The oncogenic roles of JC polyomavirus in cancer

Nanoparticle-mediated sodium butyrate delivery for repairing hypoxic-ischemic brain injury in premature infants

Hypoxic-ischemic encephalopathy of prematurity (HIEP) is a leading cause of acute mortality and chronic neurological injury in premature infants. This study investigates the molecular mechanisms by which magnetic fluorescent nanoparticles loaded with sodium butyrate (MNs@SB) repair HIEP by modulating the Sp1 and TGF-β1 signaling pathways. Untargeted metabolomics analysis revealed significant suppression of the butyrate metabolism pathway in the intestinal tissues of HIEP mice. We synthesized and characterized MNs@SB nanoparticles, with zeta potential and DLS results indicating an average nanoparticle size of approximately 79.89 nm and a zeta potential of -36.87 mV. TEM images confirmed that the nanoparticles formed polymer-coated clusters. MNs@SB demonstrated excellent biocompatibility and stable magnetic targeting behavior. The nanoparticles were delivered to the brain via tail vein injection and magnetic targeting, with focused ultrasound facilitating their diffusion. The results showed that HIEP mice exhibited a significant increase in infarct size and extensive tissue loss, whereas MNs@SB treatment effectively reversed HIEP-induced brain damage, improving both short-term and long-term neurological deficits. Single-cell RNA sequencing and high-throughput transcriptome analysis revealed that MNs@SB promoted brain repair by upregulating neuronal Sp1, activating the TGF-β1 signaling pathway, and inhibiting neuronal apoptosis. In vivo experiments further confirmed that MNs@SB treatment restored SP1 mRNA and protein expression in the brain. Additionally, MNs@SB treatment significantly restored TGF-β1, p-SMAD2, and p-SMAD3 protein expression, indicating activation of the TGF-β1/SMAD2/3 signaling pathway. This study presents a novel nanomedicine therapeutic strategy with potential clinical applications.

Polyomaviruses After Allogeneic Hematopoietic Stem Cell Transplantation

Polyomaviruses (PyVs) are non-enveloped double-stranded DNA viruses that can cause significant morbidity in allogeneic hematopoietic stem cell transplant (allo-HSCT) recipients, particularly BK polyomavirus (BKPyV) and JC polyomavirus (JCPyV). BKPyV is primarily associated with hemorrhagic cystitis (HC), while JCPyV causes progressive multifocal leukoencephalopathy (PML). The pathogenesis of these diseases involves viral reactivation under immunosuppressive conditions, leading to replication in tissues such as the kidney, bladder, and central nervous system. BKPyV-HC presents as hematuria and urinary symptoms, graded by severity. PML, though rare after allo-HSCT, manifests as neurological deficits due to JCPyV replication in glial cells. Diagnosis relies on nucleic acid amplification testing for DNAuria or DNAemia as well as clinical criteria. Management primarily involves supportive care, as no antiviral treatments have proven consistently effective for either virus and need further research. This review highlights the virology, clinical presentations, and management challenges of PyV-associated diseases post-allo-HSCT, emphasizing the need for improved diagnostic tools and therapeutic approaches to mitigate morbidity and mortality in this vulnerable population.

Clinical and molecular analysis of JCPyV and BKPyV infection and associated risk of urothelial carcinoma development in the upper tract

BACKGROUND

Human polyomaviruses (HPyVs), JC polyomavirus (JCPyV) and BK polyomavirus (BKPyV), have been found in upper tract urothelial carcinoma UTUC; however, the association of the viral oncogenic factors and clinical characteristics of UTUC remains unclear. This study aimed to investigate the prevalence of JCPyV and BKPyV in UTUC and their correlation with cancer progression among the southwest Taiwanese population from 2020 to 2022.

METHODS

A total of 72 paraffin-embedded UTUC tissue samples and 41 adjacent tissue samples were collected from 72 patients. Nested polymerase chain reaction and DNA sequencing were used to detect viral DNA and genotypes. Immunohistochemistry was performed using anti- large T (LT) and anti-p53 monoclonal antibodies to detect the expression of viral early LT protein and cellular p53 protein, respectively.

RESULTS

The overall prevalence of JCPyV and BKPyV were higher in UTUC than in adjacent tissue samples (65.3% [47/72] vs. 17.1% [7/41]). JCPyV and BKPyV were detected in 95.7% (45/47) and 4.3% (2/47) of the HPyVs-positive UTUC samples, respectively. JCPyV-TW-3 was the predominant strain of JCPyV infection. In UTUC samples, the LT protein of JCPyV and BKPyV positivity rate was 65.3%, while that of mutant p53 protein was 52.7%. JCPyV infection and LT protein expression increased the odds ratio (OR) of UTUC by 9.13-fold. The OR of UTUC was higher by 10.34-fold in patients with mutant p53 and by 10.37-fold in those with simultaneous LT and mutant p53 expression. The presence of LT protein in UTUC patients may increase the OR of mutant p53 protein expression by 2.93-fold compared to its absence. Women had a 5.19-fold higher superiority of JCPyV infection and LT expression than men. Patients with chronic kidney disease (CKD) had a 3.15-fold higher OR for mutant p53 protein expression than those without it. In the UTUC advanced stages, the OR of virus and LT expression was 3.18-fold higher compared to those who do not require chemotherapy.

CONCLUSIONS

JCPyV infection is highly prevalent in UTUC, and the presence of CKD concurrent with high expressions of LT and mutant p53 proteins in patients may be a useful indicator for chemotherapy and poor prognosis.

Exploring the genetic associations and causal relationships between antibody responses, immune cells, and various types of breast cancer

BACKGROUND

There may be potential associations between various pathogens, antibody immune responses, and breast cancer (BC), but the specific mechanisms and causal relationships remain unclear.

METHODS

First, multiple Mendelian randomization (MR) methods were used for univariable MR analysis to explore potential causal relationships between 34 antibody immune responses (related to 12 pathogens), 46 antibody immune responses (related to 13 pathogens), antibody responses post-COVID-19 vaccination, 731 immune cell types, and various BC subtypes (including overall BC, ER-positive, ER-negative, Luminal A, Luminal B, Luminal B HER2-negative, HER2-positive, and triple-negative BC). The primary results were then subjected to reverse MR analysis, heterogeneity testing using Cochran's Q, and horizontal pleiotropy testing. Robust findings were further used to design mediation pathways involving antibody immune responses, immune cells, and BC. After adjusting the effect estimates using multivariable MR (MVMR), a two-step mediation analysis was conducted to explore mediation pathways and mediation proportions. Finally, linkage disequilibrium score regression (LDSC) was applied to analyze the genetic correlation between phenotypes along mediation pathways, and cross-phenotype association analysis (CPASSOC) was performed to identify pleiotropic SNPs among three phenotypes along these pathways. Bayesian colocalization tests were conducted on pleiotropic SNPs using the multiple-trait-coloc (moloc).

RESULTS

We identified potential causal relationships between 15 antibody immune responses to 8 pathogens (Hepatitis B virus, Herpes Simplex Virus 2, Human Herpesvirus 6, Polyomavirus 2, BK polyomavirus, Cytomegalovirus, Helicobacter pylori, Chlamydia trachomatis), 250 immune cell phenotypes, and various BC subtypes. MVMR-adjusted mediation analysis revealed four potential mediation pathways. LDSC results showed no significant genetic correlation between phenotypes pairwise. CPASSOC analysis identified two potential mediation pathways with common pleiotropic SNPs (rs12121677, rs281378, rs2894250). However, none of these SNPs passed the Bayesian colocalization test by moloc. These results excluded horizontal pleiotropy, stabilizing MR analysis results.

CONCLUSION

This study utilized MR methods to analyze potential causal relationships between various antibody immune responses, immune cell types, and BC subtypes, identifying four potential regulatory mediation pathways. The findings of this study offer potential targets and research directions for virus-related and immunotherapy-related studies, providing a certain level of theoretical support. However, limitations such as GWAS sample size constraints and unclear specific pathophysiological mechanisms need further improvement and validation in future studies.

Epstein-Barr Virus BARF1 Is Expressed in Lung Cancer and Is Associated with Cancer Progression

BACKGROUND

Epstein-Barr virus (EBV) is involved in the development of lymphomas, nasopharyngeal carcinomas (NPC), and a subgroup of gastric carcinomas (GC), and has also been detected in lung carcinomas, even though the role of the virus in this malignancy has not yet been established. BamH1-A Rightward Frame 1 (BARF1), a suggested exclusive epithelial EBV oncoprotein, is detected in both EBV-associated GCs (EBVaGC) and NPC. The expression and role of BARF1 in lung cancer is unknown.

METHODS

A total of 158 lung carcinomas including 80 adenocarcinomas (AdCs) and 78 squamous cell carcinomas (SQCs) from Chilean patients were analyzed for EBV presence via polymerase chain reaction (PCR), Immunohistochemistry (IHC), or chromogenic in situ hybridization (CISH). The expression of BARF1 was evaluated using Reverse Transcription Real-Time PCR (RT-qPCR). Additionally, A549 and BEAS-2B lung epithelial cells were transfected with a construct for ectopic BARF1 expression. Cell proliferation, migration, invasion, and epithelial-mesenchymal transition (EMT) were evaluated.

RESULTS

We found that EBV was present in 37 out of 158 (23%) lung carcinomas using PCR. Considering EBV-positive specimens using PCR, IHC for Epstein-Barr nuclear antigen 1 (EBNA1) detected EBV in 24 out of 30 (80%) cases, while EBERs were detected using CISH in 13 out of 16 (81%) cases. Overall, 13 out of 158 (8%) lung carcinomas were shown to be EBV-positive using PCR/IHC/CISH. BARF1 transcripts were detected in 6 out of 13 (46%) EBV-positive lung carcinomas using RT qPCR. Finally, lung cells ectopically expressing BARF1 showed increased migration, invasion, and EMT.

CONCLUSIONS

EBV is frequently found in lung carcinomas from Chile with the expression of BARF1 in a significant subset of cases, suggesting that this viral protein may be involved in EBV-associated lung cancer progression.

A new evaluation of the rearranged non-coding control region of JC virus in patients with colorectal cancer

BACKGROUND

Several studies have reported the presence of JC virus (JCV) in human tumors, The association of JCV and CRC remains controversial. This study aimed to evaluate the rearranged NCCR region of the detected JCV DNA in CRC patients' tissue samples.

METHODS

In this case-control study, tumor tissues (n = 60), adjacent normal tissues (n = 60), and urine samples (n = 60) of the CRC patients were collected. The nested PCR was employed to detect the VP1 and NCCR regions of the JCV genome. The positive JCV PCR products were sequenced and a phylogenetic tree was constructed to determine the JCV genotypes. After extracting RNA and preparing cDNA, the expression of JCV LTAg was examined in 60 tumor tissues and 60 adjacent normal tissues. The analysis of JCV LTAg expression was performed using GraphPad Prism software version 8.

RESULTS

The analysis reveals that JCV DNA was detected in 35/60 (58.3%) tumor tissues, while 36/60 (60.0%) of adjacent normal tissues (p = 0.85). JCV DNA was detected in 42/60 (70.0%) urine samples when compared to 35/60 (58.3%) tumor tissues of CRC patients and was not found significant (P = 0.25). The phylogenetic tree analysis showed the dominant JCV genotype 3, followed by genotype 2D was distributed in tumor tissue, normal tissue, and urine samples of the CRC patients. Analysis of randomly selected NCCR sequences from JCV regions in tumor tissue samples revealed the presence of rearranged NCCR blocks of different lengths.: 431 bp, 292 bp, 449 bp, and 356 bp. These rearranged NCCR blocks differ from the rearranged NCCR blocks described in PML-type Mad-1, Mad-4, Mad-7, and Mad-8 prototypes. The expression of JCV LTAg was significantly different in tumor tissue compared to normal tissue, with a p-value of less than 0.002.

CONCLUSION

A significant proportion of 35%> of the tumor tissue and urine samples of the CRC patients was found to be positive for JCV DNA (P = 0.25). The parallel analysis of tumor and urine samples for JCV DNA further supports the potential for non-invasive screening tools. This study provides new insights into Rearranged NCCR variant isolates from patients with CRC. The significant difference in JCV LTAg expression between tumor and normal tissue indicates a latent JCV status potentially leading to cancer development.

John Cunningham Virus and Progressive Multifocal Leukoencephalopathy: A Falsely Played Diagnosis

Progressive Multifocal Leukoencephalopathy (PML) is a possibly fatal demyelinating disease and John Cunningham Polyomavirus (JCPyV) is believed to cause this condition. The so-called JCPyV was initially reported in lymphoma and Human Immunodeficiency Virus (HIV) cases, whereas nowadays, its incidence is increasing in Multiple Sclerosis (MS) cases treated with natalizumab (Tysabri). However, there are conflicting literature data on its pathology and diagnosis, whereas some misdiagnosed reports exist, giving rise to further questions towards the topic. In reality, the so-called PML and the supposed JCPyV are not what they seem to be. In addition, novel and more frequent PML-like conditions may be reported, especially after the Coronavirus Disease 2019 (COVID-19) pandemic.

Human polyomaviruses JCPyV and MCPyV in urothelial cell carcinoma: a single institution experience

Objective

Urothelial cell carcinoma (UCC) is the most common type of urinary bladder. JCPyV and BKPyV have been detected in the urine and tissue of urothelial cell carcinomas (UCC) in immunocompetent patients. Here, we investigated the presence of several HPyVs in UCC samples using diverse molecular techniques to study the prevalence of HPyVs in UCC.

Methods

A large single-institution database of urine cytology specimens (UCS; n = 22.867 UCS) has previously been searched for decoy cells (n = 30), suggesting polyomavirus infection. The available urine sediments and formalin-fixed paraffin-embedded (FFPE) tissue samples of UCC patients were tested for the presence of JCPyV-LTAg expression by immunohistochemistry (IHC) labeled with SV40-LTAg antibody (clone: PAb416) and subsequent PCR followed by sequencing. In addition, the presence of the oncogenic Merkel cell polyomavirus (MCPyV) and the presence of human polyomavirus 6 (HPyV6) and 7 (HPyV7) DNA were tested with DNA PCR or IHC.

Results

Of the 30 patients harboring decoy cells, 14 were diagnosed with UCC of the urinary bladder (14/30; 46.6%) before presenting with decoy cells in the urine. The SV40-LTAg IHC was positive in all 14 UCC urine sediments and negative in the FFPE tissues. JCPyV-DNA was identified in all five available UCS and in three FFPE samples of UCC (three of 14; 21.4%). Two UCC cases were positive for MCPyV-DNA (two of 14; 14.3%), and one of them showed protein expression by IHC (one of 14; 7.1%). All specimens were HPyV6 and HPyV7 negative.

Conclusion

Our findings show the presence of JCPyV in the urine and UCC of immunocompetent patients. Moreover, MCPyV was detected in two UCC cases. In total, five UCC cases showed the presence of either JCPyV or MCPyV. The evidence here supports the hypothesis that these viruses might sporadically be associated with UCC. Further studies are needed to confirm the relevance of JCPyV or MCPyV as a possible risk factor for UCC development.

Polyomavirus Wakes Up and Chooses Neurovirulence

JC polyomavirus (JCPyV) is a human-specific polyomavirus that establishes a silent lifelong infection in multiple peripheral organs, predominantly those of the urinary tract, of immunocompetent individuals. In immunocompromised settings, however, JCPyV can infiltrate the central nervous system (CNS), where it causes several encephalopathies of high morbidity and mortality. JCPyV-induced progressive multifocal leukoencephalopathy (PML), a devastating demyelinating brain disease, was an AIDS-defining illness before antiretroviral therapy that has "reemerged" as a complication of immunomodulating and chemotherapeutic agents. No effective anti-polyomavirus therapeutics are currently available. How depressed immune status sets the stage for JCPyV resurgence in the urinary tract, how the virus evades pre-existing antiviral antibodies to become viremic, and where/how it enters the CNS are incompletely understood. Addressing these questions requires a tractable animal model of JCPyV CNS infection. Although no animal model can replicate all aspects of any human disease, mouse polyomavirus (MuPyV) in mice and JCPyV in humans share key features of peripheral and CNS infection and antiviral immunity. In this review, we discuss the evidence suggesting how JCPyV migrates from the periphery to the CNS, innate and adaptive immune responses to polyomavirus infection, and how the MuPyV-mouse model provides insights into the pathogenesis of JCPyV CNS disease.

The potential oncogenic effect of tissue-specific expression of JC polyoma T antigen in digestive epithelial cells

JC polyoma virus (JCPyV), a ubiquitous polyoma virus that commonly infects people, is identified as the etiologic factor for progressive multifocal leukoencephalopathy and has been closely linked to various human cancers. Transgenic mice of CAG-loxp-Laz-loxp T antigen were established. T-antigen expression was specifically activated in gastroenterological target cells with a LacZ deletion using a cre-loxp system. Gastric poorly-differentiated carcinoma was observed in T antigen-activated mice using K19-cre (stem-like cells) and PGC-cre (chief cells), but not Atp4b-cre (parietal cells) or Capn8-cre (pit cells) mice. Spontaneous hepatocellular and colorectal cancers developed in Alb-cre (hepatocytes)/T antigen and villin-cre (intestinal cells)/T antigen transgenic mice respectively. Gastric, colorectal, and breast cancers were observed in PGC-cre/T antigen mice. Pancreatic insulinoma and ductal adenocarcinoma, gastric adenoma, and duodenal cancer were detected in Pdx1-cre/T antigen mice. Alternative splicing of T antigen mRNA occurred in all target organs of these transgenic mice. Our findings suggest that JCPyV T antigen might contribute to gastroenterological carcinogenesis with respect to cell specificity. Such spontaneous tumor models provide good tools for investigating the oncogenic roles of T antigen in cancers of the digestive system.

Detection of human neurotropic JCPyV DNA sequence in pediatric anaplastic xanthoastrocytoma

Due to its peculiar histopathological findings, pleomorphic xanthoastrocytoma (PXA), a rare cerebral tumor of young adults with a slow growth and a good prognosis, resembles to the lytic phase of progressive multifocal leukoencephalopathy, a fatal neurodegenerative disease caused by JC polyomavirus (JCPyV). Therefore, the presence of JCPyV DNA was examined in an 11-year-old child with xanthoastrocytoma, WHO grade 3, by quantitative PCR (qPCR) and nested PCR (nPCR) using primers amplifying sequences encoding the N- and C-terminal region of large T antigen (LTAg), the non-coding control region (NCCR), and viral protein 1 (VP1) DNA. The expression of transcripts from LTAg and VP1 genes was also evaluated. In addition, viral microRNAs' (miRNAs) expression was investigated. Cellular p53 was also searched at both DNA and RNA level. qPCR revealed the presence of JCPyV DNA with a mean value of 6.0 × 10⁴ gEq/mL. nPCR gave a positive result for the 5' region of the LTAg gene and the NCCR, whereas 3' end LTAg and VP1 DNA sequences were not amplifiable. Only LTAg transcripts of 5' end were found whereas VP1 gene transcript was undetectable. Although in most cases, either Mad-1 or Mad-4 NCCRs have been identified in association with JCPyV-positive human brain neoplasms, the archetype NCCR structure was observed in the patient's sample. Neither viral miRNA miR-J1-5p nor p53 DNA and RNA were detected. Although the expression of LTAg supports the possible role of JCPyV in PXA, further studies are warranted to better understand whether the genesis of xanthoastrocytoma could depend on the transformation capacity of LTAg by Rb sequestration.

JC polyomavirus: a short review of its biology, its association with progressive multifocal leukoencephalopathy, and the diagnostic value of different methods to manifest its activity or presence

INTRODUCTION

JC polyomavirus is the causative agent of progressive multifocal leukoencephalopathy (PML), a demyelinating disease resulting from the lytic infection of oligodendrocytes that may develop in immunosuppressed individuals: HIV1 infected or individuals under immunosuppressive therapies. Understanding the biology of JCPyV is necessary for a proper patient management, the development of diagnostic tests, and risk stratification.

AREAS COVERED

The review covers different areas of expertise including the genomic characterization of JCPyV strains detected in different body compartments (urine, plasma, and cerebrospinal fluid) of PML patients, viral mutations, molecular diagnostics, viral miRNAs, and disease.

EXPERT OPINION

The implementation of molecular biology techniques improved our understanding of JCPyV biology. Deep sequencing analysis of viral genomes revealed the presence of viral quasispecies in the cerebrospinal fluid of PML patients characterized by noncoding control region rearrangements and VP1 mutations. These neurotropic JCPyV variants present enhanced replication and an altered cell tropism that contribute to PML development. Monitoring these variants may be relevant for the identification of patients at risk of PML. Multiplex realtime PCR targeting both the LTAg and the archetype NCCR could be used to identify them. Failure to amplify NCCR should indicate the presence of a JCPyV prototype speeding up the diagnostic process.