John Cunningham virus T-antigen expression in anal carcinoma

Neoantigen identification: Technological advances and challenges

Neoantigens have emerged as promising targets for cutting-edge immunotherapies, such as cancer vaccines and adoptive cell therapy. These neoantigens are unique to tumors and arise exclusively from somatic mutations or non-genomic aberrations in tumor proteins. They encompass a wide range of alterations, including genomic mutations, post-transcriptomic variants, and viral oncoproteins. With the advancements in technology, the identification of immunogenic neoantigens has seen rapid progress, raising new opportunities for enhancing their clinical significance. Prediction of neoantigens necessitates the acquisition of high-quality samples and sequencing data, followed by mutation calling. Subsequently, the pipeline involves integrating various tools that can predict the expression, processing, binding, and recognition potential of neoantigens. However, the continuous improvement of computational tools is constrained by the availability of datasets which contain validated immunogenic neoantigens. This review article aims to provide a comprehensive summary of the current knowledge as well as limitations in neoantigen prediction and validation. Additionally, it delves into the origin and biological role of neoantigens, offering a deeper understanding of their significance in the field of cancer immunotherapy. This article thus seeks to contribute to the ongoing efforts to harness neoantigens as powerful weapons in the fight against cancer.

The Oncogenic Roles of JC Virus T Antigen in Breast Carcinogenesis

Purpose: JC virus (JCV) infects 80–90% of the population and results in progressive multifocal leukoencephalopathy upon immunodeficiency. The study aimed to pathologically clarify the oncogenic roles of T antigen in human breast cancers.

Methods: Breast cancer, dysplasia, and normal tissues were examined for T antigen of JCV by nested and real-time PCR. The positive rate or copy number of T antigen was compared with clinicopathological parameters of breast cancer. JCV existence was morphologically detected by immunohistochemistry and in situ PCR. T antigen was examined by Western blot using frozen samples of breast cancer and paired normal tissues.

Results: According to nested PCR, the positive rate of breast ductal or lobular carcinoma was lower than that of normal tissue (p < 0.05). T antigen existence was negatively correlated with E-cadherin expression and triple-negative breast cancer (p < 0.05), but positively correlated with lymph node metastasis and estrogen receptor and progestogen receptor expression (p < 0.05). Quantitative PCR showed that JCV copies were gradually decreased from normal, dysplasia to cancer tissues (p < 0.05). JCV T antigen copy number was lower in ductal adenocarcinoma than in normal tissue (p < 0.05), in line with in situ PCR and immunohistochemistry. JCV copies were negatively correlated with tumor size and E-cadherin expression (p < 0.05), but positively correlated with G grading of breast cancer (p < 0.05). Western blot also indicated weaker T antigen expression in breast cancer than normal tissues (p < 0.05).

Conclusion: JCV T antigen might play an important role in breast carcinogenesis. It can be employed as a molecular marker for the differentiation and aggressive behaviors of breast cancer.

Prevalence of JC and BK viruses in Patients with Colorectal Cancer: A Systematic Review and Meta- Analysis

INTRODUCTION

Polyomaviruses including BK virus (BKV) and JC virus (JCV) are widespread in human and have been associated with colorectal cancer (CRC) in some studies. The aim of present systematic review and meta-analysis article is to calculate the pooled prevalence of BKV and JCV in patients with CRC and assessing their association with this malignancy.

MATERIALS AND METHODS

Domestic databases and Sciences Direct, PubMed, ProQuest, Web of Sciences and Scopus were searched for relevant articles up to 2nd  June 2019Two independent reviewers extracted the related data from eligible articles. The pooled prevalence and pooled odds ratio (POR) and their 95% confidence interval (95% CI) were calculated using "metaprop" and "metan" commands in Stata 14. Where I2 statistics were >50%, the random effect model was used.

RESULTS

From 1461 relevant studies, 24 articles were eligible and included in the qualitative while 19 articles included in quantitative analysis. The pooled prevalence based on diagnostic methods varies from 29% using immunohistochemistry to 52% using nested-PCR method. The likelihood of being infected with JCV  was significantly higher in CRC patients compared to healthy (POR: 4.41, 95% CI: 2.13 - 9.13) controls, normal adjacent mucosa (POR: 2.79, 95% CI: 1.3-5.9) and colorectal adenoma (POR: 3.1, 95% CI: 1.5-6.5) but was not significant when non-CRC patients used as control group.

CONCLUSION

The prevalence of JCV in colorectal patients was substantially variable by different methods and targets. The significant association between JCV and CRC that was observed in the present study is not indicative of causation and should be studied more in large-scale prospective designs.

Study on JV Virus in Patients with Colon Cancer Type Adenocarcinoma

Introduction:

Colorectal cancer is the most repetitious malignancies with high mortality worldwide. JC virus (JCV) is ubiquitous Polyomavirus, with seroprevalence rates ranging from 70% to 90% in adult population. Recently the role of JCV have been reported in many malignant tumors worldwide. The association of JCV was reported in patients with colon and rectum cancers. Thus this study was conducted to evaluate the association of JCV DNA in patients with colon cancer type Adenocarcinoma.

Material and Methods:

A total of 120 formalin-fixed paraffin-embedded tissue blocks samples were collected including 20/40(50%) males, 20/40(50%) females patients with Colorectal Cancer(CRC), and 80 (50% males, 50% females) patients with benign tumor as a control. DNA was extracted for all the samples. Nested PCR was carried out for detection of Vp1/T-Ag junction genome in JCV genome by Nested-PCR assay. Randomly, PCR products of 6 samples were sequenced to analysis the partial JCV DNA. The phylogeny tree was constructed to determine homology identity with other JCV.

Results:

4/40(10%) samples of test group and 10/80 (12.5%) of control samples were positive for JCV DNA (P= 0.69). Out of 4 samples positive for JC DNA, 3(7.5%) were males and 1(2.4%) female (P=0.29). The frequency of JCV DNA in age group> 50 years was 4/32(10%), while in age group <50 years was 0/8 (0%) (p= 0.29).

Conclusion:

prevalence of JCV DNA was among 10% patients with CRC and 12.5% benign tumors (p=0.69). The distribution of JCV DNA was among 7.5% male and 2.5% female (p= 0.29). The frequency of JCV DNA was among 10% cases of age group >50 years and 0% of age group <50 years (P= 0.29). The subsequent T-Ag protein expression might explain the increased risk of colorectal cancer and requires further investigation.

Molecular survey on Merkel cell polyomavirus in patients with colorectal cancer

Background: Merkel cell polyomavirus (MCV) has been associated with Merkel cell carcinoma (MCC) in humans, and its role in other human cancers is under investigation. The aim of this study was to investigate MCV genome infection in patients with colorectal cancer (CRC).Methods: This retrospective, case-control study used archived formalin-fixed, paraffin-embedded (FFPE) tissue samples from colorectal cancer patients (cases) and matched healthy subjects (controls) diagnosed by an expert pathologist from hospitals affiliated with Iran University of Medical Sciences, Tehran, Iran from 2011 to 2016. After DNA extraction with a QIAamp® DNA FFPE Tissue Kit, real-time polymerase chain reaction (PCR) was used for diagnosis. A positive control was produced by cloning with the Generay Biotechnology system. SPSS v.22 was used for analysis of demographic variables.Results: There were 157 participants included in the study: 66 were cases and 91 were controls. Their mean ages (±SD) were 59.35±14.48 and 57.21±14.66, respectively. The proportion of males was 57.6% in the case group and 57.1% in the control group. None of the samples were positive for MCV expression by real-time PCR assay. Association was detected between males with CRC and tumor location in the rectum and between males with CRC and the mucinous tumor type.Conclusion: None of the tissues from the CRC or non-cancerous control groups were positive for MCV genome infection, although a low viral load, the sample type, or the method of use should not be neglected. Further studies are recommended to obtain more comprehensive results.

John Cunningham (JC) virus genotypes in kidney transplant recipients, rheumatoid arthritis patients and healthy individuals in Isfahan, Iran

In healthy individuals John Cunningham virus is latent without any clinical signs, but in the cases of the use of immunosuppressive drugs in graft recipients, autoimmune diseases and also increasing of age, that the immune system is suppressed it may cause disease in reactivation. Progressive multifocal leukoencephalopathy (PML) is the well-known disease caused by the virus. It has also been associated with nephropathy and tumorogensis. At present, based on vp1 capsid gene 7 genotypes have been detected. Genetic variations of JC virus in different geographical areas and the presence of different subtypes is a useful tool for reconstructing of the genetic information of JC virus and understanding of its evolution. The aim of this study was to investigate different genotypes of the JC virus in the urine of 100 kidney transplant recipients, 43 rheumatoid arthritis patients, and 100 healthy individuals as control group in Isfahan. DNA was extracted by phenol-chloroform method and subjected to a nested PCR using specific primer for vp1 capsid gene designed by Oligo 7 software. Fisher's exact test was used for statistical analyses. Using MEGA 6 software the sequences were aligned using Clustal W tool and phylogenetic trees were constructed by neighbor joining method. Thirty-one positive samples were sequenced. Genotypes 1, 3, and 4 of the virus were detected for the first time in Iran. For the first time genotype 3 was reported as the dominant genotype in Iran. For the first time in the world, genotype 4 was detected in rheumatoid arthritis patients. J. Med. Virol. 89:337-344, 2017. © 2016 Wiley Periodicals, Inc.

The oncogenic role of JC virus T antigen in lens tumors without cell specificity of alternative splicing of its intron

JC virus (JCV), a ubiquitous polyoma virus that commonly infects the human, is identified as the etiologic agent for progressive multifocal leukoencephalopathy and some malignancies. To clarify the oncogenic role of JCV T antigen, we established two transgenic mice of T antigen using either α-crystallin A (αAT) or cytokeratin 19(KT) promoter. Lens tumors were found in high-copy αAT mice with the immunopositivity of T antigen, p53, β-catenin and N-cadherin. Enlarged eyeballs were observed and tumor invaded into the brain by magnetic resonance imaging and hematoxylin-and-eosin staining. The overall survival time of homozygous mice was shorter than that of hemizygous mice (p<0.01), the latter than wild-type mice (p<0.01). The spontaneous salivary tumor and hepatocellular carcinoma were seen in αAT5 transgenic mice with no positivity of T antigen. KT7 mice suffered from lung tumor although JCV T antigen was strongly expressed in gastric epithelial cells. The alternative splicing of T antigen intron was detectable in the lens tumor of αAT mice, gastric mucosa of KT mice, and various cells transfected with pEGFP-N1-T antigen. It was suggested that JCV T antigen might induce carcinogenesis at a manner of cell specificity, which is not linked to alternative splicing of its intron. Both spontaneous lens and lung tumor models provide good tools to investigate the oncogenic role of JCV T antigen.

Polyomavirus infections and its clinical relevance in cancer patients: A Prospective Study

BK and JC polyomaviruses (PyV) have been demonstrated to be associated with the pathogenesis of various human cancers. We aimed to investigate the impact of BK and JC polyomavirus infections on several clinical parameters in different human cancers. A total of 150 cancer patients were included in the study (51 patients with solid tumors, 48 patients with lymphomas and 51 patients with leukemias). Amplification of PyV DNA was performed using a semi-nested version of Polymerase chain reaction targeting the T genomic region of PyV. The polyomavirus load was determined using real-time PCR assay. The clinical data were collected. Polyomavirus DNA could be detected in 84 (56%) of 150 of all cancerous patients. The solid tumors had the lowest proportion of JCV (6 (11.8%) of 51), whereas had the highest proportion of JCV (200copies/μl). JCV was more frequent among NHL patients (30%) and absent in HL patients (0%). During follow-up, PyV positivity decreased significantly (p=0.004) in lymphoma patients (n=28). Although PyV positivity decreased significantly from 39% to 7% in 28 of 48 lymphoma patients after treatment, it significantly persisted in leukemic patients after treatment (from 22% to 38%). JC was more frequent among leukemic patients with leukopenia. The presence of JC polyomavirus was more frequent among leukemic patients without any significant impact on their overall survival.

IGF axis and other factors in HPV-related and HPV-unrelated carcinogenesis (review)

The insulin-like growth factor (IGF) axis promotes the growth of cells, tissues and organs. IGF-1 is mainly produced in the liver but is also secreted from local tissues. In the circulation, IGF-1 is bound to insulin-like binding proteins (IGFBPs), and when released it activates the insulin-like growth factor receptor (IGF-1R). The signal is further transmitted by intracellular signaling pathways leading to gene expression that regulates, among others, cell proliferation and survival. This review presents the IGF axis in the context of cell transformation and cancer development. Aspects involving IGF-1 deficiency and protection from cancer are also briefly described. Furthermore, human papillomaviruses (HPVs) interplaying with IGF axis components in cervical cancer development are described. These small dsDNA viruses are divided into low-risk and high-risk HPVs with regard to the potency of their oncogenic actions; they mainly infect epithelial or mucosal cells. Special attention is drawn to expression of two major HPV oncogenes (E6 and E7) initiating and maintaining cervical carcinogenesis, which is a multistep and multifactorial process; therefore, involvement of additional factors such as mitochondrial DNA changes, sex hormones, retinoic and folic acids are also discussed. Finally, IGF axis components and HPV oncogenes as targets in anticancer treatment are presented which include IGF-1R downregulation, RNA interference and anti-HPV therapeutic vaccines. The review concludes that despite an enormous advancement in research on IGF and HPV-related cancers, more molecular studies and clinical trials are needed before commercialized therapies are widely available for oncology patients.

Prospective study of seroreactivity to JC virus T-antigen and risk of colorectal cancers and adenomas

John Cunningham virus (JCV) is a common polyomavirus classified as a possible carcinogen by the International Agency for Research on Cancer. JCV may play a role in colorectal carcinogenesis, although we previously reported no association between JCV capsid antibodies and colorectal cancer. No studies have examined the role of seroreactivity to JCV T-antigen (T-Ag) oncoprotein in colorectal cancer. A case-control study nested within a community-based prospective cohort (CLUE II) was conducted. In 1989, 25,080 residents of Washington County, Maryland, were enrolled in CLUE II, completing baseline questionnaires and providing blood samples. At follow-up, 257 incident colorectal cancer cases were identified by linkage to population-based cancer registries through 2006 and matched to controls on age, sex, race, and date of blood draw. One hundred and twenty-three colorectal adenoma cases were identified through self-report during follow-up and matched to controls on age, sex, race, date of blood draw, and colorectal cancer screening. Baseline serum samples were tested for seroreactivity to JCV T-Ag. Associations between JCV T-Ag seroreactivity and colorectal cancer/adenomas were evaluated using conditional logistic regression models. Overall, seroreactivity to JCV T-Ag was not statistically significantly associated with the risk of either colorectal cancer [OR, 1.34; 95% confidence interval (CI), 0.89-2.01] or adenoma (OR, 1.30; 95% CI, 0.70-2.42), while a borderline association with colorectal cancer was observed among women (OR, 1.82; 95% CI, 1.00-3.31). Our past evaluation of JCV capsid seropositivity, combined with current findings, does not support a notable etiologic role for JCV infection in colorectal cancer.

Immune response to JC virus T antigen in patients with and without colorectal neoplasia

JC virus (JCV) is a polyomavirus that infects approximately 75% of the population and encodes a T antigen (T-Ag) gene, which is oncogenic and inactivates the p53 and pRb/p107/p130 protein families. Previous work in our lab has identified the presence of T-Ag in colorectal neoplasms. While JCV remains in a latent state for the majority of those infected, we hypothesized that a disturbance in immunological control may permit JCV to reactivate, which may be involved in the development of colorectal neoplasia. Our aim was to determine the cell mediated immune response to JCV T-Ag, and determine if it is altered in patients with colorectal adenomatous polyps (AP) or cancers (CRC). Peripheral blood mononuclear cells (PBMCs) isolated from the blood of patients undergoing colonoscopy or colorectal surgery were stimulated by a peptide library covering the entire T-Ag protein of JCV. Cytokine production and T cell proliferation were evaluated following T-Ag stimulation using Luminex and flow cytometry assays. JCV T-Ag peptides stimulated secretion of IL-2, which induced T cell expansion in all three groups. However, stronger IL-10 and IL-13 production was seen in patients without colorectal neoplasms. IP-10 was produced at very high levels in all groups, but not significantly differently between groups. Most patients exhibited CD4(+) and CD8(+) T cells in response to stimulation by the T-Ag clusters. The combination of IL-2 and IP-10 secretion indicates the presence of T-Ag-specific Th1 cells in all patients, which is higher in patients without carcinoma.

Are human polyomaviruses co-factors for cancers induced by other oncoviruses?

Presently, 12 human polyomaviruses are known: BK polyomavirus (BKPyV), JCPyV, KIPyV, WUPyV, Merkel cell polyomavirus (MCPyV), HPyV6, HPyV7, Trichodysplasia spinulosa-associated polyomavirus, HPyV9, HPyV10, STLPyV and HPyV12. In addition, the non-human primate polyomavirus simian virus 40 (SV40) seems to circulate in the human population. MCPyV was first described in 2008 and is now accepted to be an etiological factor in about 80% of the rare but aggressive skin cancer Merkel cell carcinoma. SV40, BKPyV and JCPyV or part of their genomes can transform cells, including human cells, and induce tumours in animal models. Moreover, DNA and RNA sequences and proteins of these three viruses have been discovered in tumour tissue. Despite these observations, their role in cancer remains controversial. So far, an association between cancer and the other human polyomaviruses is lacking. Because human polyomavirus DNA has been found in a broad spectrum of cell types, simultaneous dwelling with other oncogenic viruses is possible. Co-infecting human polyomaviruses may therefore act as a co-factor in the development of cancer, including those induced by other oncoviruses. Reviewing studies that report co-infection with human polyomaviruses and other tumour viruses in cancer tissue fail to detect a clear link between co-infection and cancer. Directions for future studies to elaborate on a possible auxiliary role of human polyomaviruses in cancer are suggested, and the mechanisms by which human polyomaviruses may synergize with other viruses in oncogenic transformation are discussed.

Large T antigens of polyomaviruses: amazing molecular machines

The large tumor antigen (T antigen) encoded by simian virus 40 is an amazing molecular machine because it orchestrates viral infection by modulating multiple fundamental viral and cellular processes. T antigen is required for viral DNA replication, transcription, and virion assembly. In addition, T antigen targets multiple cellular pathways, including those that regulate cell proliferation, cell death, and the inflammatory response. Ectopic T antigen expression results in the immortalization and transformation of many cell types in culture and T antigen induces neoplasia when expressed in rodents. The analysis of the mechanisms by which T antigen carries out its many functions has proved to be a powerful way of gaining insights into cell biology. The accelerating pace at which new polyomaviruses are being discovered provides a collection of novel T antigens that, like simian virus 40, can be used to discover and study key cellular regulatory systems.

Gastrointestinal cancers reactive for the PAb416 antibody against JCV/SV40 T-Ag lack JCV DNA sequences while showing a distinctive pathologic profile

AIM

Immunohistochemical and molecular studies have suggested an oncogenic role for JCV in gastrointestinal carcinomas, but at least in colorectal cancers, the data are far from being unambiguous.

METHODS

Two large series of formalin-fixed paraffin-embedded gastric and colorectal cancers were analysed for the expression of JCV large T Antigen (T-Ag) with a panel of five antibodies, and for the presence of T-Ag DNA sequences using two PCR systems.

RESULTS

Intense nuclear staining was observed in 54/116 (46%) colorectal, and in 92/234 (39%) gastric cancers, using the PAb416 monoclonal antibody against large T-Ag. In colorectal cancers, PAb416-positivity was directly related to the presence of chromosomal instability, lymph node metastases and a more advanced tumour stage, and inversely related to proximal tumour site and the presence of microsatellite instability (MSI). In gastric cancers, the glandular histotype, the presence of lymph node metastases, a low frequency of MSI and EBV infection, and a worse prognosis were significantly associated with PAb416 immunoreactivity. Moreover, at both these sites, PAb416 expression was significantly associated with p53 nuclear accumulation. No positivity was obtained with all the other four anti-T-Ag-antibodies, and molecular analysis failed to demonstrate the presence of JCV DNA sequences in tested cases.

CONCLUSIONS

Our immunohistochemical and molecular results do not support the idea that JCV T-Ag has a role in gastrointestinal carcinogenesis. It is possible that PAb416, besides binding the viral protein, may cross-react with a hitherto undefined protein whose expression is associated with a distinct pathological profile and, at least in gastric cancers, with worse prognosis.

A peptide talk between JC virus and the human host: from silent infection to autoimmunity

Analysis of JC virus (JCV) polyprotein for peptide sharing with the human proteome reveals that the virus has hundreds of pentapeptide sequences in common with the human proteins. The datum is interesting in light of the fundamental role exerted by short amino acid sequences in protein-protein interactions and, consequently, in biochemical reactions and immune recognition. Searching for new approaches to understand the JCV infection scenarios, from the immunoevasion phenomenon underlying the viral asymptomatic stay in the human host to the (re)activation phase and associated pathogenic sequelae, the present study describes the diffuse pentapeptide communication network between JCV and the human host.