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Marshall VA, Cornejo Castro EM, Goodman CA, Labo N, Liu I, Fisher NC, Moore KN, Nair A, Immonen T, Keele BF, Polizzotto MN, Uldrick TS, Mu Y, Saswat T, Krug LT, McBride KM, Lurain K, Ramaswami R, Yarchoan R, Whitby D. Sequencing of Kaposi's Sarcoma Herpesvirus (KSHV) genomes from persons of diverse ethnicities and provenances with KSHV-associated diseases demonstrate multiple infections, novel polymorphisms, and low intra-host variance. PLoS Pathog 2024; 20:e1012338. [PMID: 39008527 PMCID: PMC11271956 DOI: 10.1371/journal.ppat.1012338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 07/25/2024] [Accepted: 06/11/2024] [Indexed: 07/17/2024] Open
Abstract
Recently published near full-length KSHV genomes from a Cameroon Kaposi sarcoma case-control study showed strong evidence of viral recombination and mixed infections, but no sequence variations associated with disease. Using the same methodology, an additional 102 KSHV genomes from 76 individuals with KSHV-associated diseases have been sequenced. Diagnoses comprise all KSHV-associated diseases (KAD): Kaposi sarcoma (KS), primary effusion lymphoma (PEL), KSHV-associated large cell lymphoma (KSHV-LCL), a type of multicentric Castleman disease (KSHV-MCD), and KSHV inflammatory cytokine syndrome (KICS). Participants originated from 22 different countries, providing the opportunity to obtain new near full-length sequences of a wide diversity of KSHV genomes. These include near full-length sequence of genomes with KSHV K1 subtypes A, B, C, and F as well as subtype E, for which no full sequence was previously available. High levels of recombination were observed. Fourteen individuals (18%) showed evidence of infection with multiple KSHV variants (from two to four unique genomes). Twenty-six comparisons of sequences, obtained from various sampling sites including PBMC, tissue biopsies, oral fluids, and effusions in the same participants, identified near complete genome conservation between different biological compartments. Polymorphisms were identified in coding and non-coding regions, including indels in the K3 and K15 genes and sequence inversions here reported for the first time. One such polymorphism in KSHV ORF46, specific to the KSHV K1 subtype E2, encoded a mutation in the leucine loop extension of the uracil DNA glycosylase that results in alteration of biochemical functions of this protein. This confirms that KSHV sequence variations can have functional consequences warranting further investigation. This study represents the largest and most diverse analysis of KSHV genome sequences to date among individuals with KAD and provides important new information on global KSHV genomics.
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Affiliation(s)
- Vickie A. Marshall
- Viral Oncology Section, AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Elena M. Cornejo Castro
- Viral Oncology Section, AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Charles A. Goodman
- Retroviral Evolution Section, AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Nazzarena Labo
- Viral Oncology Section, AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Isabella Liu
- Viral Oncology Section, AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Nicholas C. Fisher
- Viral Oncology Section, AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Kyle N. Moore
- Viral Oncology Section, AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Ananthakrishnan Nair
- Viral Oncology Section, AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Taina Immonen
- Retroviral Evolution Section, AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Brandon F. Keele
- Retroviral Evolution Section, AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Mark N. Polizzotto
- HIV and AIDS Malignancy Branch, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Thomas S. Uldrick
- HIV and AIDS Malignancy Branch, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Yunxiang Mu
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Tanuja Saswat
- HIV and AIDS Malignancy Branch, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Laurie T. Krug
- HIV and AIDS Malignancy Branch, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Kevin M. McBride
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Kathryn Lurain
- HIV and AIDS Malignancy Branch, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Ramya Ramaswami
- HIV and AIDS Malignancy Branch, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Robert Yarchoan
- HIV and AIDS Malignancy Branch, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Denise Whitby
- Viral Oncology Section, AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
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Alves PD, Rohan P, Hassan R, Abdelhay E. Lytic and Latent Genetic Diversity of the Epstein-Barr Virus Reveals Raji-Related Variants from Southeastern Brazil Associated with Recombination Markers. Int J Mol Sci 2024; 25:5002. [PMID: 38732219 PMCID: PMC11084898 DOI: 10.3390/ijms25095002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 04/27/2024] [Accepted: 05/01/2024] [Indexed: 05/13/2024] Open
Abstract
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.
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Affiliation(s)
- Paula D. Alves
- Oncovirology Laboratory, Division of Specialized Laboratories, Instituto Nacional de Câncer (INCA), Rio de Janeiro 20230-130, RJ, Brazil
- Stem Cell Laboratory, Division of Specialized Laboratories, Instituto Nacional de Câncer (INCA), Rio de Janeiro 20230-130, RJ, Brazil
| | - Paulo Rohan
- Oncovirology Laboratory, Division of Specialized Laboratories, Instituto Nacional de Câncer (INCA), Rio de Janeiro 20230-130, RJ, Brazil
- Stem Cell Laboratory, Division of Specialized Laboratories, Instituto Nacional de Câncer (INCA), Rio de Janeiro 20230-130, RJ, Brazil
| | - Rocio Hassan
- Oncovirology Laboratory, Division of Specialized Laboratories, Instituto Nacional de Câncer (INCA), Rio de Janeiro 20230-130, RJ, Brazil
| | - Eliana Abdelhay
- Stem Cell Laboratory, Division of Specialized Laboratories, Instituto Nacional de Câncer (INCA), Rio de Janeiro 20230-130, RJ, Brazil
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Alves P, Emmel V, Stefanoff G, Krsticevic F, Ezpeleta J, Murillo J, Tapia E, Delatorre E, Abdelhay E, Hassan R. Unique synapomorphies and high diversity in South American Raji-related Epstein-Barr virus genomes. Mem Inst Oswaldo Cruz 2023; 118:e230122. [PMID: 37937604 PMCID: PMC10629697 DOI: 10.1590/0074-02760230122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 10/06/2023] [Indexed: 11/09/2023] Open
Abstract
BACKGROUND Epstein-Barr virus (EBV) is a human gammaherpesvirus etiologically linked to several benign and malignant diseases. EBV-associated malignancies exhibit an unusual global distribution that might be partly attributed to virus and host genetic backgrounds. OBJECTIVES To assemble a new genome of EBV (CEMO3) from a paediatric Burkitt's lymphoma from Rio de Janeiro State (Southeast Brazil). In addition, to perform global phylogenetic analysis using complete EBV genomes, including CEMO3, and investigate the genetic relationship of some South American (SA) genomes through EBV subgenomic targets. METHODS CEMO3 was sequenced through next generation sequencing and its coverage and gaps were corrected through the Sanger method. CEMO3 and 67 EBV genomes representing diverse geographic regions were evaluated through maximum likelihood phylogenetic analysis. Further, the polymorphism of subgenomic regions of some SA EBV genomes were assessed. FINDINGS The whole bulk tumour sequencing yielded 23,217 reads related to EBV, which 172,713 base pairs of the newly EBV genome CEMO3 was assembled. The CEMO3 and most SA EBV genomes clustered within the SA subclade closely related to the African Raji strain, forming the South American/Raji clade. Notably, these Raji-related genomes exhibit significant genetic diversity, characterised by distinctive synapomorphies at some gene levels absent in the original Raji strain. CONCLUSION The CEMO3 represents a new South American EBV genome assembled. Albeit the majority of EBV genomes from SA are Raji-related, it harbours a high diversity different from the original Raji strain.
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Affiliation(s)
- Paula Alves
- Instituto Nacional de Câncer, Centro de Transplante de Medula Óssea, Rio de Janeiro, RJ, Brasil
- Universidad Nacional de Rosario, Centro Internacional Franco Argentino de Ciencias de la Información y de Sistemas, Rosario, Argentina
| | - Vanessa Emmel
- Instituto Nacional de Câncer, Centro de Transplante de Medula Óssea, Rio de Janeiro, RJ, Brasil
| | - Gustavo Stefanoff
- Instituto Nacional de Câncer, Centro de Transplante de Medula Óssea, Rio de Janeiro, RJ, Brasil
- Instituto Nacional de Câncer, Coordenação de Pesquisa Clínica, Rio de Janeiro, RJ, Brasil
| | - Flavia Krsticevic
- Instituto Nacional de Câncer, Centro de Transplante de Medula Óssea, Rio de Janeiro, RJ, Brasil
- Universidad Nacional de Rosario, Centro Internacional Franco Argentino de Ciencias de la Información y de Sistemas, Rosario, Argentina
| | - Joaquín Ezpeleta
- Universidad Nacional de Rosario, Centro Internacional Franco Argentino de Ciencias de la Información y de Sistemas, Rosario, Argentina
| | - Javier Murillo
- Universidad Nacional de Rosario, Centro Internacional Franco Argentino de Ciencias de la Información y de Sistemas, Rosario, Argentina
| | - Elizabeth Tapia
- Universidad Nacional de Rosario, Centro Internacional Franco Argentino de Ciencias de la Información y de Sistemas, Rosario, Argentina
| | - Edson Delatorre
- Universidade Federal do Espírito Santo, Centro de Ciências da Saúde, Departamento de Patologia, Laboratório de Genômica e Ecologia Viral, Vitória, ES, Brasil
| | - Eliana Abdelhay
- Instituto Nacional de Câncer, Centro de Transplante de Medula Óssea, Rio de Janeiro, RJ, Brasil
| | - Rocio Hassan
- Instituto Nacional de Câncer, Centro de Transplante de Medula Óssea, Rio de Janeiro, RJ, Brasil
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Zealiyas K, Teshome S, Haile AF, Weigel C, Alemu A, Amogne W, Yimer G, Abebe T, Berhe N, Ahmed EH, Baiocchi RA. Genotype characterization of Epstein-Barr virus among adults living with human immunodeficiency virus in Ethiopia. Front Microbiol 2023; 14:1270824. [PMID: 38029140 PMCID: PMC10644458 DOI: 10.3389/fmicb.2023.1270824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 10/16/2023] [Indexed: 12/01/2023] Open
Abstract
Background Epstein-Barr virus (EBV) is a human lymphotropic herpesvirus with a causative agent in cancer. There are two genotypes of EBV (EBV genotype 1 and EBV genotype 2) that have been shown to infect humans. This study aimed to characterize the EBV genotype among people with human immunodeficiency virus (PWH) and HIV-negative individuals in Ethiopia. Methods DNA was extracted from peripheral blood mononuclear cells (PBMCs). Conventional polymerase chain reaction (cPCR) targeting EBNA3C genes was performed for genotyping. A quantitative real-time PCR (q-PCR) assay for EBV DNA (EBNA1 ORF) detection and viral load quantification was performed. Statistical significance was determined at a value of p < 0.05. Result In this study, 155 EBV-seropositive individuals were enrolled, including 128 PWH and 27 HIV-negative individuals. Among PWH, EBV genotype 1 was the most prevalent (105/128, 82.0%) genotype, followed by EBV genotype 2 (17/128, 13.3%), and mixed infection (6/128, 4.7%). In PWH, the median log10 of EBV viral load was 4.23 copies/ml [interquartile range (IQR): 3.76-4.46], whereas it was 3.84 copies/ml (IQR: 3.74-4.02) in the HIV-negative group. The EBV viral load in PWH was significantly higher than that in HIV-negative individuals (value of p = 0.004). In PWH, the median log10 of EBV viral load was 4.25 copies/ml (IQR: 3.83-4.47) in EBV genotype 1 and higher than EBV genotype 2 and mixed infection (p = 0.032). Conclusion In Ethiopia, EBV genotype 1 was found to be the most predominant genotype, followed by EBV genotype 2. Understanding the genotype characterization of EBV in PWH is essential for developing new and innovative strategies for preventing and treating EBV-related complications in this population.
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Affiliation(s)
- Kidist Zealiyas
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Seifegebriel Teshome
- Department of Microbiology, Immunology and Parasitology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Aklilu Feleke Haile
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Christoph Weigel
- Comprehensive Cancer Center, The James Cancer Hospital and Solove Research Institute, The Ohio State University, Columbus, OH, United States
- Division of Hematology, Department of Internal Medicine, College of Medicine, The Ohio State University, Columbus, OH, United States
| | - Ayinalem Alemu
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Wondwossen Amogne
- Department of Internal Medicine, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Getnet Yimer
- Centre for Innovative Drug Development and Therapeutic Trials for Africa (CDT-Africa), College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
- Department of Genetics, Penn Center for Global Genomics & Health Equity, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Tamrat Abebe
- Department of Microbiology, Immunology and Parasitology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Nega Berhe
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Elshafa Hassan Ahmed
- Comprehensive Cancer Center, The James Cancer Hospital and Solove Research Institute, The Ohio State University, Columbus, OH, United States
| | - Robert A. Baiocchi
- Comprehensive Cancer Center, The James Cancer Hospital and Solove Research Institute, The Ohio State University, Columbus, OH, United States
- Division of Hematology, Department of Internal Medicine, College of Medicine, The Ohio State University, Columbus, OH, United States
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Barros MHM, Alves PDS. Contribution of the Epstein-Barr virus to the oncogenesis of mature T-cell lymphoproliferative neoplasms. Front Oncol 2023; 13:1240359. [PMID: 37781191 PMCID: PMC10538126 DOI: 10.3389/fonc.2023.1240359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 08/24/2023] [Indexed: 10/03/2023] Open
Abstract
EBV is a lymphotropic virus, member of the Herpesviridae family that asymptomatically infects more than 90% of the human population, establishing a latent infection in memory B cells. EBV exhibits complex survival and persistence dynamics, replicating its genome through the proliferation of infected B cells or production of the lytic virions. Many studies have documented the infection of T/NK cells by EBV in healthy individuals during and after primary infection. This feature has been confirmed in humanized mouse models. Together these results have challenged the hypothesis that the infection of T/NK cells per se by EBV could be a triggering event for lymphomagenesis. Extranodal NK/T-cell lymphoma (ENKTCL) and Epstein-Barr virus (EBV)-positive nodal T- and NK-cell lymphoma (NKTCL) are two EBV-associated lymphomas of T/NK cells. These two lymphomas display different clinical, histological and molecular features. However, they share two intriguing characteristics: the association with EBV and a geographical prevalence in East Asia and Latin America. In this review we will discuss the genetic characteristics of EBV in order to understand the possible role of this virus in the oncogenesis of ENKTCL and NKTCL. In addition, the main immunohistological, molecular, cytogenetic and epigenetic differences between ENKTCL and NKTCL will be discussed, as well as EBV differences in latency patterns and other viral molecular characteristics.
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Affiliation(s)
| | - Paula Daniela S. Alves
- Oncovirology Laboratory, Bone Marrow Transplantation Center, Instituto Nacional de Câncer (INCA), Rio de Janeiro, RJ, Brazil
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Zealiyas K, Teshome S, Berhe N, Amogne W, Haile AF, Abate E, Yimer G, Weigel C, Ahmed EH, Abebe T, Baiocchi R. The Burden of Epstein-Barr Virus (EBV) and Its Determinants among Adult HIV-Positive Individuals in Ethiopia. Viruses 2023; 15:1743. [PMID: 37632085 PMCID: PMC10458830 DOI: 10.3390/v15081743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 07/28/2023] [Accepted: 08/07/2023] [Indexed: 08/27/2023] Open
Abstract
Epstein-Barr virus (EBV) is a well-known risk factor for the development of nasopharyngeal carcinoma, Hodgkin's lymphoma (HL), and Non-Hodgkin's lymphoma (NHL). People with HIV infection (PWH) are at increased risk for EBV-associated malignancies such as HL and NHL. Nevertheless, there are limited data on the burden of EBV among this population group in Ethiopia. Hence, this study aimed to determine the burden of EBV infection among adult HIV-positive individuals in Ethiopia and assess the determinants of EBV DNA positivity. We conducted a cross-sectional study at the Tikur Anbessa Specialised Hospital from March 2020 to March 2021. Two hundred and sixty individuals were enrolled in this study, including 179 HIV-positive and 81 HIV-negative individuals. A structured questionnaire was used to capture demographic and individual attributes. In addition, the clinical data of patients were also retrieved from clinical records. EBV viral capsid antigen (VCA) IgG antibody was measured by multiplex flow immunoassay, and EBV DNA levels were tested by quantitative real-time polymerase chain reaction (q-PCR) assays targeting the EBNA-1 open reading frame (ORF). Descriptive statistics were conducted to assess each study variable. A multivariable logistic regression model was applied to evaluate the determinants of EBV infection. Statistical significance was determined at a p-value < 0.05. Two hundred and fifty-three (97.7%) study participants were seropositive for the EBV VCA IgG antibody. Disaggregated by HIV status, 99.4% of HIV-positive and 93.8% of HIV-negative participants were EBV seropositive. In this study, 49.7% of HIV-positive and 24.7% of HIV-negative individuals were EBV DNA positive. PWH had a higher risk of EBV DNA positivity at 3.05 times (AOR: 3.05, 95% CI: 1.40-6.67). Moreover, among PWH, those with an HIV viral load greater than 1000 RNA copies/mL (AOR = 5.81, 95% CI = 1.40, 24.13) had a higher likelihood of EBV DNA positivity. The prevalence of EBV among PWH was significantly higher than among HIV-negative individuals. Higher HIV viral loads in PWH were associated with an increased risk of EBV DNA positivity. Since the increases in the viral load of EBV DNA among PWH could be related to the risk of developing EBV-associated cancers, it is necessary for more research on the role of EBV in EBV-associated cancer in this population group to be carried out.
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Affiliation(s)
- Kidist Zealiyas
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa 1176, Ethiopia; (K.Z.); (N.B.); (A.F.H.)
- Ethiopian Public Health Institute, Addis Ababa 1242, Ethiopia
| | - Seifegebriel Teshome
- Department of Microbiology, Immunology and Parasitology, Addis Ababa University, Addis Ababa 9086, Ethiopia; (S.T.); (T.A.)
| | - Nega Berhe
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa 1176, Ethiopia; (K.Z.); (N.B.); (A.F.H.)
| | - Wondwossen Amogne
- Department of Internal Medicine, College of Health Sciences, Addis Ababa University, Addis Ababa 9086, Ethiopia;
| | - Aklilu Feleke Haile
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa 1176, Ethiopia; (K.Z.); (N.B.); (A.F.H.)
| | - Ebba Abate
- Global One Health Initiative, Addis Ababa 1000, Ethiopia;
| | - Getnet Yimer
- Centre for Innovative Drug Development and Therapeutic Trials for Africa (CDT-Africa), College of Health Sciences, Addis Ababa University, Addis Ababa 9086, Ethiopia;
- Center for Global Genomics and Health Equity, Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Christoph Weigel
- Comprehensive Cancer Center, The James Cancer Hospital and Solove Research Institute, The Ohio State University, Columbus, OH 43210, USA;
- Division of Hematology, Department of Internal Medicine, College of Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Elshafa Hassan Ahmed
- Comprehensive Cancer Center, The James Cancer Hospital and Solove Research Institute, The Ohio State University, Columbus, OH 43210, USA;
| | - Tamrat Abebe
- Department of Microbiology, Immunology and Parasitology, Addis Ababa University, Addis Ababa 9086, Ethiopia; (S.T.); (T.A.)
| | - Robert Baiocchi
- Comprehensive Cancer Center, The James Cancer Hospital and Solove Research Institute, The Ohio State University, Columbus, OH 43210, USA;
- Division of Hematology, Department of Internal Medicine, College of Medicine, The Ohio State University, Columbus, OH 43210, USA
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7
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Wang Y, Rong Y, Yang L, Lu Z. Genetic variability and mutation of Epstein‒Barr virus (EBV)-encoded LMP-1 and BHRF-1 genes in EBV-infected patients: identification of precise targets for development of personalized EBV vaccines. Virus Genes 2023; 59:541-553. [PMID: 37243920 PMCID: PMC10220333 DOI: 10.1007/s11262-023-02006-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 05/08/2023] [Indexed: 05/29/2023]
Abstract
The critical Epstein‒Barr virus (EBV)-encoded latent membrane protein 1 (LMP-1) and BamHI fragment H rightward open reading frame 1 (BHRF-1) genes affect EBV-mediated malignant transformation and virus replication during EBV infection. Therefore, these two genes are considered ideal targets for EBV vaccine development. However, gene mutations in LMP-1 and BHRF-1 in different cohorts may affect the biological functions of EBV, which would seriously hinder development of personalized vaccines for EBV. In the present study, by performing nested polymerase chain reaction (nested PCR) and DNA sequence techniques, we analyzed the nucleotide variability and phylogeny of LMP-1 containing a 30 bp deletion region (del-LMP-1) and BHRF-1 in EBV-infected patients (N = 382) and healthy persons receiving physical examination (N = 98; defined as the control group) in Yunnan Province, China. Three BHRF-1 subtypes were identified in this study: 79V88V, 79L88L, and 79V88L, with mutation frequencies of 58.59%, 24.24%, and 17.17%, respectively. Compared with the control group, the distribution of BHRF-1 subtypes of the three groups showed no significant difference, suggesting that BHRF-1 is highly conserved in EBV-related samples. In addition, a short fragment of del-LMP-1 was found in 133 cases, and the nucleotide variation rate was 87.50% (133/152). For del-LMP-1, a significant distribution in three groups was detected, as characterized by a high mutation rate. In conclusion, our study illustrates gene variability and mutations of EBV-encoded del-LMP-1 and BHRF-1 in clinical samples. Highly mutated LMP-1 might be associated with various types of EBV-related diseases, indicating that BHRF-1 combined with LMP-1 may be used as an ideal target for development of EBV personalized vaccines.
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Affiliation(s)
- Yue Wang
- Forensic Center of Justice, Zhongnan Hospital of Wuhan University, Wuhan, China
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yuan Rong
- Forensic Center of Justice, Zhongnan Hospital of Wuhan University, Wuhan, China
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Lijuan Yang
- Central Lab of the 2Nd, Affiliated Hospital of Kunming Medical University, Kunming, 650101 Yunnan China
| | - Zhiyan Lu
- Forensic Center of Justice, Zhongnan Hospital of Wuhan University, Wuhan, China
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
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8
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López C, Burkhardt B, Chan JKC, Leoncini L, Mbulaiteye SM, Ogwang MD, Orem J, Rochford R, Roschewski M, Siebert R. Burkitt lymphoma. Nat Rev Dis Primers 2022; 8:78. [PMID: 36522349 DOI: 10.1038/s41572-022-00404-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/19/2022] [Indexed: 12/16/2022]
Abstract
Burkitt lymphoma (BL) is an aggressive form of B cell lymphoma that can affect children and adults. The study of BL led to the identification of the first recurrent chromosomal aberration in lymphoma, t(8;14)(q24;q32), and subsequent discovery of the central role of MYC and Epstein-Barr virus (EBV) in tumorigenesis. Most patients with BL are cured with chemotherapy but those with relapsed or refractory disease usually die of lymphoma. Historically, endemic BL, non-endemic sporadic BL and the immunodeficiency-associated BL have been recognized, but differentiation of these epidemiological variants is confounded by the frequency of EBV positivity. Subtyping into EBV+ and EBV- BL might better describe the biological heterogeneity of the disease. Phenotypically resembling germinal centre B cells, all types of BL are characterized by dysregulation of MYC due to enhancer activation via juxtaposition with one of the three immunoglobulin loci. Additional molecular changes commonly affect B cell receptor and sphingosine-1-phosphate signalling, proliferation, survival and SWI-SNF chromatin remodelling. BL is diagnosed on the basis of morphology and high expression of MYC. BL can be effectively treated in children and adolescents with short durations of high dose-intensity multiagent chemotherapy regimens. Adults are more susceptible to toxic effects but are effectively treated with chemotherapy, including modified versions of paediatric regimens. The outcomes in patients with BL are good in high-income countries with low mortality and few late effects, but in low-income and middle-income countries, BL is diagnosed late and is usually treated with less-effective regimens affecting the overall good outcomes in patients with this lymphoma.
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Affiliation(s)
- Cristina López
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany
| | - Birgit Burkhardt
- Non-Hodgkin's Lymphoma Berlin-Frankfurt-Münster (NHL-BFM) Study Center and Paediatric Hematology, Oncology and BMT, University Hospital Muenster, Muenster, Germany
| | - John K C Chan
- Department of Pathology, Queen Elizabeth Hospital, Hong Kong SAR, China
| | - Lorenzo Leoncini
- Section of Pathology, Department of Medical Biotechnology, University of Siena, Siena, Italy
| | - Sam M Mbulaiteye
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, US Department of Health and Human Services, Bethesda, MD, USA
| | | | | | - Rosemary Rochford
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Mark Roschewski
- Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Reiner Siebert
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany.
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9
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Alves P, Larrate M, Garcia-Costa A, Rohan P, Gama BE, Abdelhay E, Delatorre E, Hassan R. Spatial Dispersal of Epstein-Barr Virus in South America Reveals an African American Variant in Brazilian Lymphomas. Viruses 2022; 14:v14081762. [PMID: 36016384 PMCID: PMC9412316 DOI: 10.3390/v14081762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 08/05/2022] [Accepted: 08/10/2022] [Indexed: 11/16/2022] Open
Abstract
Epstein−Barr virus (EBV) is a saliva-borne ɣ-herpesvirus associated with benign and malignant lymphoproliferation. EBV-mediated tumorigenic mechanisms are not fully understood and may be related to viral genetic variations. In this work, we characterize the genetic diversity of EBV from Brazil, assessing 82 samples derived from saliva from asymptomatic carriers (n = 45), biopsies of benign reactive hyperplasia (n = 4), and lymphomas (n = 33). Phylogenetic and phylogeographic analysis of the entire coding region of the LMP-1 was performed. Additionally, type 1/type 2 distinction by the EBNA3C gene and Zp variants were evaluated. Our results revealed a high diversity of EBV in Brazil, with the co-circulation of four main clades, described here as: Mediterranean (40.2%, n = 33), Raji/Argentine (39%, n = 32), B95-8 (6.1%, n = 5), and Asian II (1.2%, n = 1). The Raji/Argentine and Mediterranean clades were the most prevalent in South America (45% and 28%, respectively). The Raji/Argentine clade was associated with polymorphisms I124V/I152L, del30 bp, and ins15 bp (p < 0.0001, to all clades) and with a high haplotype diversity related to EBV type and Zp variants. We found that a Raji/Argentine subclade spread primarily from Brazil and later to other South American countries. Although no LMP1 variant has been directly associated with disease, the Raji/Argentine clade was predominantly clustered with lymphomas (61%) and the Mediterranean clade with non-malignant cases (59%) (p = 0.1). These data highlight the high genetic diversity of EBV circulating in Brazil, calling attention to a Raji-related variant with great recombination potential in Brazilian lymphomas.
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Affiliation(s)
- Paula Alves
- Laboratório de Oncovirologia, Centro de Transplante de Medula Óssea, Instituto Nacional de Câncer “José Alencar Gomes da Silva” (INCA), Ministério da Saúde, Rio de Janeiro 20230-130, Brazil
- Correspondence: (P.A.); (E.D.)
| | - Marcella Larrate
- Laboratório de Oncovirologia, Centro de Transplante de Medula Óssea, Instituto Nacional de Câncer “José Alencar Gomes da Silva” (INCA), Ministério da Saúde, Rio de Janeiro 20230-130, Brazil
| | - Aruanã Garcia-Costa
- Laboratório de Oncovirologia, Centro de Transplante de Medula Óssea, Instituto Nacional de Câncer “José Alencar Gomes da Silva” (INCA), Ministério da Saúde, Rio de Janeiro 20230-130, Brazil
| | - Paulo Rohan
- Laboratório de Oncovirologia, Centro de Transplante de Medula Óssea, Instituto Nacional de Câncer “José Alencar Gomes da Silva” (INCA), Ministério da Saúde, Rio de Janeiro 20230-130, Brazil
| | - Bianca Ervatti Gama
- Laboratório de Oncovirologia, Centro de Transplante de Medula Óssea, Instituto Nacional de Câncer “José Alencar Gomes da Silva” (INCA), Ministério da Saúde, Rio de Janeiro 20230-130, Brazil
| | - Eliana Abdelhay
- Laboratório de Células Tronco, Centro de Transplante de Medula Óssea, Instituto Nacional de Câncer “José Alencar Gomes da Silva” (INCA), Ministério da Saúde, Rio de Janeiro 20230-130, Brazil
| | - Edson Delatorre
- Departamento de Biologia, Centro de Ciências Exatas, Naturais e da Saúde, Universidade Federal do Espírito Santo, Alegre 29500-000, Brazil
- Correspondence: (P.A.); (E.D.)
| | - Rocio Hassan
- Laboratório de Oncovirologia, Centro de Transplante de Medula Óssea, Instituto Nacional de Câncer “José Alencar Gomes da Silva” (INCA), Ministério da Saúde, Rio de Janeiro 20230-130, Brazil
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