virus (BKV), and simian virus 40 (SV40). The host range of JCV was not expanded by the substitution of the BKV or SV40 regulatory signals; such hybrids were nonviable even in primary human fetal glial cells, the sole permissive cell for JCV. However, chimeric DNAs containing JCV regulatory sequences and BKV- or SV40-coding sequences were lytically active, indicating that the BKV and SV40 T proteins were capable of effectively interacting with the JCV replication and transcription signals to yield infectious hybrid viruses. Although JCV regulatory sequences and coding sequences both contributed to the restricted lytic activity of this virus, it appears that the latter sequences, most likely hose encoding the T protein, have a greater influence on this behavior.

Characterization of cells transformed by the human polyomavirus JC virus

One unique feature of the prototype JC virus (JCV) (Mad 1) genome is the occurrence of a second TATA sequence within the early promoter region. A naturally occurring oncogenic variant of JCV (Mad 4) lacks this second TATA box. Several cell lines transformed by Mad 1, Mad 4 and simian virus 40 were characterized, in part to investigate whether the second TATA sequence is functional. S1 nuclease mapping of early JCV gene transcription products revealed a major set of start sites common to both Mad 1 and Mad 4 mRNAs. In addition, a second set of early transcripts was found exclusively in Mad 1 transformants, presumably positioned by the second TATA box. The presence of these unique mRNAs in the Mad 1-transformed cells did not appear to have any bearing on the other parameters investigated, including size and quantity of early viral proteins, integration patterns of viral DNA and growth properties of the cells.

Isolation of JC virus capsomer-like structures from progressive multifocal leukoencephalopathy brain

Brain tissue from a patient with progressive multifocal leukoencephalopathy (PML) was analyzed by molecular biological and electron-microscopic techniques. Viral DNA was isolated directly from brain tissue, cloned into a plasmid vector, and subjected to restriction endonuclease analysis. The pattern of restriction fragments identified by gel electrophoresis was almost indistinguishable from that of prototype JC virus. By this procedure the etiologic agent of PML in this patient was identified without the isolation of infectious virus. After centrifugal clarification of brain homogenates, high speed centrifugal pellets were studied by electron microscopy. Large numbers of 9-nm polygonal particles, sometimes in paracrystalline arrays, were observed. It was thought likely that these particles were capsomer subunits of 41-43 nm JC virus virions. That the particles were capsomers was supported by negative stain electron microscopy, including reconstruction studies with simian virus 40.

Human polyomavirus JC virus genome

The complete DNA sequence of the human JC virus, which was found to consist of 5,130 nucleotide pairs, is presented. The amino acid sequence of six proteins could be deduced: the early, nonstructural proteins, large T and small t antigens; the late capsid proteins, VP1, VP2, and VP3; and the agnogene product encoded within the late leader sequence, called the agnoprotein in simian virus 40. The extent of homology between JC virus DNA and the genomes of simian virus 40 (69%) and BK virus (75%) confirmed the close evolutionary relationship of these three polyomaviruses. The sequences showing the greatest divergence in these viral DNAs occurred within the tandem repeats located to the late side of the replication origins.

Nucleotide sequence of the region encompassing the JC virus origin of DNA replication

The region of the JC virus (JCV) genome from 0.58 to 0.73 map units was sequenced by the Maxam-Gilbert technique. This segment of DNA specifies several regulatory elements and the amino-terminal portion of the early viral proteins. Comparisons with the analogous regions in the polyomaviruses simian virus 40 (SV40) and BK virus (BKV) confirm the close evolutionary relationship of these three viruses. Similarities include palindromic and symmetrical sequences near their origins of DNA replication, binding sites for their large T proteins, an AT-rich region (the Goldberg-Hogness, or TATA, box), and a large tandem duplication or triplication to the late side of their replication origins (however, these sequences differ). Homology between the sequences coding for the early proteins is also evident (79 and 93 of the first 110 amino acids are shared with SV40 and BKV, respectively). Of greater interest are features of the JCV genome which differ from those of other polyomaviruses. Absent in JCV and BKV are sequences which resemble the third T-antigen binding site of SV40. In addition, a set of sequences present in JCV and BKV DNAs (33 nucleotides in JCV and 22 nucleotides in BKV) and located near a 17-base-pair palindrome shared by all three viruses is missing in SV40 DNA. Another sequence, GGGXGGAG, which is repeated several times in many polyomaviruses and adenoviruses and which is thought to play a role in DNA replication or transcription or both, is not found near the JCV origin of replication. Finally, the tandem repeat of JCV, unlike those of BKV and SV40, includes the Goldberg-Hogness sequence.

Identification of a promoter component involved in positioning the 5' termini of simian virus 40 early mRNAs

The 5' termini of the principal early mRNAs produced in cells transformed by wild-type simian virus 40 lie 21-25 nucleotides downstream from an A-T-T-T-A-T sequence on the DNA template. The 5' termini of early mRNAs produced by five origin-defective mutants containing deletions downstream from the A-T-T-T-A-T sequence and one viable mutant dl892 with a deletion starting 15 nucleotides upstream from this sequence were determined by a method involving synthesis, separation, and determination of the sequences of DNAs complementary to 5' termini. Mutant dl892 produced early mRNAs with the same principal 5' termini as wild-type virus; the origin-defective mutants produced mRNAs with principal 5' termini shifted downstream by a distance equivalent to the length of the deleted DNA segment. These data suggest that a DNA sequence of 29 nucleotides, which includes the A-T-T-T-A-T sequence, contains a component(s) of a promoter for early transcription. This component functions in positioning the 5' ends of the principal early mRNAs 21-25 nucleotides downstream from the A-T-T-T-A-T sequence and acts independently of these downstream sequences.

Expression of early genes of origin-defective mutants of simian virus 40

The nucleotide sequences of eight origin-defective mutants of simian virus 40 have been determined. All of the mutants have suffered deletions, which range in size from 4 to 241 nucleotides. Some of the mutants induce the synthesis of tumor (T) antigen, others do not. Viral mRNA extracted from rat cells transformed by two of the T-antigen-positive mutants has been analyzed by the S1 nuclease technique of Berk and Sharp. Irrespective of the size or the location of the deletions, the 5' ends of viral mRNAs are located approximately the same distance from the A+T-rich region (A-T-T-T-A-T) rather than at a specific site in the viral genome.

Transformation of primary hamster brain cells with JC virus and its DNA

We transformed primary hamster brain cells with four isolates of JC virus and JC virus DNA. Several properties of these transformants were characterized and compared to those of simian virus 40 transformants isolated under identical conditions.

Origin-defective mutants of SV40

We have described a new technique for the isolation and propagation of nonconditionally lethal mutants. We have used this method to generate mutants of SV40 that contain a defective origin of DNA replication. Using these mutants, we have established the following: (1) SV40 DNA replication and early transcription are functionally separate. (2) A functional viral origin of DNA replication is not necessary for the maintenance of transformation. (3) The lack of the origin of SV40 DNA replication does not affect the efficiency of transformation when nonpermissive cells are transfected by DNA using the calcium technique.

Infectivity of the DNA from four isolates of JC virus

The infectivity of JC virus DNA was demonstrated in its most permissive cell culture, primary human fetal glial cells. The amount of infectivity observed in these heterogeneous cultures varied considerably between batches of cells. Contrary to results obtained with the papovaviruses simian virus 40 and BK virus, the calcium technique (F. L. Graham and A. J. van der Eb, Virology 52:456--467, 1973) was found to be more efficient at promoting JC virus DNA infectivity than the DEAE-dextran method (J. H. McCutchan and J. S. Pagano, J. Natl. Cancer Inst. 41:351--357, 1968): maximum infectivity titers of 4 x 10-(4) and 6 x 10(3) fluorescent cell units per microgram of DNA, respectively. These values represent an approximate recovery of infectivity from virus of between 0.02 and 0.14%. Comparisons of infectivity of DNAs obtained from four isolates of JC virus and which differed in their degrees of heterogeneity did not reveal significant differences. The JC virus DNA was not infectious in primary human fetal lung and kidney cells.

Restriction endonuclease cleavage map of the DNA of JC virus

A physical map of the sites cleaved by the following restriction endonucleases was derived for the DNA of JC virus, a human polyomavirus: EcoRI, HpaI, and PstI (one site each); HindII (four sites); and HindIII (three sites). By agarose gel electrophoresis of fragmented DNA, the size of full-length DNA of JC virus was estimated to be 5,125 +/- 105 base pairs (98 +/- 2% of the length of simian virus 40 DNA).