Sequence variation of Epstein-Barr virus (EBV) BZLF1 gene in EBV-associated gastric carcinomas and nasopharyngeal carcinomas in Northern China

A Comparative Genomic Analysis of Epstein-Barr Virus Strains with a Focus on EBV2 Variability

Most genomic studies on Epstein-Barr virus variability have focused on the geographic and pathological associations of EBV1 genomes. In contrast, the variability of EBV2 genomes has been less explored, mainly due to their restricted geographic circulation and the lesser number of sequenced EBV2 isolates. In this study, we sequenced and analyzed twenty-eight EBV1 and ten EBV2 genomes and a potential recombinant from Argentina, which were combined with two-hundred-and-thirty-nine downloaded complete genomes from other geographic regions, to produce an initial multi-sample.vcf file comprising 278 EBV genomes. In this context, we identified 1093/4541 positions in the viral genome that contribute to variability between viral types, mainly located in the EBNA2 and EBNA3 family of genes and the adjacent BZLF1, BZLF2, and BLLF1 genes. We further described that this variability exhibits distinct patterns across Africa, South America, and Southeast Asia. Compared to EBV1 genomes, EBV2 genomes showed fewer variable positions relative to their reference genome (Wilcoxon test, p = 0.0001). Principal component analysis revealed that EBV2 genomes from Southeast Asia segregate independently from those from South America (Wilcoxon test, Bonferroni correction; p = 1.1 × 10-7) and Africa (Wilcoxon test, Bonferroni correction; p = 2.6 × 10-9). Additionally, we identified those precise variable positions with geographic segregation strength: 1135/3666 in EBV1 and 380/3276 in EBV2. Furthermore, the distribution of variable positions along the genome disclosed a close relation for EBV2 isolates from Africa and South America as compared to isolates from Southeast Asia. Although our analysis is limited to EBV2 genomes isolated from three geographic regions, this was, to the best of our knowledge, the first study to comprehensively characterize the geographic variability of the complete EBV2 genome. These findings underscore the geographic and genetic diversity of EBV2 genomes and contribute to understanding the EBV's evolutionary dynamics and potential regional adaptations. This research enhances our understanding of EBV2 genomic variability, supporting future epidemiological studies and advancing the knowledge base for targeted treatments and vaccine development for EBV-associated diseases.

Epstein-Barr Virus and gastric carcinoma pathogenesis with emphasis on underlying epigenetic mechanisms

Gastric cancer (GC) remains one of the top causes of cancer-related mortality around the world. The pathogenesis of GC is attributed to lifestyle, family history, genetic mutations, epigenetic alterations, as well as infectious agents such as Epstein-Barr Virus (EBV). EBV, a ubiquitous human gamma herpes virus, with latent asymptomatic infection in more than 95% of the world's population, is able to infect through the oral epithelium. EBV is described as the first virus found in human neoplastic, when it was detected in Burkitt lymphoma tumor biopsy. Nowadays this virus is considered to be involved in various human malignancies such as GC. Despite comprehensive efforts and immense studies, the main underlying mechanism is not well described as there are crucial contradictions regarding the presence of this virus and the prognosis of the disease. Immunological alterations, genetic mutations, and epigenetic modifications are among the most important criteria presented in EBV- associated gastric cancer (EBVaGC), leading to its consideration as a separate subtype with unique clinical, histological, biochemical, and genetic characteristics. The current study aimed to review the association between EBV and GC with an emphasis on the role of epigenetic modifications in the suppression or progression of carcinogenesis. To put all findings in a nutshell, several genes and chromatin mutations, promoter hypermethylation and subsequent silencing of related genes, and histone modifications and aberrant micro RNAs (miRNAs) expression were considered as the major altered mechanisms in the pathogenesis of EBVaGC, most of which able to be suggested as therapeutic targets. However, the current knowledge appeared to be imperfect, hence further studies are encouraged.

The role of intratumoral microorganisms in the progression and immunotherapeutic efficacy of head and neck cancer

The effectiveness of cancer immunization is largely dependent on the tumor’s microenvironment, especially the tumor immune microenvironment. Emerging studies say microbes exist in tumor cells and immune cells, suggesting that these microbes can affect the state of the immune microenvironment of the tumor. Our comprehensive review navigates the intricate nexus between intratumoral microorganisms and their role in tumor biology and immune modulation. Beginning with an exploration of the historical acknowledgment of microorganisms within tumors, the article underscores the evolution of the tumor microenvironment (TME) and its subsequent implications. Using findings from recent studies, we delve into the unique bacterial compositions across different tumor types and their influence on tumor growth, DNA damage, and immune regulation. Furthermore, we illuminate the potential therapeutic implications of targeting these intratumoral microorganisms, emphasizing their multifaceted roles from drug delivery agents to immunotherapy enhancers. As advancements in next-generation sequencing (NGS) technology redefine our understanding of the tumor microbiome, the article underscores the importance of discerning their precise role in tumor progression and tailoring therapeutic interventions. The review culminates by emphasizing ongoing challenges and the pressing need for further research to harness the potential of intratumoral microorganisms in cancer care.

Lytic and Latent Genetic Diversity of the Epstein-Barr Virus Reveals Raji-Related Variants from Southeastern Brazil Associated with Recombination Markers

Epstein-Barr virus (EBV) is a ubiquitous gammaherpesvirus etiologically associated with benign and malignant diseases. Since the pathogenic mechanisms of EBV are not fully understood, understanding EBV genetic diversity is an ongoing goal. Therefore, the present work describes the genetic diversity of the lytic gene BZLF1 in a sampling of 70 EBV-positive cases from southeastern Brazil. Additionally, together with the genetic regions previously characterized, the aim of the present study was to determine the impact of viral genetic factors that may influence EBV genetic diversity. Accordingly, the phylogenetic analysis of the BZLF1 indicated two main clades with high support, BZ-A and BZ-B (PP > 0.85). Thus, the BZ-A clade was the most diverse clade associated with the main polymorphisms investigated, including the haplotype Type 1 + V3 (p < 0.001). Furthermore, the multigene phylogenetic analysis (MLA) between BZLF1 and the oncogene LMP1 showed specific clusters, revealing haplotypic segregation that previous single-gene phylogenies from both genes failed to demonstrate. Surprisingly, the LMP1 Raji-related variant clusters were shown to be more diverse, associated with BZ-A/B and the Type 2/1 + V3 haplotypes. Finally, due to the high haplotypic diversity of the Raji-related variants, the number of DNA recombination-inducing motifs (DRIMs) was evaluated within the different clusters defined by the MLA. Similarly, the haplotype BZ-A + Raji was shown to harbor a greater number of DRIMs (p < 0.001). These results call attention to the high haplotype diversity of EBV in southeast Brazil and strengthen the hypothesis of the recombinant potential of South American Raji-related variants via the LMP1 oncogene.

Expanding the Geographic Characterisation of Epstein-Barr Virus Variation through Gene-Based Approaches

The Epstein-Barr Virus (EBV) infects the vast majority of human individuals worldwide (~90%) and is associated with several diseases, including different types of cancer and multiple sclerosis, which show wide variation in incidence among global geographical regions. Genetic variants in EBV genomic sequences have been used to determine the geographical structure of EBV isolates, but our understanding of EBV diversity remains highly incomplete. We generated sequences for 13 pivotal EBV genes derived from 103 healthy individuals, expanding current EBV diversity datasets with respect to both geographic coverage and number of isolates per region. These newly generated sequences were integrated with the more than 250 published EBV genomes, generating the most geographically comprehensive data set of EBV strains to date. We report remarkable variation in single-gene phylogenies that, when analysed together, show robust signals of population structure. Our results not only confirm known major global patterns of geographic variation, such as the clear separation of Asian isolates from the rest, and the intermixed relationships among African, European and Australian isolates, but yield novel phylogenetic relationships with previously unreported populations. We provide a better understanding of EBV's population structure in South America, Africa and, by the inclusion of Turkey and Georgia, we also gain insight into EBV diversity in Western Asia, a crossroads connecting Europe, Africa and Asia. In summary, our results provide a detailed world-wide characterisation of EBV genetic clusters, their enrichment in specific geographic regions, novel inter-population relationships, and a catalogue of geographically informative EBV genetic variants.

Epstein-Barr Virus: From the Detection of Sequence Polymorphisms to the Recognition of Viral Types

The Epstein-Barr virus is etiologically linked with the development of benign and malignant diseases, characterized by their diversity and a heterogeneous geographic distribution across the world. The virus possesses a 170-kb-large genome that encodes for multiple proteins and non-coding RNAs. Early on there have been numerous attempts to link particular diseases with particular EBV strains, or at least with viral genetic polymorphisms. This has given rise to a wealth of information whose value has been difficult to evaluate for at least four reasons. First, most studies have looked only at one particular gene and missed the global picture. Second, they usually have not studied sufficient numbers of diseased and control cases to reach robust statistical significance. Third, the functional significance of most polymorphisms has remained unclear, although there are exceptions such as the 30-bp deletion in LMP1. Fourth, different biological properties of the virus do not necessarily equate with a different pathogenicity. This was best illustrated by the type 1 and type 2 viruses that markedly differ in terms of their transformation abilities, yet do not seem to cause different diseases. Reciprocally, environmental and genetic factors in the host are likely to influence the outcome of infections with the same virus type. However, with recent developments in recombinant virus technology and in the availability of high throughput sequencing, the tide is now turning. The availability of 23 complete or nearly complete genomes has led to the recognition of viral subtypes, some of which possess nearly identical genotypes. Furthermore, there is growing evidence that some genetic polymorphisms among EBV strains markedly influence the biological and clinical behavior of the virus. Some virus strains are endowed with biological properties that explain crucial clinical features of patients with EBV-associated diseases. Although we now have a better overview of the genetic diversity within EBV genomes, it has also become clear that defining phenotypic traits evinced by cells infected by different viruses usually result from the combination of multiple polymorphisms that will be difficult to identify in their entirety. However, the steadily increasing number of sequenced EBV genomes and cloned EBV BACS from diseased and healthy patients will facilitate the identification of the key polymorphisms that condition the biological and clinical behavior of the viruses. This will allow the development of preventative and therapeutic approaches against highly pathogenic viral strains.

Epstein-Barr Virus Strain Variation

What is wild-type Epstein-Barr virus and are there genetic differences in EBV strains that contribute to some of the EBV-associated diseases? Recent progress in DNA sequencing has resulted in many new Epstein-Barr virus (EBV) genome sequences becoming available. EBV isolates worldwide can be grouped into type 1 and type 2, a classification based on the EBNA2 gene sequence. Type 1 transforms human B cells into lymphoblastoid cell lines much more efficiently than type 2 EBV and molecular mechanisms that may account for this difference in cell transformation are now becoming understood. Study of geographic variation of EBV strains independent of the type 1/type 2 classification and systematic investigation of the relationship between viral strains, infection and disease are now becoming possible. So we should consider more directly whether viral sequence variation might play a role in the incidence of some EBV-associated diseases.

The unfolded protein response in retinal vascular diseases: implications and therapeutic potential beyond protein folding

Angiogenesis is a complex, step-wise process of new vessel formation that is involved in both normal embryonic development as well as postnatal pathological processes, such as cancer, cardiovascular disease, and diabetes. Aberrant blood vessel growth, also known as neovascularization, in the retina and the choroid is a major cause of vision loss in severe eye diseases, such as diabetic retinopathy, age-related macular degeneration, retinopathy of prematurity, and central and branch retinal vein occlusion. Yet, retinal neovascularization is causally and dynamically associated with vasodegeneration, ischemia, and vascular remodeling in retinal tissues. Understanding the mechanisms of retinal neovascularization is an urgent unmet need for developing new treatments for these devastating diseases. Accumulating evidence suggests a vital role for the unfolded protein response (UPR) in regulation of angiogenesis, in part through coordinating the secretion of pro-angiogenic growth factors, such as VEGF, and modulating endothelial cell survival and activity. Herein, we summarize current research in the context of endoplasmic reticulum (ER) stress and UPR signaling in retinal angiogenesis and vascular remodeling, highlighting potential implications of targeting these stress response pathways in the prevention and treatment of retinal vascular diseases that result in visual deficits and blindness.

Epstein-Barr virus BZLF1 gene polymorphisms: malignancy related or geographically distributed variants?

The ubiquitous Epstein-Barr virus (EBV) is related to the development of several lymphoid and epithelial malignancies and is also the aetiological agent for infectious mononucleosis (IM). BZLF1, an immediate early gene, plays a key role in modulating the switch from latency to lytic replication, hence enabling viral propagation. Polymorphic variations in the coded protein have been studied in other geographical regions in a search for viral factors that are inherent to malignancies and differ from those present in benign infections. In the present study, in samples of paediatric patients with benign IM and paediatric patients with malignant lymphomas, we detected previously described sequence variations as well as distinctive sequence polymorphisms from our region. By means of phylogenetic reconstruction, we characterized new phylogenetically distinct variants. Moreover, we described an association between specific variants and the studied pathologies in our region, particularly variant BZLF1-A2 with lymphomas and BZLF1-C with IM. Additionally, length polymorphisms within intron 1 were also assessed and compared between pathologies resulting in an association between 29-bp repeated units and lymphomas. In conclusion, this is the first report to characterize BZLF1 gene polymorphisms in paediatric patients from our geographical region and to suggest the association of these polymorphisms with malignant lymphomas.

Clinicopathological and EBV analysis of respiratory epithelial adenomatoid hamartoma

Background

To investigate the clinicopathological characteristics of respiratory epithelial adenomatoid hamartoma (REAH) in residents of Southern China and to study the correlation between REAH and Epstein-Barr virus (EBV).

Methods

Clinicopathological data of 53 cases of REAH were retrospectively analyzed. The immunoreactivity for CK 7, CK20, CEA, p53, and Ki-67, Alcian blue–periodic acid-Schiff (AB-PAS) staining and in situ hybridization for EBV-encoded RNA (EBER) were carried out.

Results

REAH lesions were covered with ciliated columnar epithelium and proliferation of subepithelial glands, which were positive for CK7, and negative for CK20, CEA, and p53. Goblet cell metaplasia was stained blue by AB-PAS. The frequency of EBER positive cases in REAH located in nasopharynx was 27.78%, compared with that in the nasal cavity (15.79%) and paranasal sinuses (12.50%), there were no statistical differences.

Conclusions

REAH is an uncommon entity with distinctive morphologic features and EBV may have nothing to do with REAH.

Virtual slides

The virtual slide(s) for this article can be found here:

http://www.diagnosticpathology.diagnomx.eu/vs/5875687401178748

Sequence analysis of EBV immediate-early gene BZLF1 and BRLF1 in lymphomas

The immediate-early (IE) genes, BZLF1 and BRLF1, play an important role in switching Epstein-Barr virus from the latent to the lytic state. The functions of the two IE genes and their respective proteins: ZEBRA and Rta have been well studied, but little is known about their DNA coding sequence variations and disease association. In order to investigate the sequence variation patterns and elucidate their association with lymphomas, BZLF1 and BRLF1 were analyzed in 26 and 33 lymphomas using PCR-direct sequencing method respectively. Three sequence variation types of BZLF1 gene were identified. The type BZLF1-A and BZLF1-B was detected in 34.6% (9/26) and 57.7% (15/26) of the tumor specimens, respectively. Among the three functional domains of ZEBRA, the transactivation domain had the most mutations. Three variation types were also identified in BRLF1 gene where type BR1-A and BR1-C were detected in 27.3% (9/33) and 69.7% (23/33) of specimens, respectively. Among the three functional domains of Rta, the dimerization domain was well conserved while multiple mutations were detected in both the DNA binding domain and the transactivation domain. The variation types BZLF1-B and BR1-C were more frequent in the lymphomas, compared with the throat washing samples from the healthy donors. These results suggest that the type BZLF1-B and BR1-C may be associated with the tumorigenesis of lymphoma.

Spontaneous lytic replication and epitheliotropism define an Epstein-Barr virus strain found in carcinomas

The Epstein-Barr virus (EBV) is found in a variety of tumors whose incidence greatly varies around the world. A poorly explored hypothesis is that particular EBV strains account for this phenomenon. We report that M81, a virus isolated from a Chinese patient with nasopharyngeal carcinoma (NPC), shows remarkable similarity to other NPC viruses but is divergent from all other known strains. M81 exhibited a reversed tropism relative to common strains with a reduced ability to infect B cells and a high propensity to infect epithelial cells, which is in agreement with its isolation from carcinomas. M81 spontaneously replicated in B cells in vitro and in vivo at unusually high levels, in line with the enhanced viral replication observed in NPC patients. Spontaneous replication and epitheliotropism could be partly ascribed to polymorphisms within viral proteins. We suggest considering M81 and its closely related isolates as an EBV subtype with enhanced pathogenic potential.

Epstein-barr virus sequence variation-biology and disease

Some key questions in Epstein-Barr virus (EBV) biology center on whether naturally occurring sequence differences in the virus affect infection or EBV associated diseases. Understanding the pattern of EBV sequence variation is also important for possible development of EBV vaccines. At present EBV isolates worldwide can be grouped into Type 1 and Type 2, a classification based on the EBNA2 gene sequence. Type 1 EBV is the most prevalent worldwide but Type 2 is common in parts of Africa. Type 1 transforms human B cells into lymphoblastoid cell lines much more efficiently than Type 2 EBV. Molecular mechanisms that may account for this difference in cell transformation are now becoming clearer. Advances in sequencing technology will greatly increase the amount of whole EBV genome data for EBV isolated from different parts of the world. Study of regional variation of EBV strains independent of the Type 1/Type 2 classification and systematic investigation of the relationship between viral strains, infection and disease will become possible. The recent discovery that specific mutation of the EBV EBNA3B gene may be linked to development of diffuse large B cell lymphoma illustrates the importance that mutations in the virus genome may have in infection and human disease.