scholarly journals The use of massively parallel sequencing to study the virome, epigenome and genome of canine and feline cancers

2019 ◽  
Author(s):  
◽  
Shirley Chu
Keyword(s):  
Massively Parallel Sequencing ◽  
Treatment Options ◽  
Telomere Maintenance ◽  
Barr Virus ◽  
Sequencing Technologies ◽  
Dna Mutations ◽  
Metastatic Lesions ◽  
Genome Wide ◽  
Epstein Barr ◽  
Genome Model

The remarkable advancements in sequencing technologies have allowed the entire mutational landscape of hundreds of different types of human cancers to be defined. This knowledge gives patients two new categories of treatment options, small molecule inhibitors and targeted immunotherapy. Veterinary oncology has been slow to enter the field of genome-wide studies, largely due to costs. Five years ago, the first whole genome of a canine cancer patient was published. Because of NIH support and the steady decline in sequencing costs, the number of published canine tumor sequences has exploded this past year as these projects are being concluded. This dissertation contributes to this growing knowledge. The scope was diverse and included exploration in metagenomics, epigenomics and transcriptomics in canine and feline cancers. This research affirmed previous notions that papillomavirus is not a common cause of feline oral squamous cell carcinoma (FOSCC) and added to the understanding that it is not caused by any other DNA or integrated dsRNA virus. In canin DLCBL (cDLBCL) we provided more evidence that the subgroups seen in human DLBCL (hDLBCL) cannot be faithfully reproduced in the methylome of cDLCBL, likely at a greater scale than DNA mutations, and neurogenic/neuroendocrine, HOX and Wnt pathways were epigenetically targeted. In canin osteosarcoma (OSA) we built upon the genome model by adding loss of heterozygosity data and illustration of metastatic lesions. We also provided support to target the CDK4, Wnt and mTOR pathways. Finally we highlight unexpected discoveries such as the discovery of Epstein Barr virus in FOSCC, stability of the methylome in Golden Retriever DLBCL, epimutations in the TBX pathway in cDLBCL, dysregulation of human melanoma pathways in canine OSA, absence of dysregulation of HER2 in canine OSA, absence of genomic evidence of a telomere maintenance mechanism, recurrent shattering of chr26 in canine OSA and HSP90AB1, MITF and NOTCH2, as potentially actionable genes. These data will provide a significant resource for the community to generate new hypotheses and answer key questions about the molecular drivers of canine and feline malignancies.

scholarly journals Genome-Wide Analysis of Wild-Type Epstein–Barr Virus Genomes Derived from Healthy Individuals of the 1000 Genomes Project

2014 ◽  
Vol 6 (4) ◽  
pp. 846-860 ◽  
Author(s):  
Gabriel Santpere ◽  
Fleur Darre ◽  
Soledad Blanco ◽  
Antonio Alcami ◽  
Pablo Villoslada ◽  
...  
Keyword(s):  
Epstein Barr Virus ◽  
Healthy Individuals ◽  
Wild Type ◽  
1000 Genomes Project ◽  
Genome Wide Analysis ◽  
Barr Virus ◽  
1000 Genomes ◽  
Genome Wide ◽  
Epstein Barr ◽  
Virus Genomes

scholarly journals How I treat EBV lymphoproliferation

Blood ◽  
2009 ◽  
Vol 114 (19) ◽  
pp. 4002-4008 ◽  
Author(s):  
Helen E. Heslop
Keyword(s):  
B Cells ◽  
Cytotoxic T Lymphocyte ◽  
Cytotoxic T Cells ◽  
Treatment Options ◽  
Solid Organ Transplantation ◽  
Solid Organ ◽  
Hematopoietic Stem ◽  
Serial Measurement ◽  
Barr Virus ◽  
Epstein Barr

Abstract Epstein-Barr virus (EBV)–associated B-cell lymphoproliferation is a life-threatening complication after hematopoietic stem cell or solid organ transplantation resulting from outgrowth of EBV-infected B cells that would normally be controlled by EBV-cytotoxic T cells. During the past decade, early detection strategies, such as serial measurement of EBV-DNA load in peripheral blood samples, have helped to identify high-risk patients and to diagnose early lymphoproliferation. Treatment options include manipulation of the balance between outgrowing EBV-infected B cells and the EBV cytotoxic T lymphocyte response and targeting the B cells with monoclonal antibodies or chemotherapy. Major challenges remain for defining indications for preemptive therapies and integrating novel and conventional therapies.

scholarly journals Epstein Barr virus genomes reveal population structure and type 1 association with endemic Burkitt lymphoma

2019 ◽  
Author(s):  
Yasin Kaymaz ◽  
Cliff I. Oduor ◽  
Ozkan Aydemir ◽  
Micah A. Luftig ◽  
Juliana A. Otieno ◽  
...  
Keyword(s):  
Population Structure ◽  
Burkitt Lymphoma ◽  
Epstein Barr Virus ◽  
Genome Wide Association ◽  
Viral Dna ◽  
Barr Virus ◽  
Genome Wide ◽  
Epstein Barr

AbstractEndemic Burkitt lymphoma (eBL), the most prevalent pediatric cancer in sub-Saharan Africa, is associated with malaria and Epstein Barr virus (EBV). In order to better understand the role of EBV in eBL, we improved viral DNA enrichment methods and generated a total of 98 new EBV genomes from both eBL cases (N=58) and healthy controls (N=40) residing in the same geographic region in Kenya. Comparing cases and controls, we found that EBV type 1 was significantly associated with eBL with 74.5% of patients (41/55) versus 47.5% of healthy children (19/40) carrying type 1 (OR=3.24, 95% CI=1.36 - 7.71,P=0.007). Controlling for EBV type, we also performed a genome-wide association study identifying 6 nonsynonymous variants in the genes EBNA1, EBNA2, BcLF1, and BARF1 that were enriched in eBL patients. Additionally, we observed that viruses isolated from plasma of eBL patients were identical to their tumor counterpart consistent with circulating viral DNA originating from the tumor. We also detected three intertypic recombinants carrying type 1 EBNA2 and type 2 EBNA3 regions as well as one novel genome with a 20 kb deletion resulting in the loss of multiple lytic and virion genes. Comparing EBV types, genes show differential variation rates as type 1 appears to be more divergent. Besides, type 2 demonstrates novel substructures. Overall, our findings address the complexities of EBV population structure and provide new insight into viral variation, which has the potential to influence eBL oncogenesis.Key PointsEBV type 1 is more prevalent in eBL patients compared to the geographically matched healthy control group.Genome-wide association analysis between cases and controls identifies 6 eBL-associated nonsynonymous variants in EBNA1, EBNA2, BcLF1, and BARF1 genes.Analysis of population structure reveals that EBV type 2 exists as two genomic sub groups.

scholarly journals Acyclovir Improves the Efficacy of Chemoradiation in Nasopharyngeal Cancer Containing the Epstein Barr Virus Genome

2020 ◽  
Author(s):  
Aditya Thandoni ◽  
Andrew Zloza ◽  
Devora Schiff ◽  
Malay Rao ◽  
Kwok-wai Lo ◽  
...  
Keyword(s):  
Epstein Barr Virus ◽  
Treatment Options ◽  
Immune Surveillance ◽  
Nasopharyngeal Cancer ◽  
Standard Of Care ◽  
Virus Genome ◽  
Barr Virus ◽  
Standard Of Care Treatment ◽  
Epstein Barr

AbstractNasopharyngeal carcinoma (NPC) is a malignancy endemic to East Asia and is caused by Epstein-Barr Virus (EBV)-mediated cancerous transformation of epithelial cells. The standard of care treatment for NPC involves radiation and chemotherapy. While treatment outcomes continue to improve, up to 50% of patients can be expected to recur by five years, and additional innovative treatment options are needed. We posit that a potential way to do this is by targeting the underlying cause of malignant transformation, namely EBV. One method by which EBV escapes immune surveillance is by undergoing latent phase replication, during which EBV expression of immunogenic proteins is reduced. However, chemoradiation is known to drive conversion of EBV from a latent to a lytic phase. This creates an opportunity for the targeting of EBV-infected cells utilizing anti-viral drugs. Indeed, we found that combining acyclovir with cisplatin and radiation significantly decreases the viability of the EBV-infected C666-1 cell line. Western blot quantification revealed a resultant increase of thymidine kinase (TK) and apoptosis-inducing mediators, cleaved PARP (cPARP) and phosphorylated ERK (pERK). These studies suggest that the addition of anti-viral drugs to frontline chemoradiation may improve outcomes in patients treated for EBV-related NPC and future in vivo and clinical studies are needed.

scholarly journals Dangerous Liaisons: Gammaherpesvirus Subversion of the Immunoglobulin Repertoire

Viruses ◽  
2020 ◽  
Vol 12 (8) ◽  
pp. 788
Author(s):  
Monika A. Zelazowska ◽  
Kevin McBride ◽  
Laurie T. Krug
Keyword(s):  
B Cells ◽  
Somatic Hypermutation ◽  
Adaptive Immune Response ◽  
Kaposi Sarcoma ◽  
Lymphoid Tissues ◽  
Barr Virus ◽  
Sequencing Technologies ◽  
Biologic Property ◽  
Epstein Barr ◽  
Immunoglobulin Repertoire

A common biologic property of the gammaherpesviruses Epstein–Barr Virus and Kaposi sarcoma herpesvirus is their use of B lymphocytes as a reservoir of latency in healthy individuals that can undergo oncogenic transformation later in life. Gammaherpesviruses (GHVs) employ an impressive arsenal of proteins and non-coding RNAs to reprogram lymphocytes for proliferative expansion. Within lymphoid tissues, the germinal center (GC) reaction is a hub of B cell proliferation and death. The goal of a GC is to generate and then select for a pool of immunoglobulin (Ig) genes that will provide a protective humoral adaptive immune response. B cells infected with GHVs are detected in GCs and bear the hallmark signatures of the mutagenic processes of somatic hypermutation and isotype class switching of the Ig genes. However, data also supports extrafollicular B cells as a reservoir engaged by GHVs. Next-generation sequencing technologies provide unprecedented detail of the Ig sequence that informs the natural history of infection at the single cell level. Here, we review recent reports from human and murine GHV systems that identify striking differences in the immunoglobulin repertoire of infected B cells compared to their uninfected counterparts. Implications for virus biology, GHV-associated cancers, and host immune dysfunction will be discussed.

Genetic loci for Epstein-Barr virus nuclear antigen-1 are associated with risk of multiple sclerosis

2016 ◽  
Vol 22 (13) ◽  
pp. 1655-1664 ◽  
Author(s):  
Yuan Zhou ◽  
Gu Zhu ◽  
Jac C Charlesworth ◽  
Steve Simpson ◽  
Rohina Rubicz ◽  
...  
Keyword(s):  
Multiple Sclerosis ◽  
Genetic Risk ◽  
Epstein Barr Virus ◽  
Meta Analysis ◽  
Nuclear Antigen ◽  
Genetic Loci ◽  
Polygenic Risk ◽  
Barr Virus ◽  
Genome Wide ◽  
Epstein Barr

Background: Infection with the Epstein-Barr virus (EBV) is associated with an increased risk of multiple sclerosis (MS). Objective: We sought genetic loci influencing EBV nuclear antigen-1 (EBNA-1) IgG titers and hypothesized that they may play a role in MS risk. Methods: We performed a genome-wide association study (GWAS) of anti-EBNA-1 IgG titers in 3599 individuals from an unselected twin family cohort, followed by a meta-analysis with data from an independent EBNA-1 GWAS. We then examined the shared polygenic risk between the EBNA-1 GWAS (effective sample size ( Neff) = 5555) and a large MS GWAS ( Neff = 15,231). Results: We identified one locus of strong association within the human leukocyte antigen (HLA) region, of which the most significantly associated genotyped single nucleotide polymorphism (SNP) was rs2516049 ( p = 4.11 × 10−9). A meta-analysis including data from another EBNA-1 GWAS in a cohort of Mexican-American families confirmed that rs2516049 remained the most significantly associated SNP ( p = 3.32 × 10−20). By examining the shared polygenic risk, we show that the genetic risk for elevated anti-EBNA-1 titers is positively correlated with the development of MS, and that elevated EBNA-1 titers are not an epiphenomena secondary to MS. In the joint meta-analysis of EBNA-1 titers and MS, loci at 1p22.1, 3p24.1, 3q13.33, and 10p15.1 reached genome-wide significance ( p < 5 × 10−8). Conclusions: Our results suggest that apart from the confirmed HLA region, the association of anti-EBNA-1 IgG titer with MS risk is also mediated through non-HLA genes, and that studies aimed at identifying genetic loci influencing EBNA immune response provides a novel opportunity to identify new and characterize existing genetic risk factors for MS.

scholarly journals Genome-wide profiling of Epstein-Barr virus integration by targeted sequencing in Epstein-Barr virus associated malignancies

Theranostics ◽  
2019 ◽  
Vol 9 (4) ◽  
pp. 1115-1124 ◽  
Author(s):  
Miao Xu ◽  
Wei-Long Zhang ◽  
Qing Zhu ◽  
You-yuan Yao ◽  
Qi-Sheng Feng ◽  
...  
Keyword(s):  
Epstein Barr Virus ◽  
Targeted Sequencing ◽  
Barr Virus ◽  
Genome Wide ◽  
Epstein Barr ◽  
Virus Integration
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