1
|
Yan X, Mischel P, Chang H. Extrachromosomal DNA in cancer. Nat Rev Cancer 2024; 24:261-273. [PMID: 38409389 DOI: 10.1038/s41568-024-00669-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/18/2024] [Indexed: 02/28/2024]
Abstract
Extrachromosomal DNA (ecDNA) has recently been recognized as a major contributor to cancer pathogenesis that is identified in most cancer types and is associated with poor outcomes. When it was discovered over 60 years ago, ecDNA was considered to be rare, and its impact on tumour biology was not well understood. The application of modern imaging and computational techniques has yielded powerful new insights into the importance of ecDNA in cancer. The non-chromosomal inheritance of ecDNA during cell division results in high oncogene copy number, intra-tumoural genetic heterogeneity and rapid tumour evolution that contributes to treatment resistance and shorter patient survival. In addition, the circular architecture of ecDNA results in altered patterns of gene regulation that drive elevated oncogene expression, potentially enabling the remodelling of tumour genomes. The generation of clusters of ecDNAs, termed ecDNA hubs, results in interactions between enhancers and promoters in trans, yielding a new paradigm in oncogenic transcription. In this Review, we highlight the rapid advancements in ecDNA research, providing new insights into ecDNA biogenesis, maintenance and transcription and its role in promoting tumour heterogeneity. To conclude, we delve into a set of unanswered questions whose answers will pave the way for the development of ecDNA targeted therapeutic approaches.
Collapse
Affiliation(s)
- Xiaowei Yan
- Department of Dermatology, Stanford University, Stanford, CA, USA
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - Paul Mischel
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA.
| | - Howard Chang
- Department of Dermatology, Stanford University, Stanford, CA, USA.
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA.
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA.
| |
Collapse
|
2
|
Li CL, Yeh SH, Chen PJ. Circulating Virus–Host Chimera DNAs in the Clinical Monitoring of Virus-Related Cancers. Cancers (Basel) 2022; 14:cancers14102531. [PMID: 35626135 PMCID: PMC9139492 DOI: 10.3390/cancers14102531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 05/18/2022] [Accepted: 05/18/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Cell-free tumor DNA (ctDNA), the DNA released into circulation from tumors, is a promising tumor marker with versatile applications. The associations of the amount, somatic mutation frequency, and epigenetic modifications of ctDNA with the tumor burden, tumor behavior, and prognosis have been widely investigated in different types of tumors. However, there are still some challenging issues to be resolved before ctDNA can complement or even replace current serum tumor markers. We propose employing exogenous viral DNA integration that produces unique virus–host chimera DNA (vh-DNA) at junction sites. Cell-free vh-DNA may become a new biomarker because it overcomes background interference detection problems, takes advantage of virus tropism to localize the tumor, and acts as a universal marker for monitoring clonal expansion or tumor loads in tumors related to oncogenic viruses. Abstract The idea of using tumor-specific cell-free DNA (ctDNA) as a tumor biomarker has been widely tested and validated in various types of human cancers and different clinical settings. ctDNA can reflect the presence or size of tumors in a real-time manner and can enable longitudinal monitoring with minimal invasiveness, allowing it to be applied in treatment response assessment and recurrence monitoring for cancer therapies. However, tumor detection by ctDNA remains a great challenge due to the difficulty in enriching ctDNA from a large amount of homologous non-tumor cell-free DNA (cfDNA). Only ctDNA with nonhuman sequences (or rearrangements) can be selected from the background of cfDNA from nontumor DNAs. This is possible for several virus-related cancers, such as hepatitis B virus (HBV)-related HCC or human papillomavirus (HPV)-related cervical or head and neck cancers, which frequently harbor randomly integrated viral DNA. The junction fragments of the integrations, namely virus–host chimera DNA (vh-DNA), can represent the signatures of individual tumors and are released into the blood. Such ctDNA can be enriched by capture with virus-specific probes and therefore exploited as a circulating biomarker to track virus-related cancers in clinical settings. Here, we review virus integrations in virus-related cancers to evaluate the feasibility of vh-DNA as a cell-free tumor marker and update studies on the development of detection and applications. vh-DNA may be a solution to the development of specific markers to manage virus-related cancers in the future.
Collapse
Affiliation(s)
- Chiao-Ling Li
- Graduate Institute of Microbiology, College of Medicine, National Taiwan University, Taipei 100, Taiwan;
| | - Shiou-Hwei Yeh
- Graduate Institute of Microbiology, College of Medicine, National Taiwan University, Taipei 100, Taiwan;
- Center for Genomic Medicine, College of Medicine, National Taiwan University, Taipei 100, Taiwan
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei 100, Taiwan
- Correspondence: (S.-H.Y.); (P.-J.C.)
| | - Pei-Jer Chen
- Center for Genomic Medicine, College of Medicine, National Taiwan University, Taipei 100, Taiwan
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei 100, Taiwan
- Division of Gastroenterology, Department of Internal Medicine, National Taiwan University Hospital, Taipei 100, Taiwan
- Correspondence: (S.-H.Y.); (P.-J.C.)
| |
Collapse
|
3
|
The Pathologic and Genetic Characteristics of Extranodal NK/T-Cell Lymphoma. Life (Basel) 2022; 12:life12010073. [PMID: 35054466 PMCID: PMC8781285 DOI: 10.3390/life12010073] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 01/01/2022] [Accepted: 01/03/2022] [Indexed: 12/14/2022] Open
Abstract
Extranodal NK/T-cell lymphoma is a neoplasm of NK cells or cytotoxic T cells presenting in extranodal sites, most often in the nasal cavity. The typical immunophenotypes are cCD3+, sCD3-, CD4-, CD5-, CD8-, CD16-, and CD56+ with the expression of cytotoxic molecules. Tumor subsets express NK cell receptors, CD95/CD95L, CD30, MYC, and PDL1. Virtually all the tumor cells harbor the EBV genome, which plays a key role in lymphomagenesis as an epigenetic driver. EBV-encoded oncoproteins modulate the host-cell epigenetic machinery, reprogramming the viral and host epigenomes using host epigenetic modifiers. NGS analysis revealed the mutational landscape of ENKTL, predominantly involving the JAK-STAT pathway, epigenetic modifications, the RNA helicase family, the RAS/MAP kinase pathway, and tumor suppressors, which indicate an important role of these pathways and this group of genes in the lymphomagenesis of ENKTL. Recently, three molecular subtypes were proposed, the tumor-suppressor/immune-modulator (TSIM), MGA-BRDT (MB), and HDAC9-EP300-ARID1A (HEA) subtypes, and they are well-correlated with the cell of origin, EBV pattern, genomic alterations, and clinical outcomes. A future investigation into the function and interaction of discovered genes would be very helpful for better understanding the molecular pathogenesis of ENKTL and establishing better treatment strategies.
Collapse
|
4
|
Janjetovic S, Hinke J, Balachandran S, Akyüz N, Behrmann P, Bokemeyer C, Dierlamm J, Murga Penas EM. Non-Random Pattern of Integration for Epstein-Barr Virus with Preference for Gene-Poor Genomic Chromosomal Regions into the Genome of Burkitt Lymphoma Cell Lines. Viruses 2022; 14:v14010086. [PMID: 35062290 PMCID: PMC8781420 DOI: 10.3390/v14010086] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 12/25/2021] [Accepted: 12/28/2021] [Indexed: 01/27/2023] Open
Abstract
Background: Epstein-Barr virus (EBV) is an oncogenic virus found in about 95% of endemic Burkitt lymphoma (BL) cases. In latently infected cells, EBV DNA is mostly maintained in episomal form, but it can also be integrated into the host genome, or both forms can coexist in the infected cells. Methods: In this study, we mapped the chromosomal integration sites of EBV (EBV-IS) into the genome of 21 EBV+ BL cell lines (BL-CL) using metaphase fluorescence in situ hybridization (FISH). The data were used to investigate the EBV-IS distribution pattern in BL-CL, its relation to the genome instability, and to assess its association to common fragile sites and episomes. Results: We detected a total of 459 EBV-IS integrated into multiple genome localizations with a preference for gene-poor chromosomes. We did not observe any preferential affinity of EBV to integrate into common and rare fragile sites or enrichment of EBV-IS at the chromosomal breakpoints of the BL-CL analyzed here, as other DNA viruses do. Conclusions: We identified a non-random integration pattern into 13 cytobands, of which eight overlap with the EBV-IS in EBV-transformed lymphoblastoid cell lines and with a preference for gene- and CpGs-poor G-positive cytobands. Moreover, it has been demonstrated that the episomal form of EBV interacts in a non-random manner with gene-poor and AT-rich regions in EBV+ cell lines, which may explain the observed affinity for G-positive cytobands in the EBV integration process. Our results provide new insights into the patterns of EBV integration in BL-CL at the chromosomal level, revealing an unexpected connection between the episomal and integrated forms of EBV.
Collapse
Affiliation(s)
- Snjezana Janjetovic
- Department of Oncology, Hematology and Bone Marrow Transplantation with Section Pneumology, University Clinic Hamburg-Eppendorf, 20251 Hamburg, Germany; (S.J.); (J.H.); (N.A.); (P.B.); (C.B.)
- Clinic of Hematology and Stem Cell Transplantation, HELIOS Clinic Berlin-Buch, 13125 Berlin, Germany
| | - Juliane Hinke
- Department of Oncology, Hematology and Bone Marrow Transplantation with Section Pneumology, University Clinic Hamburg-Eppendorf, 20251 Hamburg, Germany; (S.J.); (J.H.); (N.A.); (P.B.); (C.B.)
- Department for Psychiatry, Albertinen Hospital, 22459 Hamburg, Germany
| | - Saranya Balachandran
- Institute of Human Genetics, Christian-Albrechts-University of Kiel and University Hospital Schleswig-Holstein, Campus Kiel, 24118 Kiel, Germany;
| | - Nuray Akyüz
- Department of Oncology, Hematology and Bone Marrow Transplantation with Section Pneumology, University Clinic Hamburg-Eppendorf, 20251 Hamburg, Germany; (S.J.); (J.H.); (N.A.); (P.B.); (C.B.)
| | - Petra Behrmann
- Department of Oncology, Hematology and Bone Marrow Transplantation with Section Pneumology, University Clinic Hamburg-Eppendorf, 20251 Hamburg, Germany; (S.J.); (J.H.); (N.A.); (P.B.); (C.B.)
| | - Carsten Bokemeyer
- Department of Oncology, Hematology and Bone Marrow Transplantation with Section Pneumology, University Clinic Hamburg-Eppendorf, 20251 Hamburg, Germany; (S.J.); (J.H.); (N.A.); (P.B.); (C.B.)
| | - Judith Dierlamm
- Department of Oncology, Hematology and Bone Marrow Transplantation with Section Pneumology, University Clinic Hamburg-Eppendorf, 20251 Hamburg, Germany; (S.J.); (J.H.); (N.A.); (P.B.); (C.B.)
- Correspondence: (J.D.); (E.M.M.P.); Tel.: +49-451-500-50438 (E.M.M.P.)
| | - Eva Maria Murga Penas
- Department of Oncology, Hematology and Bone Marrow Transplantation with Section Pneumology, University Clinic Hamburg-Eppendorf, 20251 Hamburg, Germany; (S.J.); (J.H.); (N.A.); (P.B.); (C.B.)
- Institute of Human Genetics, Christian-Albrechts-University of Kiel and University Hospital Schleswig-Holstein, Campus Kiel, 24118 Kiel, Germany;
- Correspondence: (J.D.); (E.M.M.P.); Tel.: +49-451-500-50438 (E.M.M.P.)
| |
Collapse
|
5
|
Genomic Landscapes of Epstein-Barr Virus in Pulmonary Lymphoepithelioma-like Carcinoma. J Virol 2021; 96:e0169321. [PMID: 34908446 DOI: 10.1128/jvi.01693-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Epstein-Barr virus (EBV) infection is associated with multiple malignancies, including pulmonary lymphoepithelioma-like carcinoma (pLELC), a particular subtype of primary lung cancer. However, the genomic characteristics of EBV related to pLELC remain unclear. Here, we obtained the whole-genome dataset of EBV isolated from 78 pLELC patients and 37 healthy controls using EBV-captured sequencing. Compared to the reference genome (NC_007605), a total of 3995 variations were detected across pLELC-derived EBV sequences, with the mutational hotspots located in latent genes. Combined with 180 published EBV sequences derived from healthy people in Southern China, we performed a genome-wide association study and identified 32 variations significantly related to pLELC (p < 2.56×10-05, Bonferroni correction), with the top signal of SNP coordinate T7327C (OR = 1.22, p = 2.39×10-15) locating in the origin of plasmid replication (OriP). The results of population structure analysis of EBV isolates in East Asian showed the EBV strains derived from pLELC were more similar to those from nasopharyngeal carcinoma (NPC) than other EBV-associated diseases. In addition, typical latency type-II infection were recognized for EBV of pLELC at both transcription and methylation levels. Taken together, we defined the global view of EBV genomic profiles in pLELC patients for the first time, providing new insights to deepening our understanding of this rare EBV-associated primary lung carcinoma. Importance Pulmonary lymphoepithelioma-like carcinoma (pLELC) is a rarely distinctive subtype of primary lung cancer closely associated with Epstein-Barr virus (EBV) infection. Here, we gave the first overview of pLELC-derived EBV at the level of genome, methylation and transcription. We obtained the EBV sequences dataset from 78 primary pLELC patients, and revealed the sequences diversity across EBV genome and detected variability in known immune epitopes. Genome-wide association analysis combining 217 healthy controls identifies significant variations related to the risk of pLELC. Meanwhile, we characterized the integration landscapes of EBV at the genome-wide level. These results provided new insight for understanding EBV's role in pLELC tumorigenesis.
Collapse
|
6
|
Cangemi M, Zanussi S, Rampazzo E, Bidoli E, Giunco S, Tedeschi R, Pratesi C, Martorelli D, Casarotto M, Martellotta F, Schioppa O, Serraino D, Steffan A, De Rossi A, Dolcetti R, Vaccher E. Biological Predictors of De Novo Tumors in Solid Organ Transplanted Patients During Oncological Surveillance: Potential Role of Circulating TERT mRNA. Front Oncol 2021; 11:772348. [PMID: 34746013 PMCID: PMC8567137 DOI: 10.3389/fonc.2021.772348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 09/30/2021] [Indexed: 11/13/2022] Open
Abstract
Background De novo tumors are a major cause of morbidity and mortality after long-term solid organ transplantation. Chronic immunosuppression strongly affects solid organ transplanted (SOT) patients' immune system by promoting immune evasion strategies and reactivations of viruses with oncogenic potential, ultimately leading to cancer onset. In this scenario, an oncological Surveillance Protocol integrated with biobanking of peripheral blood samples and evaluation of immunovirological and molecular parameters was activated for SOT patients at CRO-IRCCS Aviano, with the aim of identifying suitable biomarkers of cancer development. Methods An exploratory longitudinal study was designed based on two serial peripheral blood samples collected at least three months apart. Forty nine SOT patients were selected and stratified by tumor onset during follow-up. Spontaneous T-cell responses to EBV, CMV and tumor associated antigens, EBV-DNA and CMV-DNA loads, and circulating TERT mRNA levels were investigated. Results Significantly higher levels of circulating TERT mRNA were observed 3.5-23.5 months before and close to the diagnosis of cancer as compared to tumor-free patients. Plasmatic TERT mRNA levels >97.73 copies/mL at baseline were significantly associated with the risk of developing de novo tumors (HR=4.0, 95%C.I. = 1.4-11.5, p=0.01). In particular, the risk significantly increased by 4% with every ten-unit increment in TERT mRNA (HR=1.04, 95%C.I. = 1.01-1.07, p=0.01). Conclusions Although obtained in an exploratory study, our data support the importance of identifying early biomarkers of tumor onset in SOT patients useful to modulate the pace of surveillance visits.
Collapse
Affiliation(s)
- Michela Cangemi
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Stefania Zanussi
- Immunopathology and Cancer Biomarkers, CRO Aviano, National Cancer Institute, IRCCS, Aviano, Italy
| | - Enrica Rampazzo
- Department of Surgery, Oncology and Gastroenterology, Section of Oncology and Immunology, University of Padova, Padova, Italy
| | - Ettore Bidoli
- Cancer Epidemiology Unit, CRO Aviano, National Cancer Institute, IRCCS, Aviano, Italy
| | - Silvia Giunco
- Department of Surgery, Oncology and Gastroenterology, Section of Oncology and Immunology, University of Padova, Padova, Italy.,Immunology and Diagnostic Molecular Oncology Unit, Veneto Institute of Oncology (IOV) - IRCCS, Padova, Italy
| | - Rosamaria Tedeschi
- Microbiology and Virology Unit, "S. Maria degli Angeli" Hospital, Pordenone, Italy
| | - Chiara Pratesi
- Clinical Pathology, "S. Maria degli Angeli" Hospital, Pordenone, Italy
| | - Debora Martorelli
- Immunopathology and Cancer Biomarkers, CRO Aviano, National Cancer Institute, IRCCS, Aviano, Italy
| | - Mariateresa Casarotto
- Immunopathology and Cancer Biomarkers, CRO Aviano, National Cancer Institute, IRCCS, Aviano, Italy
| | - Ferdinando Martellotta
- Division of Medical Oncology A, Centro di Riferimento Oncologico (CRO) Aviano, National Cancer Institute, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Aviano, Italy
| | - Ornella Schioppa
- Division of Medical Oncology A, Centro di Riferimento Oncologico (CRO) Aviano, National Cancer Institute, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Aviano, Italy
| | - Diego Serraino
- Cancer Epidemiology Unit, CRO Aviano, National Cancer Institute, IRCCS, Aviano, Italy
| | - Agostino Steffan
- Immunopathology and Cancer Biomarkers, CRO Aviano, National Cancer Institute, IRCCS, Aviano, Italy
| | - Anita De Rossi
- Department of Surgery, Oncology and Gastroenterology, Section of Oncology and Immunology, University of Padova, Padova, Italy.,Immunology and Diagnostic Molecular Oncology Unit, Veneto Institute of Oncology (IOV) - IRCCS, Padova, Italy
| | - Riccardo Dolcetti
- Centre for Cancer Immunotherapy, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC, Australia.,Department of Microbiology and Immunology, The University of Melbourne, Melbourne, VIC, Australia.,Faculty of Medicine, The University of Queensland Diamantina Institute, Brisbane, QLD, Australia
| | - Emanuela Vaccher
- Division of Medical Oncology A, Centro di Riferimento Oncologico (CRO) Aviano, National Cancer Institute, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Aviano, Italy
| |
Collapse
|
7
|
Glass MC, Smith JM, Cheng HH, Delany ME. Marek's Disease Virus Telomeric Integration Profiles of Neoplastic Host Tissues Reveal Unbiased Chromosomal Selection and Loss of Cellular Diversity during Tumorigenesis. Genes (Basel) 2021; 12:1630. [PMID: 34681024 PMCID: PMC8536068 DOI: 10.3390/genes12101630] [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: 09/19/2021] [Revised: 10/14/2021] [Accepted: 10/14/2021] [Indexed: 11/17/2022] Open
Abstract
The avian α-herpesvirus known as Marek's disease virus (MDV) linearly integrates its genomic DNA into host telomeres during infection. The resulting disease, Marek's disease (MD), is characterized by virally-induced lymphomas with high mortality. The temporal dynamics of MDV-positive (MDV+) transformed cells and expansion of MD lymphomas remain targets for further understanding. It also remains to be determined whether specific host chromosomal sites of MDV telomere integration confer an advantage to MDV-transformed cells during tumorigenesis. We applied MDV-specific fluorescence in situ hybridization (MDV FISH) to investigate virus-host cytogenomic interactions within and among a total of 37 gonad lymphomas and neoplastic splenic samples in birds infected with virulent MDV. We also determined single-cell, chromosome-specific MDV integration profiles within and among transformed tissue samples, including multiple samples from the same bird. Most mitotically-dividing cells within neoplastic samples had the cytogenomic phenotype of 'MDV telomere-integrated only', and tissue-specific, temporal changes in phenotype frequencies were detected. Transformed cell populations composing gonad lymphomas exhibited significantly lower diversity, in terms of heterogeneity of MDV integration profiles, at the latest stages of tumorigenesis (>50 days post-infection (dpi)). We further report high interindividual and lower intraindividual variation in MDV integration profiles of lymphoma cells. There was no evidence of integration hotspots into a specific host chromosome(s). Collectively, our data suggests that very few transformed MDV+ T cell populations present earlier in MDV-induced lymphomas (32-50 dpi), survive, and expand to become the dominant clonal population in more advanced MD lymphomas (51-62 dpi) and establish metastatic lymphomas.
Collapse
Affiliation(s)
- Marla C. Glass
- Department of Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Justin M. Smith
- Department of Animal Science, University of California Davis, Davis, CA 95616, USA; (J.M.S.); (M.E.D.)
| | - Hans H. Cheng
- Avian Disease and Oncology Laboratory, United States Department of Agriculture, Agricultural Research Service, East Lansing, MI 48823, USA;
| | - Mary E. Delany
- Department of Animal Science, University of California Davis, Davis, CA 95616, USA; (J.M.S.); (M.E.D.)
| |
Collapse
|
8
|
Kellogg C, Kouznetsova VL, Tsigelny IF. Implications of viral infection in cancer development. Biochim Biophys Acta Rev Cancer 2021; 1876:188622. [PMID: 34478803 DOI: 10.1016/j.bbcan.2021.188622] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 08/27/2021] [Accepted: 08/28/2021] [Indexed: 12/12/2022]
Abstract
Since the identification of the first human oncogenic virus in 1964, viruses have been studied for their potential role in aiding the development of cancer. Through the modulation of cellular pathways associated with proliferation, immortalization, and inflammation, viral proteins can mimic the effect of driver mutations and contribute to transformation. Aside from the modulation of signaling pathways, the insertion of viral DNA into the host genome and the deregulation of cellular miRNAs represent two additional mechanisms implicated in viral oncogenesis. In this review, we will discuss the role of twelve different viruses on cancer development and how these viruses utilize the abovementioned mechanisms to influence oncogenesis. The identification of specific mechanisms behind viral transformation of human cells could further elucidate the process behind cancer development.
Collapse
Affiliation(s)
- Caroline Kellogg
- REHS Program, San Diego Supercomputer Center, University of California, San Diego, CA, USA
| | - Valentina L Kouznetsova
- San Diego Supercomputer Center, University of California, San Diego, CA, USA; BiAna San Diego, CA, USA
| | - Igor F Tsigelny
- San Diego Supercomputer Center, University of California, San Diego, CA, USA; Department of Neurosciences, University of California, San Diego, CA, USA; BiAna San Diego, CA, USA.
| |
Collapse
|
9
|
Post Transplant Lymphoproliferative Disorder. Indian J Hematol Blood Transfus 2020; 36:229-237. [PMID: 32425371 DOI: 10.1007/s12288-019-01182-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Accepted: 09/05/2019] [Indexed: 12/12/2022] Open
Abstract
Posttransplant lymphoproliferative disorder is an extremely fatal complication arising in transplant recipients as a side effect of immunosuppression. PTLDs are seen after both solid organ and hematopoietic stem cell transplants though the incidence is much higher in the former. Primary Epstein-Barr virus (EBV) infection or reactivation due to a state of immune dysregulation along with intensity of immunosuppression used are of paramount importance in pathogenesis of PTLD. EBV associated PTLDs occur early in the post transplant period whereas late onset lymphomas are usually EBV negative. The uncontrolled B cell proliferation can create a spectrum of histological patterns from nondestructive lesions to destructive polymorphic or more aggressive monomorphic PTLDs. Early detection of seropositivity by serial monitoring in the recipient can prevent PTLD development by starting pre-emptive therapy. The mainstay treatment in established cases remains reduction of immunosuppression. Chemotherapeutic and immunomodulatory agents are added sequentially based on the type of PTLD and based on its response to initial therapy. Despite various treatment options available, the morbidity remains high and achieving state of disease remission without causing graft rejection can be quite challenging. Hence, a better understanding in pathobiology of EBV+ versus EBV- PTLDS may help prevent lymphomagenesis in transplant recipients.
Collapse
|
10
|
Chakravorty S, Yan B, Wang C, Wang L, Quaid JT, Lin CF, Briggs SD, Majumder J, Canaria DA, Chauss D, Chopra G, Olson MR, Zhao B, Afzali B, Kazemian M. Integrated Pan-Cancer Map of EBV-Associated Neoplasms Reveals Functional Host-Virus Interactions. Cancer Res 2019; 79:6010-6023. [PMID: 31481499 DOI: 10.1158/0008-5472.can-19-0615] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 06/24/2019] [Accepted: 08/27/2019] [Indexed: 12/20/2022]
Abstract
Epstein-Barr virus (EBV) is a complex oncogenic symbiont. The molecular mechanisms governing EBV carcinogenesis remain elusive and the functional interactions between virus and host cells are incompletely defined. Here we present a comprehensive map of the host cell-pathogen interactome in EBV-associated cancers. We systematically analyzed RNA sequencing from >1,000 patients with 15 different cancer types, comparing virus and host factors of EBV+ to EBV- tissues. EBV preferentially integrated at highly accessible regions of the cancer genome, with significant enrichment in super-enhancer architecture. Twelve EBV transcripts, including LMP1 and LMP2, correlated inversely with EBV reactivation signature. Overexpression of these genes significantly suppressed viral reactivation, consistent with a "virostatic" function. In cancer samples, hundreds of novel frequent missense and nonsense variations in virostatic genes were identified, and variant genes failed to regulate their viral and cellular targets in cancer. For example, one-third of patients with EBV+ NK/T-cell lymphoma carried two novel nonsense variants (Q322X, G342X) of LMP1 and both variant proteins failed to restrict viral reactivation, confirming loss of virostatic function. Host cell transcriptional changes in response to EBV infection classified tumors into two molecular subtypes based on patterns of IFN signature genes and immune checkpoint markers, such as PD-L1 and IDO1. Overall, these findings uncover novel points of interaction between a common oncovirus and the human genome and identify novel regulatory nodes and druggable targets for individualized EBV and cancer-specific therapies. SIGNIFICANCE: This study provides a comprehensive map of the host cell-pathogen interactome in EBV+ malignancies.See related commentary by Mbulaiteye and Prokunina-Olsson, p. 5917.
Collapse
Affiliation(s)
| | - Bingyu Yan
- Department of Biochemistry, Purdue University, West Lafayette, Indiana
| | - Chong Wang
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Luopin Wang
- Department of Computer Science, Purdue University, West Lafayette, Indiana
| | | | - Chin Fang Lin
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, Indiana
| | - Scott D Briggs
- Department of Biochemistry, Purdue University, West Lafayette, Indiana
| | - Joydeb Majumder
- Department of Chemistry, Purdue University, West Lafayette, Indiana
| | - D Alejandro Canaria
- Department of Biological Science, Purdue University, West Lafayette, Indiana
| | - Daniel Chauss
- Immunoregulation Section, Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, Maryland
| | - Gaurav Chopra
- Department of Chemistry, Purdue University, West Lafayette, Indiana
| | - Matthew R Olson
- Department of Biological Science, Purdue University, West Lafayette, Indiana
| | - Bo Zhao
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Behdad Afzali
- Immunoregulation Section, Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, Maryland
| | - Majid Kazemian
- Department of Biochemistry, Purdue University, West Lafayette, Indiana. .,Department of Computer Science, Purdue University, West Lafayette, Indiana
| |
Collapse
|
11
|
Xu M, Zhang WL, Zhu Q, Yao YY, Feng QS, Zhang Z, Peng RJ, Jia WH, He GP, Feng L, Zeng ZL, Luo B, Xu RH, Zeng MS, Zhao WL, Chen SJ, Zeng YX, Jiao Y, Zeng YX, Jiao Y. Genome-wide profiling of Epstein-Barr virus integration by targeted sequencing in Epstein-Barr virus associated malignancies. Theranostics 2019; 9:1115-1124. [PMID: 30867819 PMCID: PMC6401403 DOI: 10.7150/thno.29622] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 01/18/2019] [Indexed: 12/13/2022] Open
Abstract
Rationale: Epstein-Barr virus (EBV) is associated with multiple malignancies with expression of viral oncogenic proteins and chronic inflammation as major mechanisms contributing to tumor development. A less well-studied mechanism is the integration of EBV into the human genome possibly at sites which may disrupt gene expression or genome stability. Methods: We sequenced tumor DNA to profile the EBV sequences by hybridization-based enrichment. Bioinformatic analysis was used to detect the breakpoints of EBV integrations in the genome of cancer cells. Results: We identified 197 breakpoints in nasopharyngeal carcinomas and other EBV-associated malignancies. EBV integrations were enriched at vulnerable regions of the human genome and were close to tumor suppressor and inflammation-related genes. We found that EBV integrations into the introns could decrease the expression of the inflammation-related genes, TNFAIP3, PARK2, and CDK15, in NPC tumors. In the EBV genome, the breakpoints were frequently at oriP or terminal repeats. These breakpoints were surrounded by microhomology sequences, consistent with a mechanism for integration involving viral genome replication and microhomology-mediated recombination. Conclusion: Our finding provides insight into the potential of EBV integration as an additional mechanism mediating tumorigenesis in EBV associated malignancies.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Yi-Xin Zeng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China.,State Key Lab of Molecular Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College; Collaborative Innovation Center for Cancer Medicine, Beijing, China
| | - Yuchen Jiao
- State Key Lab of Molecular Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College; Collaborative Innovation Center for Cancer Medicine, Beijing, China
| |
Collapse
|
12
|
Maronpot RR, Nyska A, Foreman JE, Ramot Y. The legacy of the F344 rat as a cancer bioassay model (a retrospective summary of three common F344 rat neoplasms). Crit Rev Toxicol 2016; 46:641-75. [PMID: 27278595 PMCID: PMC5020328 DOI: 10.1080/10408444.2016.1174669] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The Fischer 344 (F344) rat was used by the National Toxicology Program (NTP) for over 5 decades for toxicity and carcinogenicity studies. However, in 2006, the NTP decided to switch to a different rat stock due largely to high background control incidences of Leydig cell tumors (LCTs) and mononuclear cell leukemia (MNCL), also known as large granular lymphocytic (LGL) leukemia. In the current review, we aim (1) to provide a summary of NTP bioassays with treatment-associated effects involving MNCL and LCTs in addition to male F344-specific tunica vaginalis mesothelioma (TVM); (2) to describe important pathobiological differences between these F344 rat tumor responses and similar target tissue-tumor response in humans; and (3) to present the NTP reasons for switching away from the F344 rat. We show that due to the highly variable background incidence of F344 MNCL, more reliance on historical control data than is usual for most tumor responses is warranted to evaluate potential effect of any chemical treatment in this rat strain. The high spontaneous incidence of LCTs in the testes of male F344 rats has made this tumor endpoint of little practical use in identifying potential testicular carcinogenic responses. TVM responses in F344 rats have a biological plausible relationship to LCTs unlike TVM in humans. Given their high spontaneous background incidence and species-specific biology, we contend that MNCL and LCT, along with TVM responses, in F344 rat carcinogenicity studies are inappropriate tumor types for human health risk assessment and lack relevance in predicting human carcinogenicity.
Collapse
Affiliation(s)
| | - Abraham Nyska
- b Sackler School of Medicine, Tel Aviv University, and Consultant in Toxicologic Pathology , Timrat , Israel
| | | | - Yuval Ramot
- d Hadassah-Hebrew University Medical Center , Jerusalem , Israel
| |
Collapse
|
13
|
Abstract
Post-transplant lymphoproliferative disorders (PTLDs) are a group of conditions that involve uncontrolled proliferation of lymphoid cells as a consequence of extrinsic immunosuppression after organ or haematopoietic stem cell transplant. PTLDs show some similarities to classic lymphomas in the non-immunosuppressed general population. The oncogenic Epstein-Barr virus (EBV) is a key pathogenic driver in many early-onset cases, through multiple mechanisms. The incidence of PTLD varies with the type of transplant; a clear distinction should therefore be made between the conditions after solid organ transplant and after haematopoietic stem cell transplant. Recipient EBV seronegativity and the intensity of immunosuppression are among key risk factors. Symptoms and signs depend on the localization of the lymphoid masses. Diagnosis requires histopathology, although imaging techniques can provide additional supportive evidence. Pre-emptive intervention based on monitoring EBV levels in blood has emerged as the preferred strategy for PTLD prevention. Treatment of established disease includes reduction of immunosuppression and/or administration of rituximab (a B cell-specific antibody against CD20), chemotherapy and EBV-specific cytotoxic T cells. Despite these strategies, the mortality and morbidity remains considerable. Patient outcome is influenced by the severity of presentation, treatment-related complications and risk of allograft loss. New innovative treatment options hold promise for changing the outlook in the future.
Collapse
|
14
|
Choi K, Ju H, Ko YH. Copy number analysis in EBV-positive nodal peripheral T cell lymphoma, unspecified. Methods Mol Biol 2013; 973:165-174. [PMID: 23412789 DOI: 10.1007/978-1-62703-281-0_10] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Copy number alteration was investigated in three cases of EBV + nodal peripheral T cell lymphoma of cytotoxic phenotype using Agilent array comparative genomic hybridization platform. While no recurrent abnormality among three cases was identified, genomic abnormalities involving 9p23.3, 16p13.3, and 7q34 were overlapped with changes reported in other type of NK or T cell lymphomas previously. Chromosomal region 9p23.3 contains CDKN2A and CDKN2B which are frequently mutated or deleted in various types of cancer and may be a target to find genes associated with the pathogenesis of EBV-positive nodal peripheral T cell lymphoma.
Collapse
Affiliation(s)
- Kyusam Choi
- Samsung Biomedical Research Institute, Samsung Medical Center, Seoul, Korea
| | | | | |
Collapse
|
15
|
Nickles D, Madireddy L, Yang S, Khankhanian P, Lincoln S, Hauser SL, Oksenberg JR, Baranzini SE. In depth comparison of an individual's DNA and its lymphoblastoid cell line using whole genome sequencing. BMC Genomics 2012; 13:477. [PMID: 22974163 PMCID: PMC3473256 DOI: 10.1186/1471-2164-13-477] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Accepted: 09/05/2012] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND A detailed analysis of whole genomes can be now achieved with next generation sequencing. Epstein Barr Virus (EBV) transformation is a widely used strategy in clinical research to obtain an unlimited source of a subject's DNA. Although the mechanism of transformation and immortalization by EBV is relatively well known at the transcriptional and proteomic level, the genetic consequences of EBV transformation are less well understood. A detailed analysis of the genetic alterations introduced by EBV transformation is highly relevant, as it will inform on the usefulness and limitations of this approach. RESULTS We used whole genome sequencing to assess the genomic signature of a low-passage lymphoblastoid cell line (LCL). Specifically, we sequenced the full genome (40X) of an individual using DNA purified from fresh whole blood as well as DNA from his LCL. A total of 217.33 Gb of sequence were generated from the cell line and 238.95 Gb from the normal genomic DNA. We determined with high confidence that 99.2% of the genomes were identical, with no reproducible changes in structural variation (chromosomal rearrangements and copy number variations) or insertion/deletion polymorphisms (indels). CONCLUSIONS Our results suggest that, at this level of resolution, the LCL is genetically indistinguishable from its genomic counterpart and therefore their use in clinical research is not likely to introduce a significant bias.
Collapse
Affiliation(s)
- Dorothee Nickles
- Department of Neurology, University of California San Francisco, San Francisco, CA 94143-0435, USA
| | | | | | | | | | | | | | | |
Collapse
|
16
|
Lui VWY, Yau DMS, Cheung CSF, Wong SCC, Chan AKC, Zhou Q, Wong EYL, Lau CPY, Lam EKY, Hui EP, Hong B, Hui CWC, Chan ASK, Ng PKS, Ng YK, Lo KW, Tsang CM, Tsui SKW, Tsao SW, Chan ATC. FGF8b oncogene mediates proliferation and invasion of Epstein–Barr virus-associated nasopharyngeal carcinoma cells: implication for viral-mediated FGF8b upregulation. Oncogene 2010; 30:1518-30. [DOI: 10.1038/onc.2010.529] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
|
17
|
Reisinger J, Rumpler S, Lion T, Ambros PF. Visualization of episomal and integrated Epstein-Barr virus DNA by fiber fluorescencein situ hybridization. Int J Cancer 2006; 118:1603-8. [PMID: 16217752 DOI: 10.1002/ijc.21498] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
For many Epstein-Barr virus (EBV)-associated malignancies, it is still a matter of controversy whether infected cells harbor episomal or chromosomally integrated EBV genomes or both. It is well established that the expression of EBV genes per se carries oncogenic potential, but the discrimination between episomal and integrated forms is of great relevance because integration events can contribute to the oncogenic properties of EBV, whereas host cells that exclusively harbor viral episomes may not carry the risks mediated by chromosomal integration. This notion prompted us to establish a reliable technique that not only allows to unequivocally discriminate episomal from integrated EBV DNA, but also provides detailed insights into the genomic organization of the virus. Here, we show that dynamic molecular combing of host cell DNA combined with fluorescence in situ hybridization (FISH) using EBV-specific DNA probes facilitate unambiguous discrimination of episomal from integrated viral DNA. Furthermore, the detection of highly elongated internal repeat 1 (IR1) sequences provides evidence that this method permits detection of major genomic alterations within the EBV genome. Thus, fiber FISH may also provide valuable insights into the genomic organization of viral genomes other than EBV.
Collapse
Affiliation(s)
- Jürgen Reisinger
- Children's Cancer Research Institute, St. Anna Kinderspital, Kinderspitalgasse 6, A-1090 Vienna, Austria
| | | | | | | |
Collapse
|
18
|
Luderer R, Kok M, Niesters HGM, Schuurman R, de Weerdt O, Thijsen SFT. Real-time Epstein-Barr virus PCR for the diagnosis of primary EBV infections and EBV reactivation. ACTA ACUST UNITED AC 2006; 9:195-200. [PMID: 16392898 DOI: 10.1007/bf03260091] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
BACKGROUND The serological diagnosis of primary Epstein-Barr virus (EBV) infections is often difficult, whereas the relevance of elevated immunoglobulin G (IgG) antibodies against early antigen (EA) for the diagnosis of EBV reactivation has increasingly become a matter of dispute. Recently, EBV PCR has been added as a diagnostic tool. Positive EBV PCR has been demonstrated in the serum of patients with primary EBV infections and EBV reactivation. OBJECTIVES To compare classical serological diagnosis of primary EBV infection and EBV reactivation with real-time EBV PCR. STUDY DESIGN Sera from 45 patients were selected with detectable immunoglobulin M (IgM) antibodies against EBV viral capsid antigen (VCA), and 62 sera were selected with a reactivation profile. A real-time EBV PCR was performed with DNA extracted from these sera. RESULTS Based on serological data, the diagnosis of primary EBV infection was established for 24 of the 45 IgM VCA-positive patients. By performing PCR, seven extra cases of primary infection were diagnosed for which no heterophilic antibodies could be detected. In five cases of primary infection, no EBV DNA could be detected by PCR. Only in two of the 62 sera with a reactivation seroprofile could EBV DNA be detected. CONCLUSIONS Based on these data, we suggest that for the diagnosis of primary infections, EBV PCR could lead to an increase of >16% in the number of positive diagnoses by confirming a positive IgM VCA in the absence of heterophilic antibodies. Furthermore, EBV PCR is positive in only 3% of sera with elevated antibodies against EA, raising doubt as to the utility of EA titers for diagnosing EBV reactivation.
Collapse
Affiliation(s)
- Rianne Luderer
- Unit Molecular Diagnostics, Diakonessenhuis Utrecht, Utrecht, The Netherlands.
| | | | | | | | | | | |
Collapse
|
19
|
Luderer R, Kok M, Niesters HGM, Schuurman R, de Weerdt O, Thijsen SFT. Real-time Epstein-Barr virus PCR for the diagnosis of primary EBV infections and EBV reactivation. MOLECULAR DIAGNOSIS : A JOURNAL DEVOTED TO THE UNDERSTANDING OF HUMAN DISEASE THROUGH THE CLINICAL APPLICATION OF MOLECULAR BIOLOGY 2006. [PMID: 16392898 DOI: 10.2165/00066982-200509040-00005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
BACKGROUND The serological diagnosis of primary Epstein-Barr virus (EBV) infections is often difficult, whereas the relevance of elevated immunoglobulin G (IgG) antibodies against early antigen (EA) for the diagnosis of EBV reactivation has increasingly become a matter of dispute. Recently, EBV PCR has been added as a diagnostic tool. Positive EBV PCR has been demonstrated in the serum of patients with primary EBV infections and EBV reactivation. OBJECTIVES To compare classical serological diagnosis of primary EBV infection and EBV reactivation with real-time EBV PCR. STUDY DESIGN Sera from 45 patients were selected with detectable immunoglobulin M (IgM) antibodies against EBV viral capsid antigen (VCA), and 62 sera were selected with a reactivation profile. A real-time EBV PCR was performed with DNA extracted from these sera. RESULTS Based on serological data, the diagnosis of primary EBV infection was established for 24 of the 45 IgM VCA-positive patients. By performing PCR, seven extra cases of primary infection were diagnosed for which no heterophilic antibodies could be detected. In five cases of primary infection, no EBV DNA could be detected by PCR. Only in two of the 62 sera with a reactivation seroprofile could EBV DNA be detected. CONCLUSIONS Based on these data, we suggest that for the diagnosis of primary infections, EBV PCR could lead to an increase of >16% in the number of positive diagnoses by confirming a positive IgM VCA in the absence of heterophilic antibodies. Furthermore, EBV PCR is positive in only 3% of sera with elevated antibodies against EA, raising doubt as to the utility of EA titers for diagnosing EBV reactivation.
Collapse
Affiliation(s)
- Rianne Luderer
- Unit Molecular Diagnostics, Diakonessenhuis Utrecht, Utrecht, The Netherlands.
| | | | | | | | | | | |
Collapse
|
20
|
|
21
|
Leenman EE, Panzer-Grümayer RE, Fischer S, Leitch HA, Horsman DE, Lion T, Gadner H, Ambros PF, Lestou VS. Rapid determination of Epstein-Barr virus latent or lytic infection in single human cells using in situ hybridization. Mod Pathol 2004; 17:1564-72. [PMID: 15545957 DOI: 10.1038/modpathol.3800228] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Epstein-Barr (EBV) virus is associated with malignancies such as lymphoma and carcinoma. Infection of cells with EBV may result in either lytic infection with production of viral particles, characterized by the presence of linear DNA forms, or latent infection, characterized by either episomal or integrated DNA forms. To examine whether the different lytic and latent EBV DNA forms can reliably be distinguished in single human cells, in situ hybridization was performed in EBV-positive cell lines. Immunocytochemistry and Southern blot analysis were performed supplementary to in situ hybridization. In latent infection, three in situ hybridization patterns were observed: large-disperse (episomal), small-punctate (integrated) and combined (both), signal types 1, 2 and 3 respectively. These were associated with expression of latent membrane protein 1, but not with Z fragment of Epstein-Barr replication activator or viral capsid antigen. In lytic infection, three additional in situ hybridization patterns were observed: nuclear membrane associated, bubble (filling up the nucleus) and spillover (covering the lysed cells) signals types 4, 5 and 6 respectively. Signal types 4 and 5 were associated with expression of latent membrane protein 1 and Z fragment of Epstein-Barr replication activator but not viral capsid antigen, whereas type 6 was associated with expression of viral capsid antigen only. Southern blot analysis confirmed these results; however, low copy numbers of integrated virus were often missed by Southern blot, confirming that in situ hybridization is more sensitive in determining the presence of all types of EBV DNA. In situ hybridization may prove useful in rapidly screening large series of tissue microarrays and other clinical specimens for the presence of lytic or latent EBV.
Collapse
Affiliation(s)
- Elena E Leenman
- Research Institute of Radiology and Roentgenology, St Petersburg, Russia
| | | | | | | | | | | | | | | | | |
Collapse
|
22
|
Walling DM, Andritsos LA, Etienne W, Payne DA, Aronson JF, Flaitz CM, Nichols CM. Molecular markers of clonality and identity in epstein-barr virus-associated B-cell lymphoproliferative disease. J Med Virol 2004; 74:94-101. [PMID: 15258974 DOI: 10.1002/jmv.20151] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Epstein-Barr virus (EBV)-associated B-cell lymphoproliferative disease may be polyclonal, oligoclonal, or monoclonal. The degree of tumor clonality reflects the disease pathogenesis and may have implications for disease diagnosis, prognosis, and treatment. In this study, specimens of EBV-associated B-cell lymphoproliferative disease obtained from immunocompromised hosts were analyzed for molecular markers of cellular and virologic clonality and virologic identity. Each tumor specimen was assessed for immunoglobulin gene JH region rearrangement, the structure of the EBV genome termini, and the EBV genotype(s) present using a new EBV genotyping assay based upon LMP-1 gene sequence variation. The results of the JH rearrangement and EBV termini assays were generally concordant in their assessment of tumor specimen clonality, and both assays contributed to establishing clonal identity between different tumor specimens. The EBV genotyping assay did not significantly contribute to the assessment of tumor clonality but did established clear virologic identity between different tumor specimens obtained from the same individual. In one individual, these three assays together characterized a multi-focal, monoclonal tumor that may have arisen through clonal selection after sequential infections with two different EBV genotypes. In summary, the JH rearrangement and EBV termini assays each provided different but complementary information on tumor clonality, while the EBV genotyping assay proved most useful for establishing virologic identity among tumors. Utilization of these three assays together may provide new insight into the pathogenesis of EBV-associated B-cell lymphoproliferative disease.
Collapse
Affiliation(s)
- Dennis M Walling
- Division of Infectious Diseases, Department of Internal Medicine, University of Texas Medical Branch at Galveston, 77555-0435, USA.
| | | | | | | | | | | | | |
Collapse
|
23
|
Debiec-Rychter M, Croes R, De Vos R, Marynen P, Roskams T, Hagemeijer A, Lombaerts R, Sciot R. Complex genomic rearrangement of ALK loci associated with integrated human Epstein-Barr virus in a post-transplant myogenic liver tumor. THE AMERICAN JOURNAL OF PATHOLOGY 2003; 163:913-22. [PMID: 12937132 PMCID: PMC1868245 DOI: 10.1016/s0002-9440(10)63451-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Epstein-Barr virus (EBV) is a ubiquitous viral agent, well known to be associated with lymphoid, epithelial, and smooth-muscle malignancies in immunocompromised individuals. This report describes a 10-year-old patient with an EBV-related liver tumor occurring after kidney transplantation. The neoplasm presented a phenotypic spectrum, ranging from a smooth-muscle tumor to an inflammatory pseudotumor (IPT). The neoplastic cells failed to disclose CD21, CD35, or ALK expression, the latter confirmed by reverse-transcription polymerase chain reaction. Cytogenetic analysis revealed a single clonal cell population showing 46,XY,del (2)(p23),der(3)t (2;3)(p23;q29),der(21) t(Y;21)(q12;p13) karyotype. By metaphase FISH analysis, the neoplastic cells demonstrated the presence of two molecularly different but related aberrant clones, one with the loss of one ALK allele and the second with translocation of the 3'end of ALK kinase domain on the der(3) chromosome. Using FISH with an EBV-specific and 3'end ALK DNA probes, a co-localization of the viral DNA and the ALK sequences was found on the der(3) chromosome. Metaphases with loss of rearranged ALK did not show integrated virus; instead, viral particles together with an associated 3'end ALK domain formed an ex-chromosomal, episomal-like type configuration. The interphase study, using dual-color 5'/3' end ALK FISH assay, revealed 30% of nuclei with only one fused signal, confirming the total loss of one ALK allele in the subset of tumor cells. A combined immunofluorescence and FISH study indicated this separate clonal variant to correspond to desmin-positive smooth-muscle cells. In contrast, desmin-negative myofibroblasts showed the presence of both normal and rearranged ALK alleles. Our results indicate that ALK locus may be a target of EBV integration, a hitherto unreported finding. Although the sustained clonal expansion in EBV-related smooth-muscle tumors/IPTs may depend on functions provided by the EBV oncogenic proteins, the tumor phenotype may be further modified by the secondary genomic rearrangements imposed by the virus during and/or after the integration event. In this respect, the observed phenotypic heterogeneity most likely reflects divergence during neoplastic progression, with the subsequent expansion of morphologically and molecularly distinct but cytogenetically related clones.
Collapse
Affiliation(s)
- Maria Debiec-Rychter
- Center for Human Genetics, Catholic University of Leuven, Herestraat 49, B-3000 Leuven, Belgium.
| | | | | | | | | | | | | | | |
Collapse
|
24
|
Hayashi K, Jin Z, Onoda S, Joko H, Teramoto N, Ohara N, Oda W, Tanaka T, Liu YX, Koirala TR, Oka T, Kondo E, Yoshino T, Takahashi K, Akagi T. Rabbit model for human EBV-associated hemophagocytic syndrome (HPS): sequential autopsy analysis and characterization of IL-2-dependent cell lines established from herpesvirus papio-induced fatal rabbit lymphoproliferative diseases with HPS. THE AMERICAN JOURNAL OF PATHOLOGY 2003; 162:1721-36. [PMID: 12707056 PMCID: PMC1851174 DOI: 10.1016/s0002-9440(10)64306-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Epstein-Barr virus-associated hemophagocytic syndrome (EBV-AHS) is often associated with fatal infectious mononucleosis or T-cell lymphoproliferative diseases (LPD). To elucidate the true nature of fatal LPD observed in Herpesvirus papio (HVP)-induced rabbit hemophagocytosis, reactive or neoplastic, we analyzed sequential development of HVP-induced rabbit LPD and their cell lines. All of the seven Japanese White rabbits inoculated intravenously with HVP died of fatal LPD 18 to 27 days after inoculation. LPD was also accompanied by hemophagocytic syndrome (HPS) in five of these seven rabbits. Sequential autopsy revealed splenomegaly and swollen lymph nodes, often accompanied by bleeding, which developed in the last week. Atypical lymphoid cells infiltrated many organs with a "starry sky" pattern, frequently involving the spleen, lymph nodes, and liver. HVP-small RNA-1 expression in these lymphoid cells was clearly demonstrated by a newly developed in situ hybridization (ISH) system. HVP-ISH of immunomagnetically purified lymphoid cells from spleen or lymph nodes revealed HVP-EBER1+ cells in each CD4+, CD8+, or CD79a+ fraction. Hemophagocytic histiocytosis was observed in the lymph nodes, spleen, bone marrow, and thymus. HVP-DNA was detected in the tissues and peripheral blood from the infected rabbits by PCR or Southern blot analysis. Clonality analysis of HVP-induced LPD by Southern blotting with TCR gene probe revealed polyclonal bands, suggesting polyclonal proliferation. Six IL-2-dependent rabbit T-cell lines were established from transplanted scid mouse tumors from LPD. These showed latency type I/II HVP infection and had normal karyotypes except for one line, and three of them showed tumorigenicity in nude mice. These data suggest that HVP-induced fatal LPD in rabbits is reactive polyclonally in nature.
Collapse
Affiliation(s)
- Kazuhiko Hayashi
- Department of Pathology, Okayama University Graduate School of Medicine and Dentistry, Okayama, Japan.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
25
|
Middeldorp JM, Brink AATP, van den Brule AJC, Meijer CJLM. Pathogenic roles for Epstein-Barr virus (EBV) gene products in EBV-associated proliferative disorders. Crit Rev Oncol Hematol 2003; 45:1-36. [PMID: 12482570 DOI: 10.1016/s1040-8428(02)00078-1] [Citation(s) in RCA: 137] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Epstein-Barr virus (EBV) is associated with a still growing spectrum of clinical disorders, ranging from acute and chronic inflammatory diseases to lymphoid and epithelial malignancies. Based on a combination of in vitro and in vivo findings, EBV is thought to contribute in the pathogenesis of these diseases. The different EBV gene expression patterns in the various disorders, suggest different EBV-mediated pathogenic mechanisms. In the following pages, an overview of the biology of EBV-infection is given and functional aspects of EBV-proteins are discussed and their putative role in the various EBV-associated disorders is described. EBV gene expression patterns and possible pathogenic mechanisms are discussed. In addition, expression of the cellular genes upregulated by EBV in vitro is discussed, and a comparison with the in vivo situation is made.
Collapse
Affiliation(s)
- Jaap M Middeldorp
- Department of Pathology, Vrije Universiteit Medical Center, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands.
| | | | | | | |
Collapse
|
26
|
Chang Y, Cheng SD, Tsai CH. Chromosomal integration of Epstein-Barr virus genomes in nasopharyngeal carcinoma cells. Head Neck 2002; 24:143-50. [PMID: 11891944 DOI: 10.1002/hed.10039] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Little has been known about whether Epstein-Barr virus (EBV) could persist in nasopharyngeal carcinoma (NPC) cells by chromosomal integration, and no NPC cell line harboring integrated EBV has been reported. In this study, we explored this issue through isolating EBV-infected NPC cell clones generated from an in vitro infection system and examining the configuration of EBV DNA in these cells. METHODS AND RESULTS EBV genomes were demonstrated in NPC cell clones using polymerase chain reaction and Southern hybridization. Viral nuclear antigens were also detected by use of an anticomplement immunofluorescence assay and an immunoblotting assay. Gardella gel analysis showed that two of the EBV-positive cell clones, H2B4 and H2B17-7, harbored no extrachromosomal form of the viral genome. Restriction analysis of EBV genomic termini indicated that EBV DNA in these two cell clones was not circularized, and the viral genomes were integrated into chromosomes as demonstrated by fluorescence in situ hybridization. CONCLUSIONS This is the first in vitro model of EBV persistence in NPC cells by genomic integration, which represents a unique state of virus-cell interaction. Using this model, investigation into the association between EBV integration and chromosomal abnormality in tumor cells will help to reveal the underlying biologic significance.
Collapse
Affiliation(s)
- Yao Chang
- Graduate Institute of Microbiology, College of Medicine, National Taiwan University, Number 1, Section 1, Jen-Ai Road, Taipei, Taiwan
| | | | | |
Collapse
|
27
|
Hayashi K, Akagi T. An animal model for Epstein-Barr virus (EBV)-associated lymphomagenesis in the human: malignant lymphoma induction of rabbits by EBV-related herpesvirus from cynomolgus. Pathol Int 2000; 50:85-97. [PMID: 10792766 DOI: 10.1046/j.1440-1827.2000.01018.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
It is very important to develop and analyze animal models of Epstein-Barr virus (EBV)-associated tumors in the human. However, only a few reports on the animal models of EBV infection have been reported. Here we review those previous models and describe the details on our newly developed rabbit model of malignant lymphoma induced by EBV-related virus from cynomolgus. In brief, Si-IIA-EBV or Cyno-EBV induced T-cell lymphomas in rabbits inoculated intravenously (77-90%), orally (82-89%), subcutaneously (3/3) and intraperitoneally (2/3) about 2-5 months later. EBV-DNA was detected in peripheral blood by polymerase chain reaction 2 days after oral inoculation of Cyno-EBV while antiviral capsid antigen immunoglobulin G (IgG) was raised 3 weeks after the inoculation. Rabbit lymphomas and their cell lines contained EBV-DNA and expressed EBV-encoded small RNA-1 and EBV-associated nuclear antigen. Rabbit lymphoma cell lines, some of which have specific chromosomal abnormality, showed tumorigenicity in nude mice. The significance and further research subjects of this animal model will be discussed. We believe that the present rabbit model of lymphoma with specific chromosomal abnormalities is very useful for clarifying the role of EBV in human EBV-associated lymphoma and provides a means for studying prophylactic and therapeutic regimens.
Collapse
MESH Headings
- Administration, Oral
- Animals
- Antigens, Viral/immunology
- Capsid Proteins
- DNA, Viral/analysis
- Disease Models, Animal
- Herpesviridae Infections/pathology
- Herpesviridae Infections/transmission
- Herpesviridae Infections/virology
- Herpesvirus 4, Human/genetics
- Herpesvirus 4, Human/immunology
- Herpesvirus 4, Human/isolation & purification
- Herpesvirus 4, Human/pathogenicity
- Herpesvirus 4, Human/ultrastructure
- Humans
- Injections
- Lymphoma/metabolism
- Lymphoma/pathology
- Lymphoma/virology
- Macaca fascicularis/virology
- Mice
- Mice, Nude
- Neoplasm Transplantation
- Polymerase Chain Reaction
- RNA, Viral/metabolism
- Rabbits
- Sequence Analysis, DNA
- Tumor Cells, Cultured
- Tumor Virus Infections/pathology
- Tumor Virus Infections/transmission
- Tumor Virus Infections/virology
Collapse
Affiliation(s)
- K Hayashi
- Second Department of Pathology, Okayama University Medical School, Okayama, Japan.
| | | |
Collapse
|
28
|
Suzumiya J, Ohshima K, Takeshita M, Kanda M, Kawasaki C, Kimura N, Tamura K, Kikuchi M. Nasal lymphomas in Japan: a high prevalence of Epstein-Barr virus type A and deletion within the latent membrane protein gene. Leuk Lymphoma 1999; 35:567-78. [PMID: 10609794 DOI: 10.1080/10428199909169621] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The majority of nasal lymphomas are of the natural killer (NK)/T cell lineage. We analyzed 33 specimens of nasal lymphoma from Japanese patients for Epstein-Barr virus (EBV). Phenotypic and genetic analyses showed 28 cases with NK/T cell type and 5 cases with B cell type. All NK/T lymphomas were of pleomorphic cell type except 2 large cell (centroblastoid) and one lymphoblastic lymphoma. All cases with nasal B cell lymphoma were of large (centroblastoid) cell type. EBV was detected in all cases of NK/T cell type with the exception of one lymphoblastic case, and was monoclonally integrated in all cases examined (14/14 cases). All but one case had subtype A of EBV infection with 30-base paired deleted LMP-1 gene. One case of B cell lymphoma showed the presence of EBV infection with subtype A and deletion of LMP-1. Our results indicate that the majority of nasal lymphomas in Japanese patients are of the nasal NK/T cell type, have pleomorphic morphology, a high prevalence of EBV with a monoclonal integration, subtype A and deleted LMP-1 gene. In contrast, nasal B cell lymphoma showed monomorphic appearance and rare EBV infection.
Collapse
Affiliation(s)
- J Suzumiya
- First Department of Pathology, School of Medicine, Fukuoka University, Japan.
| | | | | | | | | | | | | | | |
Collapse
|