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Tang KW, Tian Y, Xie G, Bäckerholm A, Holmqvist I, Vracar D, Lin J, Carlsten J, Abrahamsson S, Liu Z, Huang Y, Shair K. Landscape of Epstein-Barr virus gene expression and perturbations in cancer. Res Sq 2024:rs.3.rs-3911441. [PMID: 38352479 PMCID: PMC10862949 DOI: 10.21203/rs.3.rs-3911441/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/24/2024]
Abstract
Epstein-Barr virus (EBV) is the causative agent for multiple neoplastic diseases of epithelial and lymphocytic origin1-3. The heterogeneity of the viral elements expressed and the mechanisms by which these coding and non-coding genes maintain cancer cell properties in vivo remain elusive4,5. Here we conducted a multi-modal transcriptomic analysis of EBV-associated neoplasms and identified that the ubiquitously expressed RPMS1 non-coding RNAs support cancer cell properties by disruption of the interferon response. Our map of EBV expression shows a variable, but pervasive expression of BNLF2 discerned from the overlapping LMP1 RNA in bulk sequencing data. Using long-read single-molecule sequencing, we identified three new viral elements within the RPMS1 gene. Furthermore, single-cell sequencing datasets allowed for the separation of cancer cells and healthy cells from the same tissue biopsy and the characterization of a microenvironment containing interferon gamma excreted by EBV-stimulated T-lymphocytes. In comparison with healthy epithelium, EBV-transformed cancer cells exhibited increased proliferation and inhibited immune response induced by the RPMS1-encoded microRNAs. Our atlas of EBV expression shows that the EBV-transformed cancer cells express high levels of non-coding RNAs originating from RPMS1 and that the oncogenic properties are maintained by RPMS1 microRNAs. Through bioinformatic disentanglement of single cells from cancer tissues we identified a positive feedback loop where EBV-activated immune cells stimulate cancer cells to proliferate, which in turn undergo viral reactivation and trigger an immune response.
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Paudel S, Warner BE, Wang R, Adams-Haduch J, Reznik AS, Dou J, Huang Y, Gao YT, Koh WP, Bäckerholm A, Yuan JM, Shair KHY. Serologic Profiling Using an Epstein-Barr Virus Mammalian Expression Library Identifies EBNA1 IgA as a Prediagnostic Marker for Nasopharyngeal Carcinoma. Clin Cancer Res 2022; 28:5221-5230. [PMID: 36165913 PMCID: PMC9722633 DOI: 10.1158/1078-0432.ccr-22-1600] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 08/22/2022] [Accepted: 09/22/2022] [Indexed: 01/24/2023]
Abstract
PURPOSE The favorable prognosis of stage I and II nasopharyngeal carcinoma (NPC) has motivated a search for biomarkers for the early detection and risk assessment of Epstein-Barr virus (EBV)-associated NPC. Although EBV seropositivity is ubiquitous among adults, a spike in antibodies against select EBV proteins is a harbinger of NPC. A serologic survey would likely reveal which EBV antibodies could discriminate those at risk of developing NPC. EXPERIMENTAL DESIGN Lysates from a new EBV mammalian expression library were used in a denaturing multiplex immunoblot assay to survey antibodies against EBV in sera collected from healthy individuals who later developed NPC (incident cases) in a prospective cohort from Singapore and validated in an independent cohort from Shanghai, P.R. China. RESULTS We show that IgA against EBV nuclear antigen 1 (EBNA1) discriminated incident NPC cases from matched controls with 100% sensitivity and 100% specificity up to 4 years before diagnosis in both Singapore and Shanghai cohorts. Incident NPC cases had a greater IgG repertoire against lytic-classified EBV proteins, and the assortment of IgA against EBV proteins detected by the immunoblot assay increased closer to diagnosis. CONCLUSIONS Although NPC tumors consistently harbor latent EBV, the observed heightened systemic and mucosal immunity against lytic-classified antigens years prior to clinical diagnosis is consistent with enhanced lytic transcription. We conclude that an expanding EBV mucosal reservoir (which can be latent and/or lytic) is a risk factor for NPC. This presents an opportunity to identify those at risk of developing NPC using IgA against EBNA1 as a biomarker.
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Affiliation(s)
- Sarita Paudel
- Cancer Virology Program, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Division of Cancer Control and Population Sciences, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Benjamin E Warner
- Cancer Virology Program, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Division of Cancer Control and Population Sciences, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Renwei Wang
- Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Division of Cancer Control and Population Sciences, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Jennifer Adams-Haduch
- Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Division of Cancer Control and Population Sciences, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Alex S Reznik
- Cancer Virology Program, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Jason Dou
- Department of Electrical and Computer Engineering, Swanson School of Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Yufei Huang
- Cancer Virology Program, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Department of Electrical and Computer Engineering, Swanson School of Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Yu-Tang Gao
- Department of Epidemiology, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Woon-Puay Koh
- Healthy Longevity Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Alan Bäckerholm
- Cancer Virology Program, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Jian-Min Yuan
- Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Division of Cancer Control and Population Sciences, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Kathy H Y Shair
- Cancer Virology Program, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Corresponding author: Kathy H Y Shair, UPMC Hillman Cancer Center, 5117 Centre Avenue, Suite 1.8, Pittsburgh, PA 15213,Tel: 412-623 7717,
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Holmqvist I, Bäckerholm A, Tian Y, Xie G, Thorell K, Tang KW. FLAME: long-read bioinformatics tool for comprehensive spliceome characterization. RNA 2021; 27:1127-1139. [PMID: 34253685 PMCID: PMC8457008 DOI: 10.1261/rna.078800.121] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 06/28/2021] [Indexed: 06/13/2023]
Abstract
Comprehensive characterization of differentially spliced RNA transcripts with nanopore sequencing is limited by bioinformatics tools that are reliant on existing annotations. We have developed FLAME, a bioinformatics pipeline for alternative splicing analysis of gene-specific or transcriptome-wide long-read sequencing data. FLAME is a Python-based tool aimed at providing comprehensible quantification of full-length splice variants, reliable de novo recognition of splice sites and exons, and representation of consecutive exon connectivity in the form of a weighted adjacency matrix. Notably, this workflow circumvents issues related to inadequate reference annotations and allows for incorporation of short-read sequencing data to improve the confidence of nanopore sequencing reads. In this study, the Epstein-Barr virus long noncoding RNA RPMS1 was used to demonstrate the utility of the pipeline. RPMS1 is ubiquitously expressed in Epstein-Barr virus associated cancer and known to undergo ample differential splicing. To fully resolve the RPMS1 spliceome, we combined gene-specific nanopore sequencing reads from a primary gastric adenocarcinoma and a nasopharyngeal carcinoma cell line with matched publicly available short-read sequencing data sets. All previously reported splice variants, including putative ORFs, were detected using FLAME. In addition, 32 novel exons, including two intron retentions and a cassette exon, were discovered within the RPMS1 gene.
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MESH Headings
- Benchmarking
- Cell Line, Tumor
- Computational Biology/methods
- Epstein-Barr Virus Infections/genetics
- Epstein-Barr Virus Infections/metabolism
- Epstein-Barr Virus Infections/pathology
- Epstein-Barr Virus Infections/virology
- Exons
- Herpesvirus 4, Human/genetics
- Herpesvirus 4, Human/pathogenicity
- High-Throughput Nucleotide Sequencing
- Humans
- Introns
- Nanopore Sequencing
- Nasopharyngeal Carcinoma/genetics
- Nasopharyngeal Carcinoma/metabolism
- Nasopharyngeal Carcinoma/pathology
- Nasopharyngeal Carcinoma/virology
- Nasopharyngeal Neoplasms/genetics
- Nasopharyngeal Neoplasms/metabolism
- Nasopharyngeal Neoplasms/pathology
- Nasopharyngeal Neoplasms/virology
- RNA Splicing
- RNA, Long Noncoding/genetics
- RNA, Long Noncoding/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Viral/genetics
- RNA, Viral/metabolism
- Sequence Analysis, RNA
- Software
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Affiliation(s)
- Isak Holmqvist
- Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, 413 46 Gothenburg, Sweden
| | - Alan Bäckerholm
- Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, 413 46 Gothenburg, Sweden
| | - Yarong Tian
- Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, 413 46 Gothenburg, Sweden
| | - Guojiang Xie
- Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, 413 46 Gothenburg, Sweden
| | - Kaisa Thorell
- Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, 413 46 Gothenburg, Sweden
| | - Ka-Wei Tang
- Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, 413 46 Gothenburg, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, Sahlgrenska Center for Cancer Research, Västra Götaland Region, Department of Clinical Microbiology, Sahlgrenska University Hospital, 413 46 Gothenburg, Sweden
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Ziegler P, Tian Y, Bai Y, Abrahamsson S, Bäckerholm A, Reznik AS, Green A, Moore JA, Lee SE, Myerburg MM, Park HJ, Tang KW, Shair KHY. A primary nasopharyngeal three-dimensional air-liquid interface cell culture model of the pseudostratified epithelium reveals differential donor- and cell type-specific susceptibility to Epstein-Barr virus infection. PLoS Pathog 2021; 17:e1009041. [PMID: 33914843 PMCID: PMC8112674 DOI: 10.1371/journal.ppat.1009041] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 05/11/2021] [Accepted: 04/01/2021] [Indexed: 02/07/2023] Open
Abstract
Epstein-Barr virus (EBV) is a ubiquitous γ-herpesvirus with latent and lytic cycles. EBV replicates in the stratified epithelium but the nasopharynx is also composed of pseudostratified epithelium with distinct cell types. Latent infection is associated with nasopharyngeal carcinoma (NPC). Here, we show with nasopharyngeal conditionally reprogrammed cells cultured at the air-liquid interface that pseudostratified epithelial cells are susceptible to EBV infection. Donors varied in susceptibility to de novo EBV infection, but susceptible cultures also displayed differences with respect to pathogenesis. The cultures from one donor yielded lytic infection but cells from two other donors were positive for EBV-encoded EBERs and negative for other lytic infection markers. All cultures stained positive for the pseudostratified markers CK7, MUC5AC, α-tubulin in cilia, and the EBV epithelial cell receptor Ephrin receptor A2. To define EBV transcriptional programs by cell type and to elucidate latent/lytic infection-differential changes, we performed single cell RNA-sequencing on one EBV-infected culture that resulted in alignment with many EBV transcripts. EBV transcripts represented a small portion of the total transcriptome (~0.17%). All cell types in the pseudostratified epithelium had detectable EBV transcripts with suprabasal cells showing the highest number of reads aligning to many EBV genes. Several restriction factors (IRF1, MX1, STAT1, C18orf25) known to limit lytic infection were expressed at lower levels in the lytic subcluster. A third of the differentially-expressed genes in NPC tumors compared to an uninfected pseudostratified ALI culture overlapped with the differentially-expressed genes in the latent subcluster. A third of these commonly perturbed genes were specific to EBV infection and changed in the same direction. Collectively, these findings suggest that the pseudostratified epithelium could harbor EBV infection and that the pseudostratified infection model mirrors many of the transcriptional changes imposed by EBV infection in NPC. It has been known for over 50 years that EBV infection is associated with NPC. Despite many advances from studies in 2-dimensional cell culture, many aspects of EBV molecular pathogenesis in the nasopharynx remain undefined because the cell types and the biology of the nasopharyngeal epithelium can only be faithfully captured in 3-dimensional cell culture. In the stratified epithelium, cellular differentiation triggers lytic infection but it is not clear to what degree the pseudostratified epithelium is involved. The pseudostratified epithelium is abundant in the lateral wall where the lymphoid-rich fossa of Rosenmüller is located and is a site where NPC tumors most often arises. While the oral epithelium is a site of EBV replication, whether the nasopharyngeal epithelium is a major source of EBV shedding in the nasopharynx is not well defined. Here, we present a 3-dimensional organoid model of the nasopharyngeal pseudostratified epithelium showing that such cells can be infected with EBV in some donor cultures, with examples of both latent and lytic infection. We propose that the cell types of the pseudostratified epithelium should be considered a component of EBV pathogenesis in the nasopharynx and that the difference in donor susceptibility and latent/lytic infection could influence EBV’s fitness in the nasopharynx.
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Affiliation(s)
- Phillip Ziegler
- Cancer Virology Program, University of Pittsburgh Medical Center (UPMC), University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Yarong Tian
- Wallenberg Centre for Molecular and Translational Medicine, Sahlgrenska Center for Cancer Research, Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Yulong Bai
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Sanna Abrahamsson
- Wallenberg Centre for Molecular and Translational Medicine, Sahlgrenska Center for Cancer Research, Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Alan Bäckerholm
- Wallenberg Centre for Molecular and Translational Medicine, Sahlgrenska Center for Cancer Research, Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Alex S. Reznik
- Cancer Virology Program, University of Pittsburgh Medical Center (UPMC), University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Anthony Green
- University of Pittsburgh Research Histology Services, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - John A. Moore
- UPMC Department of Otolaryngology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Stella E. Lee
- UPMC Department of Otolaryngology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Michael M. Myerburg
- Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Hyun Jung Park
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Ka-Wei Tang
- Wallenberg Centre for Molecular and Translational Medicine, Sahlgrenska Center for Cancer Research, Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Region Västra Götaland, Sahlgrenska University Hospital, Department of Clinical Microbiology, Gothenburg, Sweden
| | - Kathy Ho Yen Shair
- Cancer Virology Program, University of Pittsburgh Medical Center (UPMC), University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- * E-mail:
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