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Katti PD, Jasuja H. Current Advances in the Use of Tissue Engineering for Cancer Metastasis Therapeutics. Polymers (Basel) 2024; 16:617. [PMID: 38475301 DOI: 10.3390/polym16050617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 02/16/2024] [Accepted: 02/20/2024] [Indexed: 03/14/2024] Open
Abstract
Cancer is a leading cause of death worldwide and results in nearly 10 million deaths each year. The global economic burden of cancer from 2020 to 2050 is estimated to be USD 25.2 trillion. The spread of cancer to distant organs through metastasis is the leading cause of death due to cancer. However, as of today, there is no cure for metastasis. Tissue engineering is a promising field for regenerative medicine that is likely to be able to provide rehabilitation procedures to patients who have undergone surgeries, such as mastectomy and other reconstructive procedures. Another important use of tissue engineering has emerged recently that involves the development of realistic and robust in vitro models of cancer metastasis, to aid in drug discovery and new metastasis therapeutics, as well as evaluate cancer biology at metastasis. This review covers the current studies in developing tissue-engineered metastasis structures. This article reports recent developments in in vitro models for breast, prostate, colon, and pancreatic cancer. The review also identifies challenges and opportunities in the use of tissue engineering toward new, clinically relevant therapies that aim to reduce the cancer burden.
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Affiliation(s)
- Preeya D Katti
- American University of Caribbean, Miramar, FL 33025, USA
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2
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Burnet AM, Brunetti T, Rochford R. Hemin treatment drives viral reactivation and plasma cell differentiation of EBV latently infected B cells. PLoS Pathog 2023; 19:e1011561. [PMID: 37639483 PMCID: PMC10491393 DOI: 10.1371/journal.ppat.1011561] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 09/08/2023] [Accepted: 07/16/2023] [Indexed: 08/31/2023] Open
Abstract
Epstein-Barr virus (EBV) and Plasmodium falciparum have a well described role in the development of endemic Burkitt lymphoma (BL), yet the mechanisms involved remain unknown. A major hallmark of malarial disease is hemolysis and bystander eryptosis of red blood cells, which causes release of free heme in large quantities into peripheral blood. We hypothesized that heme released during malaria infection drives differentiation of latently infected EBV-positive B cells, resulting in viral reactivation and release of infectious virus. To test this hypothesis, we used the EBV-positive Mutu I B-cell line and treated with hemin (the oxidized form of heme) and evaluated evidence of EBV reactivation. Hemin treatment resulted in the expression of EBV immediate early, early and late lytic gene transcripts. In addition, expression of CD138, a marker of plasma cells was co-expressed with the late lytic protein gp350 on hemin treated Mutu I cells. Finally, DNase-resistant EBV DNA indicative of virion production was detected in supernatant. To assess the transcriptional changes induced by hemin treatment, RNA sequencing was performed on mock- and hemin-treated Mutu I cells, and a shift from mature B cell transcripts to plasma cell transcripts was identified. To identify the mechanism of hemin-induced B cell differentiation, we measured levels of the plasma cell transcriptional repressor, BACH2, that contains specific heme binding sites. Hemin treatment caused significant degradation of BACH2 by 24 hours post-treatment in four BL cell lines (two EBV positive, two EBV negative). Knockdown of BACH2 in Mutu I cells using siRNAs significantly increased CD138+gp350+ cells to levels similar to treatment with hemin. This suggested that hemin induced BACH2 degradation was responsible for plasma cell differentiation and viral reactivation. Together, these data support a model where EBV reactivation can occur during malaria infection via heme modulation, providing a mechanistic link between malaria and EBV.
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Affiliation(s)
- Anna M. Burnet
- Department of Immunology and Microbiology, University of Colorado, School of Medicine, Aurora, Colorado, United States of America
| | - Tonya Brunetti
- Department of Immunology and Microbiology, University of Colorado, School of Medicine, Aurora, Colorado, United States of America
| | - Rosemary Rochford
- Department of Immunology and Microbiology, University of Colorado, School of Medicine, Aurora, Colorado, United States of America
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3
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Pereira GC. An Automated Strategy to Handle Antigenic Variability in Immunisation Protocols, Part I: Nanopore Sequencing of Infectious Agent Variants. Methods Mol Biol 2023; 2575:305-321. [PMID: 36301483 DOI: 10.1007/978-1-0716-2716-7_16] [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] [Indexed: 06/16/2023]
Abstract
Infectious agents often challenge therapeutics, from antibiotics resistance to antigenic variability affecting inoculation measures. Over the last decades, genome sequencing arose as an important ally to address such challenges. In bacterial infection, whole-genome-sequencing (WGS) supports tracking pathogenic alterations affecting the human microbiome. In viral infection, the analysis of the relevant sequence of nucleotides helps with determining historical variants of a virus and elucidates details about infection clusters and their distribution. Additionally, genome sequencing is now an important step in inoculation protocols, isolating target genes to design more robust immunisation assays. Ultimately, genetic engineering has empowered repurposing at scale, allowing long-lasting repeating clinical trials to be automated within a much shorter time-frame, by adjusting existing protocols. This is particularly important during sanitary emergencies as the ones caused by the 2014 West African Ebola outbreak, the Zika virus rapid spread in both South and North America in 2015, followed by Asia in 2016, and the pandemic caused by the SARS-CoV-2, which has infected more than 187 million people and caused more than 4 million deaths, worldwide, as per July 2021 statistics. In this scenery, this chapter presents a novel fully automated strategy to handle antigenic variability in immunisation protocols. The methodology comprises of two major steps (1) nanopore sequencing of infectious agent variants - the focus is on the SARS-CoV-2 and its variants; followed by (2) mRNA vector design for immunotherapy. This chapter presents the nanopore sequencing step and Chapter 17 introduces a protocol for mRNA vector design.
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4
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Javadzadeh S, Rajkumar U, Nguyen N, Sarmashghi S, Luebeck J, Shang J, Bafna V. FastViFi: Fast and accurate detection of (Hybrid) Viral DNA and RNA. NAR Genom Bioinform 2022; 4:lqac032. [PMID: 35493723 PMCID: PMC9041341 DOI: 10.1093/nargab/lqac032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 03/04/2022] [Accepted: 03/06/2022] [Indexed: 11/13/2022] Open
Abstract
DNA viruses are important infectious agents known to mediate a large number of human diseases, including cancer. Viral integration into the host genome and the formation of hybrid transcripts are also associated with increased pathogenicity. The high variability of viral genomes, however requires the use of sensitive ensemble hidden Markov models that add to the computational complexity, often requiring > 40 CPU-hours per sample. Here, we describe FastViFi, a fast 2-stage filtering method that reduces the computational burden. On simulated and cancer genomic data, FastViFi improved the running time by 2 orders of magnitude with comparable accuracy on challenging data sets. Recently published methods have focused on identification of location of viral integration into the human host genome using local assembly, but do not extend to RNA. To identify human viral hybrid transcripts, we additionally developed ensemble Hidden Markov Models for the Epstein Barr virus (EBV) to add to the models for Hepatitis B (HBV), Hepatitis C (HCV) viruses and the Human Papillomavirus (HPV), and used FastViFi to query RNA-seq data from Gastric cancer (EBV) and liver cancer (HBV/HCV). FastViFi ran in <10 minutes per sample and identified multiple hybrids that fuse viral and human genes suggesting new mechanisms for oncoviral pathogenicity. FastViFi is available at https://github.com/sara-javadzadeh/FastViFi.
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Affiliation(s)
- Sara Javadzadeh
- Department of Computer Science & Engineering, UC San Diego, La Jolla, California, USA
| | - Utkrisht Rajkumar
- Department of Computer Science & Engineering, UC San Diego, La Jolla, California, USA
| | - Nam Nguyen
- Boundless Bio, Inc. 11099 N Torrey Pines Rd, La Jolla, CA, USA
| | - Shahab Sarmashghi
- Department of Electrical and Computer Engineering, UC San Diego, La Jolla, California, USA
| | - Jens Luebeck
- Bioinformatics & Systems Biology Graduate Program, UC San Diego, La Jolla, California, USA
| | - Jingbo Shang
- Department of Computer Science & Engineering, UC San Diego, La Jolla, California, USA
| | - Vineet Bafna
- Department of Computer Science & Engineering, UC San Diego, La Jolla, California, USA
- Boundless Bio, Inc. 11099 N Torrey Pines Rd, La Jolla, CA, USA
- Moores Cancer Center, UC San Diego, La Jolla, California, USA
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5
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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.
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Gaglia MM. Kaposi's sarcoma-associated herpesvirus at 27. Tumour Virus Res 2021; 12:200223. [PMID: 34153523 PMCID: PMC8250455 DOI: 10.1016/j.tvr.2021.200223] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 06/16/2021] [Accepted: 06/17/2021] [Indexed: 01/25/2023] Open
Abstract
Kaposi's sarcoma-associated herpesvirus (KSHV) was discovered 27 years ago and its link to several pathologies - Kaposi's sarcoma, primary effusion lymphoma, and the B cell variant of Multicentric Castleman disease - is now well established. However, many questions remain about how KSHV causes tumors. Here, I will review studies from the last few years (primarily 2019-2021) that report new information about KSHV biology and tumorigenesis, including new results about KSHV proteins implicated in tumorigenesis, genetic and environmental variability in KSHV-related tumor development, and potential vulnerabilities of KSHV-caused tumors that could be novel therapeutic targets.
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Affiliation(s)
- Marta Maria Gaglia
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, 02111, USA.
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Jurasz H, Pawłowski T, Perlejewski K. Contamination Issue in Viral Metagenomics: Problems, Solutions, and Clinical Perspectives. Front Microbiol 2021; 12:745076. [PMID: 34745046 PMCID: PMC8564396 DOI: 10.3389/fmicb.2021.745076] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 09/17/2021] [Indexed: 12/16/2022] Open
Abstract
We describe the most common internal and external sources and types of contamination encountered in viral metagenomic studies and discuss their negative impact on sequencing results, particularly for low-biomass samples and clinical applications. We also propose some basic recommendations for reducing the background noise in viral shotgun metagenomic (SM) studies, which would limit the bias introduced by various classes of contaminants. Regardless of the specific viral SM protocol, contamination cannot be totally avoided; in particular, the issue of reagent contamination should always be addressed with high priority. There is an urgent need for the development and validation of standards for viral metagenomic studies especially if viral SM protocols will be more widely applied in diagnostics.
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Affiliation(s)
- Henryk Jurasz
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Tomasz Pawłowski
- Division of Psychotherapy and Psychosomatic Medicine, Department of Psychiatry, Wrocław Medical University, Wrocław, Poland
| | - Karol Perlejewski
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
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Islam S, Espitia CM, Persky DO, Carew JS, Nawrocki ST. Targeting JAK/STAT Signaling Antagonizes Resistance to Oncolytic Reovirus Therapy Driven by Prior Infection with HTLV-1 in Models of T-Cell Lymphoma. Viruses 2021; 13:1406. [PMID: 34372612 PMCID: PMC8310324 DOI: 10.3390/v13071406] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Revised: 07/11/2021] [Accepted: 07/14/2021] [Indexed: 12/12/2022] Open
Abstract
Human T-cell leukemia virus type 1 (HTLV-1) is a retrovirus that infects at least 10 million people worldwide and is associated with the development of T-cell lymphoma (TCL). The treatment of TCL remains challenging and new treatment options are urgently needed. With the goal of developing a novel therapeutic approach for TCL, we investigated the activity of the clinical formulation of oncolytic reovirus (Reolysin, Pelareorep) in TCL models. Our studies revealed that HTLV-1-negative TCL cells were highly sensitive to Reolysin-induced cell death, but HTLV-1-positive TCL cells were resistant. Consistent with these data, reovirus displayed significant viral accumulation in HTLV-1-negative cells, but failed to efficiently replicate in HTLV-1-positive cells. Transcriptome analyses of HTLV-1-positive vs. negative cells revealed a significant increase in genes associated with retroviral infection including interleukin-13 and signal transducer and activator of transcription 5 (STAT5). To investigate the relationship between HTLV-1 status and sensitivity to Reolysin, we infected HTLV-1-negative cells with HTLV-1. The presence of HTLV-1 resulted in significantly decreased sensitivity to Reolysin. Treatment with the JAK inhibitor ruxolitinib suppressed STAT5 phosphorylation and expression of the key anti-viral response protein MX1 and enhanced the anti-TCL activity of Reolysin in both HTLV-1-positive and negative cells. Our data demonstrate that the inhibition of the JAK/STAT pathway can be used as a novel approach to antagonize the resistance of HTLV-1-positive cells to oncolytic virus therapy.
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Affiliation(s)
- Shariful Islam
- Division of Translational and Regenerative Medicine, Department of Medicine, The University of Arizona Cancer Center, Tucson, AZ 85724, USA; (S.I.); (C.M.E.); (J.S.C.)
| | - Claudia M. Espitia
- Division of Translational and Regenerative Medicine, Department of Medicine, The University of Arizona Cancer Center, Tucson, AZ 85724, USA; (S.I.); (C.M.E.); (J.S.C.)
| | - Daniel O. Persky
- Division of Hematology and Oncology, Department of Medicine, The University of Arizona Cancer Center, Tucson, AZ 85724, USA;
| | - Jennifer S. Carew
- Division of Translational and Regenerative Medicine, Department of Medicine, The University of Arizona Cancer Center, Tucson, AZ 85724, USA; (S.I.); (C.M.E.); (J.S.C.)
| | - Steffan T. Nawrocki
- Division of Translational and Regenerative Medicine, Department of Medicine, The University of Arizona Cancer Center, Tucson, AZ 85724, USA; (S.I.); (C.M.E.); (J.S.C.)
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9
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Riquier S, Bessiere C, Guibert B, Bouge AL, Boureux A, Ruffle F, Audoux J, Gilbert N, Xue H, Gautheret D, Commes T. Kmerator Suite: design of specific k-mer signatures and automatic metadata discovery in large RNA-seq datasets. NAR Genom Bioinform 2021; 3:lqab058. [PMID: 34179780 PMCID: PMC8221386 DOI: 10.1093/nargab/lqab058] [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: 11/17/2020] [Revised: 05/10/2021] [Accepted: 06/17/2021] [Indexed: 11/12/2022] Open
Abstract
The huge body of publicly available RNA-sequencing (RNA-seq) libraries is a treasure of functional information allowing to quantify the expression of known or novel transcripts in tissues. However, transcript quantification commonly relies on alignment methods requiring a lot of computational resources and processing time, which does not scale easily to large datasets. K-mer decomposition constitutes a new way to process RNA-seq data for the identification of transcriptional signatures, as k-mers can be used to quantify accurately gene expression in a less resource-consuming way. We present the Kmerator Suite, a set of three tools designed to extract specific k-mer signatures, quantify these k-mers into RNA-seq datasets and quickly visualize large dataset characteristics. The core tool, Kmerator, produces specific k-mers for 97% of human genes, enabling the measure of gene expression with high accuracy in simulated datasets. KmerExploR, a direct application of Kmerator, uses a set of predictor gene-specific k-mers to infer metadata including library protocol, sample features or contaminations from RNA-seq datasets. KmerExploR results are visualized through a user-friendly interface. Moreover, we demonstrate that the Kmerator Suite can be used for advanced queries targeting known or new biomarkers such as mutations, gene fusions or long non-coding RNAs for human health applications.
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Affiliation(s)
- Sébastien Riquier
- IRMB, University of Montpellier, INSERM, 80 rue Augustin Fliche, 34295, Montpellier, France
| | - Chloé Bessiere
- IRMB, University of Montpellier, INSERM, 80 rue Augustin Fliche, 34295, Montpellier, France
| | - Benoit Guibert
- IRMB, University of Montpellier, INSERM, 80 rue Augustin Fliche, 34295, Montpellier, France
| | | | - Anthony Boureux
- IRMB, University of Montpellier, INSERM, 80 rue Augustin Fliche, 34295, Montpellier, France
| | - Florence Ruffle
- IRMB, University of Montpellier, INSERM, 80 rue Augustin Fliche, 34295, Montpellier, France
| | | | - Nicolas Gilbert
- IRMB, University of Montpellier, INSERM, 80 rue Augustin Fliche, 34295, Montpellier, France
| | - Haoliang Xue
- Institute for Integrative Biology of the Cell, CEA, CNRS, Université Paris-Saclay, 91198, Gif sur Yvette, France
| | - Daniel Gautheret
- Institute for Integrative Biology of the Cell, CEA, CNRS, Université Paris-Saclay, 91198, Gif sur Yvette, France
| | - Thérèse Commes
- IRMB, University of Montpellier, INSERM, 80 rue Augustin Fliche, 34295, Montpellier, France
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Liang J, Cui Z, Wu C, Yu Y, Tian R, Xie H, Jin Z, Fan W, Xie W, Huang Z, Xu W, Zhu J, You Z, Guo X, Qiu X, Ye J, Lang B, Li M, Tan S, Hu Z. DeepEBV: A deep learning model to predict Epstein-Barr virus (EBV) integration sites. Bioinformatics 2021; 37:3405-3411. [PMID: 34009299 DOI: 10.1093/bioinformatics/btab388] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 03/26/2021] [Accepted: 05/17/2021] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Epstein-Barr virus (EBV) is one of the most prevalent DNA oncogenic viruses. The integration of EBV into the host genome has been reported to play an important role in cancer development. The preference of EBV integration showed strong dependence on the local genomic environment, which enables the prediction of EBV integration sites. RESULTS An attention-based deep learning model, DeepEBV, was developed to predict EBV integration sites by learning local genomic features automatically. First, DeepEBV was trained and tested using the data from the dsVIS database. The results showed that DeepEBV with EBV integration sequences plus Repeat peaks and 2 fold data augmentation performed the best on the training dataset. Furthermore, the performance of the model was validated in an independent dataset. In addition, the motifs of DNA-binding proteins could influence the selection preference of viral insertional mutagenesis. Furthermore, the results showed that DeepEBV can predict EBV integration hotspot genes accurately. In summary, DeepEBV is a robust, accurate and explainable deep learning model, providing novel insights into EBV integration preferences and mechanisms. AVAILABILITY DeepEBV is available as open-source software and can be downloaded from https://github.com/JiuxingLiang/DeepEBV.gitSupplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Jiuxing Liang
- Key Laboratory of Brain, Cognition and Education Sciences, Ministry of Education, China; Institute for Brain Research and Rehabilitation, South China Normal University, Guangzhou 510631, China
| | - Zifeng Cui
- Department of Gynaecological oncology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, Guangdong, China
| | - Canbiao Wu
- Key Laboratory of Brain, Cognition and Education Sciences, Ministry of Education, China; Institute for Brain Research and Rehabilitation, South China Normal University, Guangzhou 510631, China
| | - Yao Yu
- Department of Urology, The First Medical Center of Chinese PLA General Hospital, Beijing 100853 China.,School of Medicine, Nankai University, Tianjin 300071, China
| | - Rui Tian
- Center for Translational Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, Guangdong, China
| | - Hongxian Xie
- STech Company Bio-X Lab, Zhuhai 519000, Guangdong, China
| | - Zhuang Jin
- Department of Gynaecological oncology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, Guangdong, China
| | - Weiwen Fan
- Department of Gynaecological oncology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, Guangdong, China
| | - Weiling Xie
- Department of Gynaecological oncology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, Guangdong, China
| | - Zhaoyue Huang
- Department of Gynaecological oncology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, Guangdong, China
| | - Wei Xu
- Department of Gynaecological oncology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, Guangdong, China
| | - Jingjing Zhu
- Department of Gynaecological oncology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, Guangdong, China
| | - Zeshan You
- Department of Gynaecological oncology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, Guangdong, China
| | - Xiaofang Guo
- Department of Medical Oncology of the Eastern Hospital, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510700, China
| | - Xiaofan Qiu
- Key Laboratory of Brain, Cognition and Education Sciences, Ministry of Education, China; Institute for Brain Research and Rehabilitation, South China Normal University, Guangzhou 510631, China
| | - Jiahao Ye
- Key Laboratory of Brain, Cognition and Education Sciences, Ministry of Education, China; Institute for Brain Research and Rehabilitation, South China Normal University, Guangzhou 510631, China.,School of Computer Science, South China Normal University, Guangzhou 510631, China
| | - Bin Lang
- School of Health Sciences and Sports, Macao Polytechnic Institute, China
| | - Mengyuan Li
- Department of Gynaecological oncology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, Guangdong, China
| | - Songwei Tan
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Zheng Hu
- Department of Gynaecological oncology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, Guangdong, China.,Department of Obstetrics and Gynaecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei, China
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11
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Pathogenic Role of Epstein-Barr Virus in Lung Cancers. Viruses 2021; 13:v13050877. [PMID: 34064727 PMCID: PMC8151745 DOI: 10.3390/v13050877] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 04/27/2021] [Accepted: 05/07/2021] [Indexed: 01/02/2023] Open
Abstract
Human oncogenic viruses account for at least 12% of total cancer cases worldwide. Epstein–Barr virus (EBV) is the first identified human oncogenic virus and it alone causes ~200,000 cancer cases and ~1.8% of total cancer-related death annually. Over the past 40 years, increasing lines of evidence have supported a causal link between EBV infection and a subgroup of lung cancers (LCs). In this article, we review the current understanding of the EBV-LC association and the etiological role of EBV in lung carcinogenesis. We also discuss the clinical impact of the knowledge gained from previous research, challenges, and future directions in this field. Given the high clinical relevance of EBV-LC association, there is an urgent need for further investigation on this topic.
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12
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Avilala J, Becnel D, Abdelghani R, Nanbo A, Kahn J, Li L, Lin Z. Role of Virally Encoded Circular RNAs in the Pathogenicity of Human Oncogenic Viruses. Front Microbiol 2021; 12:657036. [PMID: 33959113 PMCID: PMC8093803 DOI: 10.3389/fmicb.2021.657036] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 03/05/2021] [Indexed: 12/14/2022] Open
Abstract
Human oncogenic viruses are a group of important pathogens that etiologically contribute to at least 12% of total cancer cases in the world. As an emerging class of non-linear regulatory RNA molecules, circular RNAs (circRNAs) have gained increasing attention as a crucial player in the regulation of signaling pathways involved in viral infection and oncogenesis. With the assistance of current circRNA enrichment and detection technologies, numerous novel virally-encoded circRNAs (vcircRNAs) have been identified in the human oncogenic viruses, initiating an exciting new era of vcircRNA research. In this review, we discuss the current understanding of the roles of vcircRNAs in the respective viral infection cycles and in virus-associated pathogenesis.
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Affiliation(s)
- Janardhan Avilala
- Tulane University Health Sciences Center and Tulane Cancer Center, New Orleans, LA, United States
| | - David Becnel
- Department of Medicine, Tulane University Health Sciences Center, New Orleans, LA, United States
| | - Ramsy Abdelghani
- Department of Medicine, Tulane University Health Sciences Center, New Orleans, LA, United States
| | - Asuka Nanbo
- National Research Center for the Control and Prevention of Infectious Diseases, Nagasaki University, Nagasaki, Japan
| | - Jacob Kahn
- Tulane University Health Sciences Center and Tulane Cancer Center, New Orleans, LA, United States
| | - Li Li
- Institute of Translational Research, Ochsner Clinic Foundation, New Orleans, LA, United States
| | - Zhen Lin
- Tulane University Health Sciences Center and Tulane Cancer Center, New Orleans, LA, United States
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13
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Loiseau V, Cordaux R, Giraud I, Beby-Defaux A, Lévêque N, Gilbert C. Characterization of a new case of XMLV (Bxv1) contamination in the human cell line Hep2 (clone 2B). Sci Rep 2020; 10:16046. [PMID: 32994520 PMCID: PMC7524804 DOI: 10.1038/s41598-020-73169-y] [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: 10/04/2019] [Accepted: 08/31/2020] [Indexed: 11/09/2022] Open
Abstract
The use of misidentified cell lines contaminated by other cell lines and/or microorganisms has generated much confusion in the scientific literature. Detailed characterization of such contaminations is therefore crucial to avoid misinterpretation and ensure robustness and reproducibility of research. Here we use DNA-seq data produced in our lab to first confirm that the Hep2 (clone 2B) cell line (Sigma-Aldrich catalog number: 85011412-1VL) is indistinguishable from the HeLa cell line by mapping integrations of the human papillomavirus 18 (HPV18) at their expected loci on chromosome 8. We then show that the cell line is also contaminated by a xenotropic murine leukemia virus (XMLV) that is nearly identical to the mouse Bxv1 provirus and we characterize one Bxv1 provirus, located in the second intron of the pseudouridylate synthase 1 (PUS1) gene. Using an RNA-seq dataset, we confirm the high expression of the E6 and E7 HPV18 oncogenes, show that the entire Bxv1 genome is moderately expressed, and retrieve a Bxv1 splicing event favouring expression of the env gene. Hep2 (clone 2B) is the fourth human cell line so far known to be contaminated by the Bxv1 XMLV. This contamination has to be taken into account when using the cell line in future experiments.
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Affiliation(s)
- Vincent Loiseau
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, 91198, Gif-sur-Yvette, France
| | - Richard Cordaux
- Université de Poitiers, CNRS UMR 7267 Laboratoire Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, 5 Rue Albert Turpain, TSA 51106, 86073, Poitiers Cedex 9, France
| | - Isabelle Giraud
- Université de Poitiers, CNRS UMR 7267 Laboratoire Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, 5 Rue Albert Turpain, TSA 51106, 86073, Poitiers Cedex 9, France
| | - Agnès Beby-Defaux
- Laboratoire de Virologie et de Mycobactériologie, CHU de Poitiers, Poitiers, France.,Unité de Microbiologie Moléculaire et Séquençage, CHU de Poitiers, Poitiers, France
| | - Nicolas Lévêque
- Laboratoire de Virologie et de Mycobactériologie, CHU de Poitiers, Poitiers, France.,EA4331-LITEC, Université de Poitiers, Poitiers, France
| | - Clément Gilbert
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, 91198, Gif-sur-Yvette, France.
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14
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Andrews RJ, O’Leary CA, Moss WN. A survey of RNA secondary structural propensity encoded within human herpesvirus genomes: global comparisons and local motifs. PeerJ 2020; 8:e9882. [PMID: 32974099 PMCID: PMC7487152 DOI: 10.7717/peerj.9882] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 08/16/2020] [Indexed: 12/13/2022] Open
Abstract
There are nine herpesviruses known to infect humans, of which Epstein-Barr virus (EBV) is the most widely distributed (>90% of adults infected). This ubiquitous virus is implicated in a variety of cancers and autoimmune diseases. Previous analyses of the EBV genome revealed numerous regions with evidence of generating unusually stable and conserved RNA secondary structures and led to the discovery of a novel class of EBV non-coding (nc)RNAs: the stable intronic sequence (sis)RNAs. To gain a better understanding of the roles of RNA structure in EBV biology and pathogenicity, we revisit EBV using recently developed tools for genome-wide motif discovery and RNA structural characterization. This corroborated previous results and revealed novel motifs with potential functionality; one of which has been experimentally validated. Additionally, since many herpesviruses increasingly rival the seroprevalence of EBV (VZV, HHV-6 and HHV-7 being the most notable), analyses were expanded to include all sequenced human Herpesvirus RefSeq genomes, allowing for genomic comparisons. In total 10 genomes were analyzed, for EBV (types 1 and 2), HCMV, HHV-6A, HHV-6B, HHV-7, HSV-1, HSV-2, KSHV, and VZV. All resulting data were archived in the RNAStructuromeDB (https://structurome.bb.iastate.edu/herpesvirus) to make them available to a wide array of researchers.
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Affiliation(s)
- Ryan J. Andrews
- The Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, United States of America
| | - Collin A. O’Leary
- The Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, United States of America
| | - Walter N. Moss
- The Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, United States of America
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15
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Chen X, Kost J, Li D. Comprehensive comparative analysis of methods and software for identifying viral integrations. Brief Bioinform 2020; 20:2088-2097. [PMID: 30102374 DOI: 10.1093/bib/bby070] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 07/02/2018] [Accepted: 07/12/2018] [Indexed: 12/13/2022] Open
Abstract
Many viruses are capable of integrating in the human genome, particularly viruses involved in tumorigenesis. Viral integrations can be considered genetic markers for discovering virus-caused cancers and inferring cancer cell development. Next-generation sequencing (NGS) technologies have been widely used to screen for viral integrations in cancer genomes, and a number of bioinformatics tools have been developed to detect viral integrations using NGS data. However, there has been no systematic comparison of the methods or software. In this study, we performed a comprehensive comparative analysis of the designs, performance, functionality and limitations among the existing methods and software for detecting viral integrations. We further compared the sensitivity, precision and runtime of integration detection of four representative tools. Our analyses showed that each of the existing software had its own merits; however, none of them were sufficient for parallel or accurate virome-wide detection. After carefully evaluating the limitations shared by the existing methods, we proposed strategies and directions for developing virome-wide integration detection.
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Affiliation(s)
- Xun Chen
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont 05405, USA
| | - Jason Kost
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont 05405, USA
| | - Dawei Li
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont 05405, USA.,Department of Computer Science, University of Vermont, Burlington, Vermont 05405, USA.,Neuroscience, Behavior, and Health Initiative, University of Vermont, Burlington, Vermont 05405, USA.,Cancer Center, University of Vermont, Burlington, Vermont 05405, USA
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16
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Mollerup S, Asplund M, Friis-Nielsen J, Kjartansdóttir KR, Fridholm H, Hansen TA, Herrera JAR, Barnes CJ, Jensen RH, Richter SR, Nielsen IB, Pietroni C, Alquezar-Planas DE, Rey-Iglesia A, Olsen PVS, Rajpert-De Meyts E, Groth-Pedersen L, von Buchwald C, Jensen DH, Gniadecki R, Høgdall E, Langhoff JL, Pete I, Vereczkey I, Baranyai Z, Dybkaer K, Johnsen HE, Steiniche T, Hokland P, Rosenberg J, Baandrup U, Sicheritz-Pontén T, Willerslev E, Brunak S, Lund O, Mourier T, Vinner L, Izarzugaza JMG, Nielsen LP, Hansen AJ. High-Throughput Sequencing-Based Investigation of Viruses in Human Cancers by Multienrichment Approach. J Infect Dis 2020; 220:1312-1324. [PMID: 31253993 PMCID: PMC6743825 DOI: 10.1093/infdis/jiz318] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Accepted: 06/27/2019] [Indexed: 01/10/2023] Open
Abstract
Background Viruses and other infectious agents cause more than 15% of human cancer cases. High-throughput sequencing-based studies of virus-cancer associations have mainly focused on cancer transcriptome data. Methods In this study, we applied a diverse selection of presequencing enrichment methods targeting all major viral groups, to characterize the viruses present in 197 samples from 18 sample types of cancerous origin. Using high-throughput sequencing, we generated 710 datasets constituting 57 billion sequencing reads. Results Detailed in silico investigation of the viral content, including exclusion of viral artefacts, from de novo assembled contigs and individual sequencing reads yielded a map of the viruses detected. Our data reveal a virome dominated by papillomaviruses, anelloviruses, herpesviruses, and parvoviruses. More than half of the included samples contained 1 or more viruses; however, no link between specific viruses and cancer types were found. Conclusions Our study sheds light on viral presence in cancers and provides highly relevant virome data for future reference.
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Affiliation(s)
- Sarah Mollerup
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
| | - Maria Asplund
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
| | - Jens Friis-Nielsen
- Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark
| | | | - Helena Fridholm
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
| | - Thomas Arn Hansen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
| | - José Alejandro Romero Herrera
- Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark.,Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | | | - Randi Holm Jensen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
| | - Stine Raith Richter
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
| | - Ida Broman Nielsen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
| | - Carlotta Pietroni
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
| | - David E Alquezar-Planas
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
| | - Alba Rey-Iglesia
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
| | - Pernille V S Olsen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
| | - Ewa Rajpert-De Meyts
- Department of Growth and Reproduction, Copenhagen University Hospital (Rigshospitalet), Denmark
| | - Line Groth-Pedersen
- Department of Pediatrics and Adolescent Medicine, University Hospital Rigshospitalet, Denmark
| | - Christian von Buchwald
- Department of Otorhinolaryngology, Head and Neck Surgery and Audiology, Rigshospitalet, Copenhagen University Hospital
| | - David H Jensen
- Department of Otorhinolaryngology, Head and Neck Surgery and Audiology, Rigshospitalet, Copenhagen University Hospital
| | - Robert Gniadecki
- Department of Dermato-Venerology, Faculty of Health Sciences, Copenhagen University Hospital, Bispebjerg Hospital, Denmark
| | - Estrid Høgdall
- Department of Pathology, Herlev and Gentofte Hospital, University of Copenhagen, Denmark
| | - Jill Levin Langhoff
- Department of Pathology, Herlev and Gentofte Hospital, University of Copenhagen, Denmark
| | - Imre Pete
- National Institute of Oncology, Department of Gynecology, Budapest, Hungary
| | - Ildikó Vereczkey
- National Institute of Oncology, Department of Gynecology, Budapest, Hungary
| | - Zsolt Baranyai
- 1st Department of Surgery, Semmelweis University, Budapest, Hungary
| | - Karen Dybkaer
- Department of Clinical Medicine, Aalborg University, Denmark
| | | | | | - Peter Hokland
- Department of Clinical Medicine, Department of Haematology, Aarhus University Hospital, Denmark
| | - Jacob Rosenberg
- Department of Surgery, Herlev and Gentofte Hospital, University of Copenhagen, Denmark
| | - Ulrik Baandrup
- Center for Clinical Research, North Denmark Regional Hospital and Department of Clinical Medicine, Aalborg University, Hjørring, Denmark
| | - Thomas Sicheritz-Pontén
- Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark.,Centre of Excellence for Omics-Driven Computational Biodiscovery, AIMST University, Kedah, Malaysia
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
| | - Søren Brunak
- Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark.,Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Ole Lund
- Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark
| | - Tobias Mourier
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
| | - Lasse Vinner
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
| | - Jose M G Izarzugaza
- Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark
| | - Lars Peter Nielsen
- Department of Autoimmunology and Biomarkers, Statens Serum Institut, Copenhagen S, Denmark
| | - Anders Johannes Hansen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
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17
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Selitsky SR, Marron D, Hollern D, Mose LE, Hoadley KA, Jones C, Parker JS, Dittmer DP, Perou CM. Virus expression detection reveals RNA-sequencing contamination in TCGA. BMC Genomics 2020; 21:79. [PMID: 31992194 PMCID: PMC6986043 DOI: 10.1186/s12864-020-6483-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 01/10/2020] [Indexed: 02/06/2023] Open
Abstract
Background Contamination of reagents and cross contamination across samples is a long-recognized issue in molecular biology laboratories. While often innocuous, contamination can lead to inaccurate results. Cantalupo et al., for example, found HeLa-derived human papillomavirus 18 (H-HPV18) in several of The Cancer Genome Atlas (TCGA) RNA-sequencing samples. This work motivated us to assess a greater number of samples and determine the origin of possible contaminations using viral sequences. To detect viruses with high specificity, we developed the publicly available workflow, VirDetect, that detects virus and laboratory vector sequences in RNA-seq samples. We applied VirDetect to 9143 RNA-seq samples sequenced at one TCGA sequencing center (28/33 cancer types) over 5 years. Results We confirmed that H-HPV18 was present in many samples and determined that viral transcripts from H-HPV18 significantly co-occurred with those from xenotropic mouse leukemia virus-related virus (XMRV). Using laboratory metadata and viral transcription, we determined that the likely contaminant was a pool of cell lines known as the “common reference”, which was sequenced alongside TCGA RNA-seq samples as a control to monitor quality across technology transitions (i.e. microarray to GAII to HiSeq), and to link RNA-seq to previous generation microarrays that standardly used the “common reference”. One of the cell lines in the pool was a laboratory isolate of MCF-7, which we discovered was infected with XMRV; another constituent of the pool was likely HeLa cells. Conclusions Altogether, this indicates a multi-step contamination process. First, MCF-7 was infected with an XMRV. Second, this infected cell line was added to a pool of cell lines, which contained HeLa. Finally, RNA from this pool of cell lines contaminated several TCGA tumor samples most-likely during library construction. Thus, these human tumors with H-HPV or XMRV reads were likely not infected with H-HPV 18 or XMRV.
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Affiliation(s)
- Sara R Selitsky
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA.,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA
| | - David Marron
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA
| | - Daniel Hollern
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA.,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA
| | - Lisle E Mose
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA
| | - Katherine A Hoadley
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA.,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA
| | - Corbin Jones
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Joel S Parker
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA.,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA
| | - Dirk P Dittmer
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA.,Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Charles M Perou
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA. .,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA.
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18
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Park SJ, Onizuka S, Seki M, Suzuki Y, Iwata T, Nakai K. A systematic sequencing-based approach for microbial contaminant detection and functional inference. BMC Biol 2019; 17:72. [PMID: 31519179 PMCID: PMC6743104 DOI: 10.1186/s12915-019-0690-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 08/20/2019] [Indexed: 12/16/2022] Open
Abstract
Background Microbial contamination poses a major difficulty for successful data analysis in biological and biomedical research. Computational approaches utilizing next-generation sequencing (NGS) data offer promising diagnostics to assess the presence of contaminants. However, as host cells are often contaminated by multiple microorganisms, these approaches require careful attention to intra- and interspecies sequence similarities, which have not yet been fully addressed. Results We present a computational approach that rigorously investigates the genomic origins of sequenced reads, including those mapped to multiple species that have been discarded in previous studies. Through the analysis of large-scale synthetic and public NGS samples, we estimate that 1000–100,000 contaminating microbial reads are detected per million host reads sequenced by RNA-seq. The microbe catalog we established included Cutibacterium as a prevalent contaminant, suggesting that contamination mostly originates from the laboratory environment. Importantly, by applying a systematic method to infer the functional impact of contamination, we revealed that host-contaminant interactions cause profound changes in the host molecular landscapes, as exemplified by changes in inflammatory and apoptotic pathways during Mycoplasma infection of lymphoma cells. Conclusions We provide a computational method for profiling microbial contamination on NGS data and suggest that sources of contamination in laboratory reagents and the experimental environment alter the molecular landscape of host cells leading to phenotypic changes. These findings reinforce the concept that precise determination of the origins and functional impacts of contamination is imperative for quality research and illustrate the usefulness of the proposed approach to comprehensively characterize contamination landscapes. Electronic supplementary material The online version of this article (10.1186/s12915-019-0690-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sung-Joon Park
- Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, 108-8693, Japan
| | - Satoru Onizuka
- Institute of Advanced Biomedical Engineering and Science, Tokyo Women's Medical University, Tokyo, 162-8666, Japan.,Division of Periodontology, Department of Oral Function, Kyushu Dental University, Fukuoka, 803-8580, Japan
| | - Masahide Seki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 277-8568, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 277-8568, Japan
| | - Takanori Iwata
- Institute of Advanced Biomedical Engineering and Science, Tokyo Women's Medical University, Tokyo, 162-8666, Japan.,Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, 113-8549, Japan
| | - Kenta Nakai
- Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, 108-8693, Japan. .,Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 277-8568, Japan.
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19
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Nakhoul H, Lin Z, Wang X, Roberts C, Dong Y, Flemington E. High-Throughput Sequence Analysis of Peripheral T-Cell Lymphomas Indicates Subtype-Specific Viral Gene Expression Patterns and Immune Cell Microenvironments. mSphere 2019; 4:e00248-19. [PMID: 31292228 PMCID: PMC6620372 DOI: 10.1128/msphere.00248-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 06/24/2019] [Indexed: 12/11/2022] Open
Abstract
Certain peripheral T-cell lymphomas (PTCLs) have been associated with viral infection, particularly infection with Epstein-Barr virus (EBV). However, a comprehensive virome analysis across PTCLs has not previously been reported. Here we utilized published whole-transcriptome RNA sequencing (RNA-seq) data sets from seven different PTCL studies and new RNA-seq data from our laboratory to screen for virus association, to analyze viral gene expression, and to assess B- and T-cell receptor diversity paradigms across PTCL subtypes. In addition to identifying EBV in angioimmunoblastic T-cell lymphoma (AITL) and extranodal NK/T-cell lymphoma (ENKTL), two PTCL subtypes with well-established EBV associations, we also detected EBV in several cases of anaplastic large-cell lymphoma (ALCL), and we found evidence of infection by the oncogenic viruses Kaposi's sarcoma-associated herpesvirus and human T-cell leukemia virus type 1 in isolated PTCL cases. In AITLs, EBV gene expression analysis showed expression of immediate early, early, and late lytic genes, suggesting either low-level lytic gene expression or productive infection in a subset of EBV-infected B-lymphocyte stromal cells. Deconvolution of immune cell subpopulations demonstrated a greater B-cell signal in AITLs than in other PTCL subtypes, consistent with a larger role for B-cell support in the pathogenesis of AITL. Reconstructed T-cell receptor (TCR) and B-cell receptor (BCR) repertoires demonstrated increased BCR diversity in AITLs, consistent with a possible EBV-driven polyclonal response. These findings indicate potential alternative roles for EBV in PTCLs, in addition to the canonical oncogenic mechanisms associated with EBV latent infection. Our findings also suggest the involvement of other viruses in PTCL pathogenesis and demonstrate immunological alterations associated with these cancers.IMPORTANCE In this study, we utilized next-generation sequencing data from 7 different studies of peripheral T-cell lymphoma (PTCL) patient samples to globally assess viral associations, provide insights into the contributions of EBV gene expression to the tumor phenotype, and assess the unique roles of EBV in modulating the immune cell tumor microenvironment. These studies revealed potential roles for EBV replication genes in some PTCL subtypes, the possible role of additional human tumor viruses in rare cases of PTCLs, and a role for EBV in providing a unique immune microenvironmental niche in one subtype of PTCLs. Together, these studies provide new insights into the understudied role of tumor viruses in PTCLs.
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Affiliation(s)
- Hani Nakhoul
- Department of Pathology, Tulane Cancer Center, Tulane University School of Medicine, New Orleans, Louisiana, USA
| | - Zhen Lin
- Department of Pathology, Tulane Cancer Center, Tulane University School of Medicine, New Orleans, Louisiana, USA
| | - Xia Wang
- Department of Pathology, Tulane Cancer Center, Tulane University School of Medicine, New Orleans, Louisiana, USA
| | - Claire Roberts
- Department of Pathology, Tulane Cancer Center, Tulane University School of Medicine, New Orleans, Louisiana, USA
| | - Yan Dong
- Department of Structural and Cellular Biology, Tulane Cancer Center, Tulane University School of Medicine, New Orleans, Louisiana, USA
| | - Erik Flemington
- Department of Pathology, Tulane Cancer Center, Tulane University School of Medicine, New Orleans, Louisiana, USA
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20
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Multidimensional analysis of Gammaherpesvirus RNA expression reveals unexpected heterogeneity of gene expression. PLoS Pathog 2019; 15:e1007849. [PMID: 31166996 PMCID: PMC6576797 DOI: 10.1371/journal.ppat.1007849] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 06/17/2019] [Accepted: 05/17/2019] [Indexed: 11/19/2022] Open
Abstract
Virus-host interactions are frequently studied in bulk cell populations, obscuring cell-to-cell variation. Here we investigate endogenous herpesvirus gene expression at the single-cell level, combining a sensitive and robust fluorescent in situ hybridization platform with multiparameter flow cytometry, to study the expression of gammaherpesvirus non-coding RNAs (ncRNAs) during lytic replication, latent infection and reactivation in vitro. This method allowed robust detection of viral ncRNAs of murine gammaherpesvirus 68 (γHV68), Kaposi’s sarcoma associated herpesvirus and Epstein-Barr virus, revealing variable expression at the single-cell level. By quantifying the inter-relationship of viral ncRNA, viral mRNA, viral protein and host mRNA regulation during γHV68 infection, we find heterogeneous and asynchronous gene expression during latency and reactivation, with reactivation from latency identified by a distinct gene expression profile within rare cells. Further, during lytic replication with γHV68, we find many cells have limited viral gene expression, with only a fraction of cells showing robust gene expression, dynamic RNA localization, and progressive infection. Lytic viral gene expression was enhanced in primary fibroblasts and by conditions associated with enhanced viral replication, with multiple subpopulations of cells present in even highly permissive infection conditions. These findings, powered by single-cell analysis integrated with automated clustering algorithms, suggest inefficient or abortive γHV infection in many cells, and identify substantial heterogeneity in viral gene expression at the single-cell level. The gammaherpesviruses are a group of DNA tumor viruses that establish lifelong infection. How these viruses infect and manipulate cells has frequently been studied in bulk populations of cells. While these studies have been incredibly insightful, there is limited understanding of how virus infection proceeds within a single cell. Here we present a new approach to quantify gammaherpesvirus gene expression at the single-cell level. This method allows us to detect cell-to-cell variation in the expression of virus non-coding RNAs, an important and understudied class of RNAs which do not encode for proteins. By examining multiple features of virus gene expression, this method further reveals significant variation in infection between cells across multiple stages of infection, even in conditions generally thought to be highly uniform. These studies emphasize that gammaherpesvirus infection can be surprisingly heterogeneous when viewed at the level of the individual cell. Because this approach can be broadly applied across diverse viruses, this study affords new opportunities to understand the complexity of virus infection within single cells.
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21
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Hancock MH, Skalsky RL. Roles of Non-coding RNAs During Herpesvirus Infection. Curr Top Microbiol Immunol 2019; 419:243-280. [PMID: 28674945 DOI: 10.1007/82_2017_31] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Non-coding RNAs (ncRNAs) play essential roles in multiple aspects of the life cycles of herpesviruses and contribute to lifelong persistence of herpesviruses within their respective hosts. In this chapter, we discuss the types of ncRNAs produced by the different herpesvirus families during infection, some of the cellular ncRNAs manipulated by these viruses, and the overall contributions of ncRNAs to the viral life cycle, influence on the host environment, and pathogenesis.
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Affiliation(s)
- Meaghan H Hancock
- Vaccine and Gene Therapy Institute at Oregon Health and Science University, Beaverton, OR, USA
| | - Rebecca L Skalsky
- Vaccine and Gene Therapy Institute at Oregon Health and Science University, Beaverton, OR, USA.
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22
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Chen X, Kost J, Sulovari A, Wong N, Liang WS, Cao J, Li D. A virome-wide clonal integration analysis platform for discovering cancer viral etiology. Genome Res 2019; 29:819-830. [PMID: 30872350 PMCID: PMC6499315 DOI: 10.1101/gr.242529.118] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 03/11/2019] [Indexed: 12/31/2022]
Abstract
Oncoviral infection is responsible for 12%–15% of cancer in humans. Convergent evidence from epidemiology, pathology, and oncology suggests that new viral etiologies for cancers remain to be discovered. Oncoviral profiles can be obtained from cancer genome sequencing data; however, widespread viral sequence contamination and noncausal viruses complicate the process of identifying genuine oncoviruses. Here, we propose a novel strategy to address these challenges by performing virome-wide screening of early-stage clonal viral integrations. To implement this strategy, we developed VIcaller, a novel platform for identifying viral integrations that are derived from any characterized viruses and shared by a large proportion of tumor cells using whole-genome sequencing (WGS) data. The sensitivity and precision were confirmed with simulated and benchmark cancer data sets. By applying this platform to cancer WGS data sets with proven or speculated viral etiology, we newly identified or confirmed clonal integrations of hepatitis B virus (HBV), human papillomavirus (HPV), Epstein-Barr virus (EBV), and BK Virus (BKV), suggesting the involvement of these viruses in early stages of tumorigenesis in affected tumors, such as HBV in TERT and KMT2B (also known as MLL4) gene loci in liver cancer, HPV and BKV in bladder cancer, and EBV in non-Hodgkin's lymphoma. We also showed the capacity of VIcaller to identify integrations from some uncharacterized viruses. This is the first study to systematically investigate the strategy and method of virome-wide screening of clonal integrations to identify oncoviruses. Searching clonal viral integrations with our platform has the capacity to identify virus-caused cancers and discover cancer viral etiologies.
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Affiliation(s)
- Xun Chen
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont 05405, USA
| | - Jason Kost
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont 05405, USA
| | - Arvis Sulovari
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont 05405, USA
| | - Nathalie Wong
- Department of Anatomical and Cellular Pathology, Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, NT, Hong Kong 999077, P.R. China
| | - Winnie S Liang
- Translational Genomics Research Institute, Phoenix, Arizona 85004, USA
| | - Jian Cao
- Division of Medical Oncology, Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08903, USA.,Department of Medicine, Rutgers Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08903, USA
| | - Dawei Li
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont 05405, USA.,Neuroscience, Behavior, and Health Initiative, University of Vermont, Burlington, Vermont 05405, USA.,Department of Computer Science, University of Vermont, Burlington, Vermont 05405, USA
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23
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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.
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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
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24
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Uphoff CC, Pommerenke C, Denkmann SA, Drexler HG. Screening human cell lines for viral infections applying RNA-Seq data analysis. PLoS One 2019; 14:e0210404. [PMID: 30629668 PMCID: PMC6328144 DOI: 10.1371/journal.pone.0210404] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 12/21/2018] [Indexed: 01/09/2023] Open
Abstract
Monitoring viral infections of cell cultures is largely neglected although the viruses may have an impact on the physiology of cells and may constitute a biohazard regarding laboratory safety and safety of bioactive agents produced by cell cultures. PCR, immunological assays, and enzyme activity tests represent common methods to detect virus infections. We have screened more than 300 Cancer Cell Line Encyclopedia RNA sequencing and 60 whole exome sequencing human cell lines data sets for specific viral sequences and general viral nucleotide and protein sequence assessment applying the Taxonomer bioinformatics tool developed by IDbyDNA. The results were compared with our previous findings from virus specific PCR analyses. Both, the results obtained from the direct alignment method and the Taxonomer alignment method revealed a complete concordance with the PCR results: twenty cell lines were found to be infected with five virus species. Taxonomer further uncovered a bovine polyomavirus infection in the breast cancer cell line SK-BR-3 most likely introduced by contaminated fetal bovine serum. RNA-Seq data sets were more sensitive for virus detection although a significant proportion of cell lines revealed low numbers of virus specific alignments attributable to low level nucleotide contamination during RNA preparation or sequencing procedure. Low quality reads leading to Taxonomer false positive results can be eliminated by trimming the sequence data before analysis. One further important result is that no viruses were detected that had never been shown to occur in cell cultures. The results prove that the currently applied testing of cell cultures is adequate for the detection of contamination and for the risk assessment of cell cultures. The results emphasize that next generation sequencing is an efficient tool to determine the viral infection status of human cells.
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Affiliation(s)
- Cord C. Uphoff
- Department of Human and Animal Cell Lines, Leibniz Institute DSMZ—German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Claudia Pommerenke
- Department of Human and Animal Cell Lines, Leibniz Institute DSMZ—German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Sabine A. Denkmann
- Department of Human and Animal Cell Lines, Leibniz Institute DSMZ—German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Hans G. Drexler
- Department of Human and Animal Cell Lines, Leibniz Institute DSMZ—German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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25
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Tan KT, Ding LW, Sun QY, Lao ZT, Chien W, Ren X, Xiao JF, Loh XY, Xu L, Lill M, Mayakonda A, Lin DC, Yang H, Koeffler HP. Profiling the B/T cell receptor repertoire of lymphocyte derived cell lines. BMC Cancer 2018; 18:940. [PMID: 30285677 PMCID: PMC6167786 DOI: 10.1186/s12885-018-4840-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2018] [Accepted: 09/19/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Clonal VDJ rearrangement of B/T cell receptors (B/TCRs) occurring during B/T lymphocyte development has been used as a marker to track the clonality of B/T cell populations. METHODS We systematically profiled the B/T cell receptor repertoire of 936 cancer cell lines across a variety of cancer types as well as 462 Epstein-Barr Virus (EBV) transformed normal B lymphocyte lines using RNA sequencing data. RESULTS Rearranged B/TCRs were readily detected in cell lines derived from lymphocytes, and subclonality or potential biclonality were found in a number of blood cancer cell lines. Clonal BCR/TCR rearrangements were detected in several blast phase CML lines and unexpectedly, one gastric cancer cell line (KE-97), reflecting a lymphoid origin of these cells. Notably, clonality was highly prevalent in EBV transformed B lymphocytes, suggesting either transformation only occurred in a few B cells or those with a growth advantage dominated the transformed population through clonal evolution. CONCLUSIONS Our analysis reveals the complexity and heterogeneity of the BCR/TCR rearrangement repertoire and provides a unique insight into the clonality of lymphocyte derived cell lines.
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Affiliation(s)
- Kar-Tong Tan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Ling-Wen Ding
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.
| | - Qiao-Yang Sun
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Zhen-Tang Lao
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,Department of Haematology, Singapore General Hospital, Singapore, Singapore
| | - Wenwen Chien
- Division of Hematology/Oncology, Cedars-Sinai Medical Center, UCLA School of Medicine, Los Angeles, USA
| | - Xi Ren
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Jin-Fen Xiao
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Xin Yi Loh
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Liang Xu
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Michael Lill
- Division of Hematology/Oncology, Cedars-Sinai Medical Center, UCLA School of Medicine, Los Angeles, USA
| | - Anand Mayakonda
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - De-Chen Lin
- Division of Hematology/Oncology, Cedars-Sinai Medical Center, UCLA School of Medicine, Los Angeles, USA
| | - Henry Yang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.
| | - H Phillip Koeffler
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,Division of Hematology/Oncology, Cedars-Sinai Medical Center, UCLA School of Medicine, Los Angeles, USA
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26
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Epstein-Barr Virus-Positive Cancers Show Altered B-Cell Clonality. mSystems 2018; 3:mSystems00081-18. [PMID: 30271878 PMCID: PMC6156273 DOI: 10.1128/msystems.00081-18] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 08/29/2018] [Indexed: 12/14/2022] Open
Abstract
Around 20% of human cancers are associated with viruses. Epstein-Barr virus (EBV) contributes to gastric cancer, nasopharyngeal carcinoma, and certain lymphomas, but its role in other cancer types remains controversial. We assessed the prevalence of EBV in RNA-seq from 32 tumor types in the Cancer Genome Atlas Project (TCGA) and found EBV to be present in >5% of samples in 12 tumor types. EBV infects epithelial cells and B cells and in B cells causes proliferation. We hypothesized that the low expression of EBV in most of the tumor types was due to infiltration of B cells into the tumor. The increase in B-cell abundance and diversity in subjects where EBV was detected in the tumors strengthens this hypothesis. Overall, we found that EBV was associated with an increased and altered immune response. This result is not evidence of causality, but a potential novel biomarker for tumor immune status. Epstein-Barr virus (EBV) is convincingly associated with gastric cancer, nasopharyngeal carcinoma, and certain lymphomas, but its role in other cancer types remains controversial. To test the hypothesis that there are additional cancer types with high prevalence of EBV, we determined EBV viral expression in all the Cancer Genome Atlas Project (TCGA) mRNA sequencing (mRNA-seq) samples (n = 10,396) from 32 different tumor types. We found that EBV was present in gastric adenocarcinoma and lymphoma, as expected, and was also present in >5% of samples in 10 additional tumor types. For most samples, EBV transcript levels were low, which suggests that EBV was likely present due to infected infiltrating B cells. In order to determine if there was a difference in the B-cell populations, we assembled B-cell receptors for each sample and found B-cell receptor abundance (P ≤ 1.4 × 10−20) and diversity (P ≤ 8.3 × 10−27) were significantly higher in EBV-positive samples. Moreover, diversity was independent of B-cell abundance, suggesting that the presence of EBV was associated with an increased and altered B-cell population. IMPORTANCE Around 20% of human cancers are associated with viruses. Epstein-Barr virus (EBV) contributes to gastric cancer, nasopharyngeal carcinoma, and certain lymphomas, but its role in other cancer types remains controversial. We assessed the prevalence of EBV in RNA-seq from 32 tumor types in the Cancer Genome Atlas Project (TCGA) and found EBV to be present in >5% of samples in 12 tumor types. EBV infects epithelial cells and B cells and in B cells causes proliferation. We hypothesized that the low expression of EBV in most of the tumor types was due to infiltration of B cells into the tumor. The increase in B-cell abundance and diversity in subjects where EBV was detected in the tumors strengthens this hypothesis. Overall, we found that EBV was associated with an increased and altered immune response. This result is not evidence of causality, but a potential novel biomarker for tumor immune status.
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27
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Ungerleider N, Concha M, Lin Z, Roberts C, Wang X, Cao S, Baddoo M, Moss WN, Yu Y, Seddon M, Lehman T, Tibbetts S, Renne R, Dong Y, Flemington EK. The Epstein Barr virus circRNAome. PLoS Pathog 2018; 14:e1007206. [PMID: 30080890 PMCID: PMC6095625 DOI: 10.1371/journal.ppat.1007206] [Citation(s) in RCA: 100] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 08/16/2018] [Accepted: 07/11/2018] [Indexed: 11/18/2022] Open
Abstract
Our appreciation for the extent of Epstein Barr virus (EBV) transcriptome complexity continues to grow through findings of EBV encoded microRNAs, new long non-coding RNAs as well as the more recent discovery of over a hundred new polyadenylated lytic transcripts. Here we report an additional layer to the EBV transcriptome through the identification of a repertoire of latent and lytic viral circular RNAs. Utilizing RNase R-sequencing with cell models representing latency types I, II, and III, we identified EBV encoded circular RNAs expressed from the latency Cp promoter involving backsplicing from the W1 and W2 exons to the C1 exon, from the EBNA BamHI U fragment exon, and from the latency long non-coding RPMS1 locus. In addition, we identified circular RNAs expressed during reactivation including backsplicing from exon 8 to exon 2 of the LMP2 gene and a highly expressed circular RNA derived from intra-exonic backsplicing within the BHLF1 gene. While expression of most of these circular RNAs was found to depend on the EBV transcriptional program utilized and the transcription levels of the associated loci, expression of LMP2 exon 8 to exon 2 circular RNA was found to be cell model specific. Altogether we identified over 30 unique EBV circRNAs candidates and we validated and determined the structural features, expression profiles and nuclear/cytoplasmic distributions of several predominant and notable viral circRNAs. Further, we show that two of the EBV circular RNAs derived from the RPMS1 locus are detected in EBV positive clinical stomach cancer specimens. This study increases the known EBV latency and lytic transcriptome repertoires to include viral circular RNAs and it provides an essential foundation and resource for investigations into the functions and roles of this new class of EBV transcripts in EBV biology and diseases.
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Affiliation(s)
- Nathan Ungerleider
- Department of Pathology, Tulane University School of Medicine, Tulane Cancer Center, New Orleans, LA, United States of America
| | - Monica Concha
- Department of Pathology, Tulane University School of Medicine, Tulane Cancer Center, New Orleans, LA, United States of America
| | - Zhen Lin
- Department of Pathology, Tulane University School of Medicine, Tulane Cancer Center, New Orleans, LA, United States of America
| | - Claire Roberts
- Department of Pathology, Tulane University School of Medicine, Tulane Cancer Center, New Orleans, LA, United States of America
| | - Xia Wang
- Department of Pathology, Tulane University School of Medicine, Tulane Cancer Center, New Orleans, LA, United States of America
| | - Subing Cao
- Department of Structural and Cellular Biology, Tulane University School of Medicine, Tulane Cancer Center, New Orleans, LA, United States of America
| | - Melody Baddoo
- Department of Pathology, Tulane University School of Medicine, Tulane Cancer Center, New Orleans, LA, United States of America
| | - Walter N. Moss
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, United States of America
| | - Yi Yu
- Department of Pathology, Tulane University School of Medicine, Tulane Cancer Center, New Orleans, LA, United States of America
| | | | - Terri Lehman
- Reprocell USA, Beltsville, MD, United States of America
| | - Scott Tibbetts
- Department of Biochemistry and Molecular Biology, University of Florida College of Medicine, Gainesville, FL, United States of America
| | - Rolf Renne
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL, United States of America
| | - Yan Dong
- Department of Structural and Cellular Biology, Tulane University School of Medicine, Tulane Cancer Center, New Orleans, LA, United States of America
| | - Erik K. Flemington
- Department of Pathology, Tulane University School of Medicine, Tulane Cancer Center, New Orleans, LA, United States of America
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28
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Jia Ng SS, Zheng RT, Osman I, Pek JW. Generation of Drosophila sisRNAs by Independent Transcription from Cognate Introns. iScience 2018; 4:68-75. [PMID: 30240754 PMCID: PMC6146417 DOI: 10.1016/j.isci.2018.05.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 04/25/2018] [Accepted: 05/14/2018] [Indexed: 01/26/2023] Open
Abstract
Although stable intronic sequence RNAs (sisRNAs) are conserved in plants and animals, their functional significance is still unclear. We identify a pool of polyadenylated maternally deposited sisRNAs in Drosophila melanogaster. These sisRNAs can be generated by independent transcription from the cognate introns. The ovary-specific poly(A) polymerase Wispy mediates the polyadenylation of maternal sisRNAs and confers their stability as maternal transcripts. A developmentally regulated sisRNA sisR-3 represses the expression of a long noncoding RNA CR44148 and is required during development. Our results expand the pool of sisRNAs and suggest that sisRNAs perform regulatory functions during development in Drosophila. Identification of polyadenylated sisRNAs sisRNAs can be produced from independent transcription sisR-3 regulates a long noncoding RNA sisR-3 is required during development
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Affiliation(s)
- Sharon Si Jia Ng
- Temasek Polytechnic, 21 Tampines Avenue 1, Singapore 529757, Singapore
| | - Ruther Teo Zheng
- Ngee Ann Polytechnic, 535 Clementi Road, Singapore 599489, Singapore
| | - Ismail Osman
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604, Singapore; Department of Biological Sciences, National University of Singapore 117543, Singapore, Singapore
| | - Jun Wei Pek
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604, Singapore.
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29
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Williams M, Ariza ME. EBV Positive Diffuse Large B Cell Lymphoma and Chronic Lymphocytic Leukemia Patients Exhibit Increased Anti-dUTPase Antibodies. Cancers (Basel) 2018; 10:E129. [PMID: 29723986 PMCID: PMC5977102 DOI: 10.3390/cancers10050129] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 04/20/2018] [Accepted: 04/25/2018] [Indexed: 12/22/2022] Open
Abstract
The Epstein-Barr virus (EBV), which is a ubiquitous γ-herpesvirus, establishes a latent infection in more than 90% of the global adult population. EBV-associated malignancies have increased by 14.6% over the last 20 years, and account for approximately 1.5% of all cancers worldwide and 1.8% of all cancer deaths. However, the potential involvement/contribution of lytic proteins to the pathophysiology of EBV-associated cancers is not well understood. We have previously demonstrated that the EBV-deoxyuridine triphosphate nucleotidohydrolase (dUTPase) modulates innate and adaptive immune responses by engaging the Toll-Like Receptor 2 (TLR2), which leads to the modulation of downstream genes involved in oncogenesis, chronic inflammation, and in effector T-cell function. Furthermore, examination of serum samples from diffuse large B-cell lymphoma (DLBCL) and chronic lymphocytic leukemia patients revealed the presence of increased levels of anti-dUTPase antibodies in both cohorts compared to controls with the highest levels (3.67-fold increase) observed in DLBCL female cases and the lowest (2.12-fold increase) in DLBCL males. Using computer-generated algorithms, dUTPase amino acid sequence alignments, and functional studies of BLLF3 mutants, we identified a putative amino acid motif involved with TLR2 interaction. These findings suggest that the EBV-dUTPase: TLR2 interaction is a potential molecular target that could be used for developing novel therapeutics (small molecules/vaccines).
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Affiliation(s)
- Marshall Williams
- Department of Cancer Biology and Genetics, The Ohio State University College of Medicine, Columbus, OH 43210, USA.
- Institute for Behavioral Medicine Research, The Ohio State University College of Medicine, Columbus, OH 43210, USA.
| | - Maria Eugenia Ariza
- Department of Cancer Biology and Genetics, The Ohio State University College of Medicine, Columbus, OH 43210, USA.
- Institute for Behavioral Medicine Research, The Ohio State University College of Medicine, Columbus, OH 43210, USA.
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30
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Shioda S, Kasai F, Watanabe K, Kawakami K, Ohtani A, Iemura M, Ozawa M, Arakawa A, Hirayama N, Kawaguchi E, Tano T, Miyata S, Satoh M, Shimizu N, Kohara A. Screening for 15 pathogenic viruses in human cell lines registered at the JCRB Cell Bank: characterization of in vitro human cells by viral infection. ROYAL SOCIETY OPEN SCIENCE 2018; 5:172472. [PMID: 29892436 PMCID: PMC5990783 DOI: 10.1098/rsos.172472] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 03/23/2018] [Indexed: 05/04/2023]
Abstract
Human cell lines have been used in a variety of research fields as an in vitro model. These cells are all derived from human tissue samples, thus there is a possibility of virus infection. Virus tests are routinely performed in clinical practice, but are limited in cell lines. In this study, we investigated 15 kinds of viruses in 844 human cell lines registered at the Japanese Collection of Research Bioresources (JCRB) Cell Bank. Our real-time PCR analysis revealed that six viruses, EBV, HTLV-1, HBV, B19V, HHV-6 and HHV-7, were detected in 43 cell lines. Of them, 20 cell lines were transformed by intentional infection in vitro with EBV or HTLV-1. Viruses in the other 23 cell lines and one EBV transformed cell line are derived from an in vivo infection, including five de novo identifications of EBV, B19V or HHV-7 carriers. Among them, 17 cell lines were established from patients diagnosed with virus-associated diseases. However, the other seven cell lines originated from in vivo cells unrelated to disease or cellular tropism. Our approach to screen for a set of 15 viruses in each cell line has worked efficiently to identify these rare cases. Virus tests in cell lines contribute not only to safety assessments but also to investigation of in vivo viral infection which can be a characteristic feature of cell lines.
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Affiliation(s)
- Setsuko Shioda
- Japanese Collection of Research Bioresources (JCRB) Cell Bank, Laboratory of Cell Cultures, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Fumio Kasai
- Japanese Collection of Research Bioresources (JCRB) Cell Bank, Laboratory of Cell Cultures, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
- Author for correspondence: Fumio Kasai e-mail:
| | - Ken Watanabe
- Department of Virology, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Kohei Kawakami
- Japanese Collection of Research Bioresources (JCRB) Cell Bank, Laboratory of Cell Cultures, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Azusa Ohtani
- Japanese Collection of Research Bioresources (JCRB) Cell Bank, Laboratory of Cell Cultures, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Masashi Iemura
- Japanese Collection of Research Bioresources (JCRB) Cell Bank, Laboratory of Cell Cultures, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Midori Ozawa
- Japanese Collection of Research Bioresources (JCRB) Cell Bank, Laboratory of Cell Cultures, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Akemi Arakawa
- Japanese Collection of Research Bioresources (JCRB) Cell Bank, Laboratory of Cell Cultures, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Noriko Hirayama
- Japanese Collection of Research Bioresources (JCRB) Cell Bank, Laboratory of Cell Cultures, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Eiko Kawaguchi
- Japanese Collection of Research Bioresources (JCRB) Cell Bank, Laboratory of Cell Cultures, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Tomoko Tano
- Japanese Collection of Research Bioresources (JCRB) Cell Bank, Laboratory of Cell Cultures, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Sayaka Miyata
- Japanese Collection of Research Bioresources (JCRB) Cell Bank, Laboratory of Cell Cultures, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Motonobu Satoh
- Japanese Collection of Research Bioresources (JCRB) Cell Bank, Laboratory of Cell Cultures, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Norio Shimizu
- Department of Virology, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Arihiro Kohara
- Japanese Collection of Research Bioresources (JCRB) Cell Bank, Laboratory of Cell Cultures, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
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31
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Nakagawa H, Fujita M. Whole genome sequencing analysis for cancer genomics and precision medicine. Cancer Sci 2018; 109:513-522. [PMID: 29345757 PMCID: PMC5834793 DOI: 10.1111/cas.13505] [Citation(s) in RCA: 196] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Revised: 01/05/2018] [Accepted: 01/11/2018] [Indexed: 12/12/2022] Open
Abstract
Explosive advances in next-generation sequencer (NGS) and computational analyses have enabled exploration of somatic protein-altered mutations in most cancer types, with coding mutation data intensively accumulated. However, there is limited information on somatic mutations in non-coding regions, including introns, regulatory elements and non-coding RNA. Structural variants and pathogen in cancer genomes remain widely unexplored. Whole genome sequencing (WGS) approaches can be used to comprehensively explore all types of genomic alterations in cancer and help us to better understand the whole landscape of driver mutations and mutational signatures in cancer genomes and elucidate the functional or clinical implications of these unexplored genomic regions and mutational signatures. This review describes recently developed technical approaches for cancer WGS and the future direction of cancer WGS, and discusses its utility and limitations as an analysis platform and for mutation interpretation for cancer genomics and cancer precision medicine. Taking into account the diversity of cancer genomes and phenotypes, interpretation of abundant mutation information from WGS, especially non-coding and structure variants, requires the analysis of large-scale WGS data integrated with RNA-Seq, epigenomics, immuno-genomic and clinic-pathological information.
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Affiliation(s)
- Hidewaki Nakagawa
- Laboratory for Genome Sequencing AnalysisRIKEN Center for Integrative Medical SciencesTokyoJapan
| | - Masashi Fujita
- Laboratory for Genome Sequencing AnalysisRIKEN Center for Integrative Medical SciencesTokyoJapan
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Tompkins VS, Valverde DP, Moss WN. Human regulatory proteins associate with non-coding RNAs from the EBV IR1 region. BMC Res Notes 2018; 11:139. [PMID: 29458410 PMCID: PMC5819218 DOI: 10.1186/s13104-018-3250-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 02/12/2018] [Indexed: 12/11/2022] Open
Abstract
Objective The function of Epstein–Barr virus (EBV) stable intronic sequence (sis)RNAs, non-coding RNAs transcribed from a region required for EBV-mediated cellular transformation, remain unknown. To better understand the function of ebv-sisRNA-1 and ebv-sisRNA-2 from the internal repeat (IR)1 region of EBV, we used a combination of bioinformatics and biochemistry to identify associated RNA binding proteins. The findings reported here are part of ongoing studies to determine the functions of non-coding RNAs from the IR1 region of EBV. Results Human regulatory proteins HNRNPA1 (heterogeneous nuclear ribonucleoprotein A1), HNRNPC, HNRNPL, HuR (human antigen R), and protein LIN28A (lin-28 homolog A) were predicted to bind ebv-sisRNA-1 and/or ebv-sisRNA-2; FUS (fused in sarcoma) was predicted to associate with ebv-sisRNA-2. Protein interactions were validated using a combination of RNA immunoprecipitation and biotin pulldown assays. Both sisRNAs also precipitated with HNRNPD and NONO (non-POU domain-containing octamer-binding protein). Interestingly, each of these interacting proteins also precipitated non-spliced non-coding RNA sequences transcribed from the IR1 region. Our findings suggest interesting roles for sisRNAs (through their interactions with regulatory proteins) and provide further evidence for the existence of non-spliced stable non-coding RNAs. Electronic supplementary material The online version of this article (10.1186/s13104-018-3250-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- V S Tompkins
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, 2437 Pammel Drive, Ames, IA, 50011, USA
| | - D P Valverde
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT, 06536, USA
| | - W N Moss
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, 2437 Pammel Drive, Ames, IA, 50011, USA.
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Juskevicius D, Müller A, Hashwah H, Lundberg P, Tzankov A, Menter T. Characterization of the mutational profile of 11 diffuse large B-cell lymphoma cell lines. Leuk Lymphoma 2017; 59:1710-1716. [DOI: 10.1080/10428194.2017.1387903] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Darius Juskevicius
- Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - Anne Müller
- Institute of Molecular Cancer Research, University of Zürich, Zürich, Switzerland
| | - Hind Hashwah
- Institute of Molecular Cancer Research, University of Zürich, Zürich, Switzerland
| | - Pontus Lundberg
- Department of Hematology, University Hospital Basel, Basel, Switzerland
| | - Alexandar Tzankov
- Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - Thomas Menter
- Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
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Moustafa A, Xie C, Kirkness E, Biggs W, Wong E, Turpaz Y, Bloom K, Delwart E, Nelson KE, Venter JC, Telenti A. The blood DNA virome in 8,000 humans. PLoS Pathog 2017; 13:e1006292. [PMID: 28328962 PMCID: PMC5378407 DOI: 10.1371/journal.ppat.1006292] [Citation(s) in RCA: 199] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Revised: 04/03/2017] [Accepted: 03/14/2017] [Indexed: 02/06/2023] Open
Abstract
The characterization of the blood virome is important for the safety of blood-derived transfusion products, and for the identification of emerging pathogens. We explored non-human sequence data from whole-genome sequencing of blood from 8,240 individuals, none of whom were ascertained for any infectious disease. Viral sequences were extracted from the pool of sequence reads that did not map to the human reference genome. Analyses sifted through close to 1 Petabyte of sequence data and performed 0.5 trillion similarity searches. With a lower bound for identification of 2 viral genomes/100,000 cells, we mapped sequences to 94 different viruses, including sequences from 19 human DNA viruses, proviruses and RNA viruses (herpesviruses, anelloviruses, papillomaviruses, three polyomaviruses, adenovirus, HIV, HTLV, hepatitis B, hepatitis C, parvovirus B19, and influenza virus) in 42% of the study participants. Of possible relevance to transfusion medicine, we identified Merkel cell polyomavirus in 49 individuals, papillomavirus in blood of 13 individuals, parvovirus B19 in 6 individuals, and the presence of herpesvirus 8 in 3 individuals. The presence of DNA sequences from two RNA viruses was unexpected: Hepatitis C virus is revealing of an integration event, while the influenza virus sequence resulted from immunization with a DNA vaccine. Age, sex and ancestry contributed significantly to the prevalence of infection. The remaining 75 viruses mostly reflect extensive contamination of commercial reagents and from the environment. These technical problems represent a major challenge for the identification of novel human pathogens. Increasing availability of human whole-genome sequences will contribute substantial amounts of data on the composition of the normal and pathogenic human blood virome. Distinguishing contaminants from real human viruses is challenging. Novel sequencing technologies offer insight into the virome in human samples. Here, we identify the viral DNA sequences in blood of over 8,000 individuals undergoing whole genome sequencing. This approach serves to identify 94 viruses; however, many are shown to reflect widespread DNA contamination of commercial reagents or of environmental origin. While this represents a significant limitation to reliably identify novel viruses infecting humans, we could confidently detect sequences and quantify abundance of 19 human viruses in 42% of individuals. Ancestry, sex, and age were important determinants of viral prevalence. This large study calls attention on the challenge of interpreting next generation sequencing data for the identification of novel viruses. However, it serves to categorize the abundance of human DNA viruses using an unbiased technique.
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Affiliation(s)
- Ahmed Moustafa
- Human Longevity Inc., San Diego, California, United States of America
| | - Chao Xie
- Human Longevity Singapore Pte. Ltd., Singapore
| | - Ewen Kirkness
- Human Longevity Inc., San Diego, California, United States of America
| | - William Biggs
- Human Longevity Inc., San Diego, California, United States of America
| | - Emily Wong
- Human Longevity Inc., San Diego, California, United States of America
| | | | - Kenneth Bloom
- Human Longevity Inc., San Diego, California, United States of America
| | - Eric Delwart
- Blood Systems Research Institute, Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Karen E. Nelson
- J. Craig Venter Institute, La Jolla, California, United States of America
| | - J. Craig Venter
- Human Longevity Inc., San Diego, California, United States of America
- J. Craig Venter Institute, La Jolla, California, United States of America
- * E-mail: (JCV); (AT)
| | - Amalio Telenti
- Human Longevity Inc., San Diego, California, United States of America
- J. Craig Venter Institute, La Jolla, California, United States of America
- * E-mail: (JCV); (AT)
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Quantitative Analysis of the KSHV Transcriptome Following Primary Infection of Blood and Lymphatic Endothelial Cells. Pathogens 2017; 6:pathogens6010011. [PMID: 28335496 PMCID: PMC5371899 DOI: 10.3390/pathogens6010011] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 03/07/2017] [Accepted: 03/15/2017] [Indexed: 12/14/2022] Open
Abstract
The transcriptome of the Kaposi’s sarcoma-associated herpesvirus (KSHV/HHV8) after primary latent infection of human blood (BEC), lymphatic (LEC) and immortalized (TIME) endothelial cells was analyzed using RNAseq, and compared to long-term latency in BCBL-1 lymphoma cells. Naturally expressed transcripts were obtained without artificial induction, and a comprehensive annotation of the KSHV genome was determined. A set of unique coding sequence (UCDS) features and a process to resolve overlapping transcripts were developed to accurately quantitate transcript levels from specific promoters. Similar patterns of KSHV expression were detected in BCBL-1 cells undergoing long-term latent infections and in primary latent infections of both BEC and LEC cultures. High expression levels of poly-adenylated nuclear (PAN) RNA and spliced and unspliced transcripts encoding the K12 Kaposin B/C complex and associated microRNA region were detected, with an elevated expression of a large set of lytic genes in all latently infected cultures. Quantitation of non-overlapping regions of transcripts across the complete KSHV genome enabled for the first time accurate evaluation of the KSHV transcriptome associated with viral latency in different cell types. Hierarchical clustering applied to a gene correlation matrix identified modules of co-regulated genes with similar correlation profiles, which corresponded with biological and functional similarities of the encoded gene products. Gene modules were differentially upregulated during latency in specific cell types indicating a role for cellular factors associated with differentiated and/or proliferative states of the host cell to influence viral gene expression.
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Zheng LL, Deng KW, Deng AC, Wu J, Yang JH, Lun ZR, Qu LH. Exo-miRExplorer: A Comprehensive Resource for Exploring and Comparatively Analyzing Exogenous MicroRNAs. Front Microbiol 2017; 8:126. [PMID: 28203233 PMCID: PMC5285362 DOI: 10.3389/fmicb.2017.00126] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 01/18/2017] [Indexed: 12/21/2022] Open
Abstract
MicroRNAs (miRNAs) are small regulatory RNAs that play important roles in animals, plants, and viruses. Deep-sequencing technology has been widely adopted in miRNA investigations. However, it is still a big mysterious why nearly all sequencing data contain miRNA sequences from exogenous species, called exo-miRNAs. In this study, we developed a novel platform, exo-miRExplorer, for mining and identifying exo-miRNAs from high-throughput small RNA sequencing experiments which originated from tissues and cell lines of multiple organisms. Thousands of exo-miRNAs are characterized with their expression abundance, the RNA families, original organisms and the sequencing platforms presented in exo-miRExplorer. Subsequently, we used exo-miRExplorer to perform further analysis. Comparative analysis of the exo-miRNAs between different sequencing datasets revealed significant correlation of exo-miRNAs between experiments in the same study. The plant-derived exo-miRNAs analysis provided robust evidence for non-diet source of exo-miRNAs. Virus-derived exo-miRNA analysis showed that pathogen RNAs could transfer to host cells and exist in deep-sequencing result at abundance level. In conclusion, exo-miRExplorer provides users with an integrative resource to facilitate detection and analysis of exo-miRNAs. exo-miRExplorer is available at the following URL: http://rna.sysu.edu.cn/exomiRDB/.
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Affiliation(s)
- Ling-Ling Zheng
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, RNA Information Center, School of Life Sciences, Sun Yat-sen University Guangzhou, China
| | - Kai-Wen Deng
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, RNA Information Center, School of Life Sciences, Sun Yat-sen University Guangzhou, China
| | - An-Cheng Deng
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, RNA Information Center, School of Life Sciences, Sun Yat-sen University Guangzhou, China
| | - Jie Wu
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, RNA Information Center, School of Life Sciences, Sun Yat-sen University Guangzhou, China
| | - Jian-Hua Yang
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, RNA Information Center, School of Life Sciences, Sun Yat-sen University Guangzhou, China
| | - Zhao-Rong Lun
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, RNA Information Center, School of Life Sciences, Sun Yat-sen University Guangzhou, China
| | - Liang-Hu Qu
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, RNA Information Center, School of Life Sciences, Sun Yat-sen University Guangzhou, China
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Abstract
Epstein-Barr virus (EBV) infection is associated with several distinct hematological and epithelial malignancies, e.g., Burkitt lymphoma, Hodgkin lymphoma, nasopharyngeal carcinoma, gastric carcinoma, and others. The association with several malignant tumors of local and worldwide distribution makes EBV one of the most important tumor viruses. Furthermore, because EBV can cause posttransplant lymphoproliferative disease, transplant medicine has to deal with EBV as a major pathogenic virus second only to cytomegalovirus. In this review, we summarize briefly the natural history of EBV infection and outline some of the recent advances in the pathogenesis of the major EBV-associated neoplasms. We present alternative scenarios and discuss them in the light of most recent experimental data. Emerging research areas including EBV-induced patho-epigenetic alterations in host cells and the putative role of exosome-mediated information transfer in disease development are also within the scope of this review. This book contains an in-depth description of a series of modern methodologies used in EBV research. In this introductory chapter, we thoroughly refer to the applications of these methods and demonstrate how they contributed to the understanding of EBV-host cell interactions. The data gathered using recent technological advancements in molecular biology and immunology as well as the application of sophisticated in vitro and in vivo experimental models certainly provided deep and novel insights into the pathogenetic mechanisms of EBV infection and EBV-associated tumorigenesis. Furthermore, the development of adoptive T cell immunotherapy has provided a novel approach to the therapy of viral disease in transplant medicine and hematology.
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Affiliation(s)
- Janos Minarovits
- Faculty of Dentistry, Department of Oral Biology and Experimental Dental Research, University of Szeged, Tisza Lajos krt. 64, H-6720, Szeged, Hungary.
| | - Hans Helmut Niller
- Institute of Medical Microbiology and Hygiene, University of Regensburg, D-93053, Regensburg, Germany
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Williamson SJ, Nicol SM, Stürzl M, Sabbah S, Hislop AD. Azidothymidine Sensitizes Primary Effusion Lymphoma Cells to Kaposi Sarcoma-Associated Herpesvirus-Specific CD4+ T Cell Control and Inhibits vIRF3 Function. PLoS Pathog 2016; 12:e1006042. [PMID: 27893813 PMCID: PMC5125715 DOI: 10.1371/journal.ppat.1006042] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Accepted: 11/04/2016] [Indexed: 01/06/2023] Open
Abstract
Kaposi sarcoma-associated herpesvirus (KSHV) is linked with the development of Kaposi sarcoma and the B lymphocyte disorders primary effusion lymphoma (PEL) and multi-centric Castleman disease. T cell immunity limits KSHV infection and disease, however the virus employs multiple mechanisms to inhibit efficient control by these effectors. Thus KSHV-specific CD4+ T cells poorly recognize most PEL cells and even where they can, they are unable to kill them. To make KSHV-infected cells more sensitive to T cell control we treated PEL cells with the thymidine analogue azidothymidine (AZT), which sensitizes PEL lines to Fas-ligand and TRAIL challenge; effector mechanisms which T cells use. PELs co-cultured with KSHV-specific CD4+ T cells in the absence of AZT showed no control of PEL outgrowth. However in the presence of AZT PEL outgrowth was controlled in an MHC-restricted manner. To investigate how AZT sensitizes PELs to immune control we first examined BJAB cells transduced with individual KSHV-latent genes for their ability to resist apoptosis mediated by stimuli delivered through Fas and TRAIL receptors. This showed that in addition to the previously described vFLIP protein, expression of vIRF3 also inhibited apoptosis delivered by these stimuli. Importantly vIRF3 mediated protection from these apoptotic stimuli was inhibited in the presence of AZT as was a second vIRF3 associated phenotype, the downregulation of surface MHC class II. Although both vFLIP and vIRF3 are expressed in PELs, we propose that inhibiting vIRF3 function with AZT may be sufficient to restore T cell control of these tumor cells. Kaposi sarcoma-associated herpesvirus (KSHV) can cause disease in humans in the form of B lymphocyte disorders such as primary effusion lymphoma (PEL) and multicentric Castleman disease. Where tested, these are highly resistant to immune control by KSHV-specific T cells. To investigate how such KSHV-infected cells can be made more sensitive to T cell control we treated PEL lines with azidothymidine (AZT), which has been shown to induce sensitivity in such lines to the mechanisms which T cells use to kill targets. We found this allowed the T cells to control in vitro lymphoma growth. The ability of the T cells to control PEL cell growth was found to correlate with AZT mediated inhibition of function of the KSHV protein vIRF3 which we show has the ability to protect cells from killing by immune effector mechanisms. These studies suggest that the therapeutic drug AZT may be of use to tip the virus host balance away from the virus by interfering with this immune evasion and pro-survival protein, potentially allowing better control by the host.
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Affiliation(s)
- Samantha J. Williamson
- Institute of Immunology and Immunotherapy, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Samantha M. Nicol
- Institute of Immunology and Immunotherapy, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Michael Stürzl
- Division of Molecular and Experimental Surgery, Department of Surgery, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
| | - Shereen Sabbah
- Department of Immunobiology, King's College London, London, United Kingdom
| | - Andrew D. Hislop
- Institute of Immunology and Immunotherapy, University of Birmingham, Edgbaston, Birmingham, United Kingdom
- * E-mail:
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O'Grady T, Wang X, Höner Zu Bentrup K, Baddoo M, Concha M, Flemington EK. Global transcript structure resolution of high gene density genomes through multi-platform data integration. Nucleic Acids Res 2016; 44:e145. [PMID: 27407110 PMCID: PMC5062983 DOI: 10.1093/nar/gkw629] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 07/02/2016] [Indexed: 12/11/2022] Open
Abstract
Annotation of herpesvirus genomes has traditionally been undertaken through the detection of open reading frames and other genomic motifs, supplemented with sequencing of individual cDNAs. Second generation sequencing and high-density microarray studies have revealed vastly greater herpesvirus transcriptome complexity than is captured by existing annotation. The pervasive nature of overlapping transcription throughout herpesvirus genomes, however, poses substantial problems in resolving transcript structures using these methods alone. We present an approach that combines the unique attributes of Pacific Biosciences Iso-Seq long-read, Illumina short-read and deepCAGE (Cap Analysis of Gene Expression) sequencing to globally resolve polyadenylated isoform structures in replicating Epstein-Barr virus (EBV). Our method, Transcriptome Resolution through Integration of Multi-platform Data (TRIMD), identifies nearly 300 novel EBV transcripts, quadrupling the size of the annotated viral transcriptome. These findings illustrate an array of mechanisms through which EBV achieves functional diversity in its relatively small, compact genome including programmed alternative splicing (e.g. across the IR1 repeats), alternative promoter usage by LMP2 and other latency-associated transcripts, intergenic splicing at the BZLF2 locus, and antisense transcription and pervasive readthrough transcription throughout the genome.
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Affiliation(s)
- Tina O'Grady
- Department of Pathology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Xia Wang
- Department of Pathology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Kerstin Höner Zu Bentrup
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Melody Baddoo
- Department of Pathology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Monica Concha
- Department of Pathology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Erik K Flemington
- Department of Pathology, Tulane University School of Medicine, New Orleans, LA 70112, USA Tulane Cancer Center, New Orleans, LA 70112, USA
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Complete Unique Genome Sequence, Expression Profile, and Salivary Gland Tissue Tropism of the Herpesvirus 7 Homolog in Pigtailed Macaques. J Virol 2016; 90:6657-6674. [PMID: 27170755 PMCID: PMC4944276 DOI: 10.1128/jvi.00651-16] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 05/03/2016] [Indexed: 11/20/2022] Open
Abstract
Human herpesvirus 6A (HHV-6A), HHV-6B, and HHV-7 are classified as roseoloviruses and are highly prevalent in the human population. Roseolovirus reactivation in an immunocompromised host can cause severe pathologies. While the pathogenic potential of HHV-7 is unclear, it can reactivate HHV-6 from latency and thus contributes to severe pathological conditions associated with HHV-6. Because of the ubiquitous nature of roseoloviruses, their roles in such interactions and the resulting pathological consequences have been difficult to study. Furthermore, the lack of a relevant animal model for HHV-7 infection has hindered a better understanding of its contribution to roseolovirus-associated diseases. Using next-generation sequencing analysis, we characterized the unique genome of an uncultured novel pigtailed macaque roseolovirus. Detailed genomic analysis revealed the presence of gene homologs to all 84 known HHV-7 open reading frames. Phylogenetic analysis confirmed that the virus is a macaque homolog of HHV-7, which we have provisionally named Macaca nemestrina herpesvirus 7 (MneHV7). Using high-throughput RNA sequencing, we observed that the salivary gland tissue samples from nine different macaques had distinct MneHV7 gene expression patterns and that the overall number of viral transcripts correlated with viral loads in parotid gland tissue and saliva. Immunohistochemistry staining confirmed that, like HHV-7, MneHV7 exhibits a natural tropism for salivary gland ductal cells. We also observed staining for MneHV7 in peripheral nerve ganglia present in salivary gland tissues, suggesting that HHV-7 may also have a tropism for the peripheral nervous system. Our data demonstrate that MneHV7-infected macaques represent a relevant animal model that may help clarify the causality between roseolovirus reactivation and diseases. IMPORTANCE Human herpesvirus 6A (HHV-6A), HHV-6B, and HHV-7 are classified as roseoloviruses. We have recently discovered that pigtailed macaques are naturally infected with viral homologs of HHV-6 and HHV-7, which we provisionally named MneHV6 and MneHV7, respectively. In this study, we confirm that MneHV7 is genetically and biologically similar to its human counterpart, HHV-7. We determined the complete unique MneHV7 genome sequence and provide a comprehensive annotation of all genes. We also characterized viral transcription profiles in salivary glands from naturally infected macaques. We show that broad transcriptional activity across most of the viral genome is associated with high viral loads in infected parotid glands and that late viral protein expression is detected in salivary duct cells and peripheral nerve ganglia. Our study provides new insights into the natural behavior of an extremely prevalent virus and establishes a basis for subsequent investigations of the mechanisms that cause HHV-7 reactivation and associated disease.
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Strong MJ, Blanchard E, Lin Z, Morris CA, Baddoo M, Taylor CM, Ware ML, Flemington EK. A comprehensive next generation sequencing-based virome assessment in brain tissue suggests no major virus - tumor association. Acta Neuropathol Commun 2016; 4:71. [PMID: 27402152 PMCID: PMC4940872 DOI: 10.1186/s40478-016-0338-z] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 06/15/2016] [Indexed: 12/15/2022] Open
Abstract
Next generation sequencing (NGS) can globally interrogate the genetic composition of biological samples in an unbiased yet sensitive manner. The objective of this study was to utilize the capabilities of NGS to investigate the reported association between glioblastoma multiforme (GBM) and human cytomegalovirus (HCMV). A large-scale comprehensive virome assessment was performed on publicly available sequencing datasets from the Cancer Genome Atlas (TCGA), including RNA-seq datasets from primary GBM (n = 157), recurrent GBM (n = 13), low-grade gliomas (n = 514), recurrent low-grade gliomas (n = 17), and normal brain (n = 5), and whole genome sequencing (WGS) datasets from primary GBM (n = 51), recurrent GBM (n = 10), and normal matched blood samples (n = 20). In addition, RNA-seq datasets from MRI-guided biopsies (n = 92) and glioma stem-like cell cultures (n = 9) were analyzed. Sixty-four DNA-seq datasets from 11 meningiomas and their corresponding blood control samples were also analyzed. Finally, three primary GBM tissue samples were obtained, sequenced using RNA-seq, and analyzed. After in-depth analysis, the most robust virus findings were the detection of papillomavirus (HPV) and hepatitis B reads in the occasional LGG sample (4 samples and 1 sample, respectively). In addition, low numbers of virus reads were detected in several datasets but detailed investigation of these reads suggest that these findings likely represent artifacts or non-pathological infections. For example, all of the sporadic low level HCMV reads were found to map to the immediate early promoter intimating that they likely originated from laboratory expression vector contamination. Despite the detection of low numbers of Epstein-Barr virus reads in some samples, these likely originated from infiltrating B-cells. Finally, human herpesvirus 6 and 7 aligned viral reads were identified in all DNA-seq and a few RNA-seq datasets but detailed analysis demonstrated that these were likely derived from the homologous human telomeric-like repeats. Other low abundance viral reads were detected in some samples but for most viruses, the reads likely represent artifacts or incidental infections. This analysis argues against associations between most known viruses and GBM or mengiomas. Nevertheless, there may be a low percentage association between HPV and/or hepatitis B and LGGs.
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Flippot R, Malouf GG, Su X, Khayat D, Spano JP. Oncogenic viruses: Lessons learned using next-generation sequencing technologies. Eur J Cancer 2016; 61:61-8. [PMID: 27156225 DOI: 10.1016/j.ejca.2016.03.086] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2015] [Revised: 03/25/2016] [Accepted: 03/30/2016] [Indexed: 01/04/2023]
Abstract
Fifteen percent of cancers are driven by oncogenic human viruses. Four of those viruses, hepatitis B virus, human papillomavirus, Merkel cell polyomavirus, and human T-cell lymphotropic virus, integrate the host genome. Viral oncogenesis is the result of epigenetic and genetic alterations that happen during viral integration. So far, little data have been available regarding integration mechanisms and modifications in the host genome. However, the emergence of high-throughput sequencing and bioinformatic tools enables researchers to establish the landscape of genomic alterations and predict the events that follow viral integration. Cooperative working groups are currently investigating these factors in large data sets. Herein, we provide novel insights into the initiating events of cancer onset during infection with integrative viruses. Although much remains to be discovered, many improvements are expected from the clinical point of view, from better prognosis classifications to better therapeutic strategies.
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Affiliation(s)
- Ronan Flippot
- University Hospital Pitié Salpêtrière, Department of Medical Oncology, University Pierre and Marie Curie, Paris, France
| | - Gabriel G Malouf
- University Hospital Pitié Salpêtrière, Department of Medical Oncology, University Pierre and Marie Curie, Paris, France.
| | - Xiaoping Su
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, U.S.A
| | - David Khayat
- University Hospital Pitié Salpêtrière, Department of Medical Oncology, University Pierre and Marie Curie, Paris, France
| | - Jean-Philippe Spano
- University Hospital Pitié Salpêtrière, Department of Medical Oncology, University Pierre and Marie Curie, Paris, France
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Phan AT, Fernandez SG, Somberg JJ, Keck KM, Miranda JL. Epstein-Barr virus latency type and spontaneous reactivation predict lytic induction levels. Biochem Biophys Res Commun 2016; 474:71-75. [PMID: 27091426 DOI: 10.1016/j.bbrc.2016.04.070] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Revised: 04/13/2016] [Accepted: 04/14/2016] [Indexed: 11/18/2022]
Abstract
The human Epstein-Barr virus (EBV) evades the immune system by entering a transcriptionally latent phase in B cells. EBV in tumor cells expresses distinct patterns of genes referred to as latency types. Viruses in tumor cells also display varying levels of lytic transcription resulting from spontaneous reactivation out of latency. We measured this dynamic range of lytic transcription with RNA deep sequencing and observed no correlation with EBV latency types among genetically different viruses, but type I cell lines reveal more spontaneous reactivation than isogenic type III cultures. We further determined that latency type and spontaneous reactivation levels predict the relative amount of induced reactivation generated by cytotoxic chemotherapy drugs. Our work has potential implications for personalizing medicine against EBV-transformed malignancies. Identifying latency type or measuring spontaneous reactivation may provide predictive power in treatment contexts where viral production should be either avoided or coerced.
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Affiliation(s)
- An T Phan
- Gladstone Institute of Virology and Immunology, San Francisco, CA, USA
| | | | - Jessica J Somberg
- Gladstone Institute of Virology and Immunology, San Francisco, CA, USA
| | - Kristin M Keck
- Gladstone Institute of Virology and Immunology, San Francisco, CA, USA
| | - Jj L Miranda
- Gladstone Institute of Virology and Immunology, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA.
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Nicol SM, Sabbah S, Brulois KF, Jung JU, Bell AI, Hislop AD. Primary B Lymphocytes Infected with Kaposi's Sarcoma-Associated Herpesvirus Can Be Expanded In Vitro and Are Recognized by LANA-Specific CD4+ T Cells. J Virol 2016; 90:3849-3859. [PMID: 26819313 PMCID: PMC4810529 DOI: 10.1128/jvi.02377-15] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 01/20/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Kaposi's sarcoma-associated herpesvirus (KSHV) has tropism for B lymphocytes, in which it establishes latency, and can also cause lymphoproliferative disorders of these cells manifesting as primary effusion lymphoma (PEL) and multicentric Castleman disease (MCD). T cell immunity is vital for the control of KSHV infection and disease; however, few models of B lymphocyte infection exist to study immune recognition of such cells. Here, we developed a model of B lymphocyte infection with KSHV in which infected tonsillar B lymphocytes were expanded by providing mitogenic stimuli and then challenged with KSHV-specific CD4(+)T cells. The infected cells expressed viral proteins found in PELs, namely, LANA and viral IRF3 (vIRF3), albeit at lower levels, with similar patterns of gene expression for the major latency, viral interleukin 6 (vIL-6), and vIRF3 transcripts. Despite low-level expression of open reading frame 50 (ORF50), transcripts for the immune evasion genes K3 and K5 were detected, with some downregulation of cell surface-expressed CD86 and ICAM. The vast majority of infected lymphocytes expressed IgM heavy chains with Igλ light chains, recapitulating the features seen in infected cells in MCD. We assessed the ability of the infected lymphocytes to be targeted by a panel of major histocompatibility complex (MHC) class II-matched CD4(+)T cells and found that LANA-specific T cells restricted to different epitopes recognized these infected cells. Given that at least some KSHV latent antigens are thought to be poor targets for CD8(+)T cells, we suggest that CD4(+)T cells are potentially important effectors for thein vivocontrol of KSHV-infected B lymphocytes. IMPORTANCE KSHV establishes a latent reservoir within B lymphocytes, but few models exist to study KSHV-infected B cells other than the transformed PEL cell lines, which have likely accrued mutations during the transformation process. We developed a model of KSHV-infected primary B lymphocytes that recapitulates features seen in PEL and MCD by gene expression and cell phenotype analysis, allowing the study of T cell recognition of these cells. Challenge of KSHV-infected B cells with CD4(+)T cells specific for LANA, a protein expressed in all KSHV-infected cells and malignanciesin vivo, showed that these effectors could efficiently recognize such targets. Given that the virus expresses immune evasion genes or uses proteins with intrinsic properties, such as LANA, that minimize epitope recognition by CD8(+)T cells, CD4(+)T cell immunity to KSHV may be important for maintaining the virus-host balance.
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Affiliation(s)
- Samantha M Nicol
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, United Kingdom
| | - Shereen Sabbah
- Department of Immunobiology, King's College London, London, United Kingdom
| | - Kevin F Brulois
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Jae U Jung
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Andrew I Bell
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Andrew D Hislop
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, United Kingdom
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Strahan R, Uppal T, Verma SC. Next-Generation Sequencing in the Understanding of Kaposi's Sarcoma-Associated Herpesvirus (KSHV) Biology. Viruses 2016; 8:92. [PMID: 27043613 PMCID: PMC4848587 DOI: 10.3390/v8040092] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Revised: 03/21/2016] [Accepted: 03/23/2016] [Indexed: 12/16/2022] Open
Abstract
Non-Sanger-based novel nucleic acid sequencing techniques, referred to as Next-Generation Sequencing (NGS), provide a rapid, reliable, high-throughput, and massively parallel sequencing methodology that has improved our understanding of human cancers and cancer-related viruses. NGS has become a quintessential research tool for more effective characterization of complex viral and host genomes through its ever-expanding repertoire, which consists of whole-genome sequencing, whole-transcriptome sequencing, and whole-epigenome sequencing. These new NGS platforms provide a comprehensive and systematic genome-wide analysis of genomic sequences and a full transcriptional profile at a single nucleotide resolution. When combined, these techniques help unlock the function of novel genes and the related pathways that contribute to the overall viral pathogenesis. Ongoing research in the field of virology endeavors to identify the role of various underlying mechanisms that control the regulation of the herpesvirus biphasic lifecycle in order to discover potential therapeutic targets and treatment strategies. In this review, we have complied the most recent findings about the application of NGS in Kaposi’s sarcoma-associated herpesvirus (KSHV) biology, including identification of novel genomic features and whole-genome KSHV diversities, global gene regulatory network profiling for intricate transcriptome analyses, and surveying of epigenetic marks (DNA methylation, modified histones, and chromatin remodelers) during de novo, latent, and productive KSHV infections.
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Affiliation(s)
- Roxanne Strahan
- Department of Microbiology and Immunology, School of Medicine, University of Nevada, 1664 N, Virginia Street, MS 320, Reno, NV 89557, USA.
| | - Timsy Uppal
- Department of Microbiology and Immunology, School of Medicine, University of Nevada, 1664 N, Virginia Street, MS 320, Reno, NV 89557, USA.
| | - Subhash C Verma
- Department of Microbiology and Immunology, School of Medicine, University of Nevada, 1664 N, Virginia Street, MS 320, Reno, NV 89557, USA.
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Maldarelli F. The role of HIV integration in viral persistence: no more whistling past the proviral graveyard. J Clin Invest 2016; 126:438-47. [PMID: 26829624 DOI: 10.1172/jci80564] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
A substantial research effort has been directed to identifying strategies to eradicate or control HIV infection without a requirement for combination antiretroviral therapy (cART). A number of obstacles prevent HIV eradication, including low-level viral persistence during cART, long-term persistence of HIV-infected cells, and latent infection of resting CD4+ T cells. Mechanisms of persistence remain uncertain, but integration of the provirus into the host genome represents a central event in replication and pathogenesis of all retroviruses, including HIV. Analysis of HIV proviruses in CD4+ lymphocytes from individuals after prolonged cART revealed that a substantial proportion of the infected cells that persist have undergone clonal expansion and frequently have proviruses integrated in genes associated with regulation of cell growth. These data suggest that integration may influence persistence and clonal expansion of HIV-infected cells after cART is introduced, and these processes may represent key mechanisms for HIV persistence. Determining the diversity of host genes with integrants in HIV-infected cells that persist for prolonged periods may yield useful information regarding pathways by which infected cells persist for prolonged periods. Moreover, many integrants are defective, and new studies are required to characterize the role of clonal expansion in the persistence of replication-competent HIV.
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Bernhardt K, Haar J, Tsai MH, Poirey R, Feederle R, Delecluse HJ. A Viral microRNA Cluster Regulates the Expression of PTEN, p27 and of a bcl-2 Homolog. PLoS Pathog 2016; 12:e1005405. [PMID: 26800049 PMCID: PMC4723338 DOI: 10.1371/journal.ppat.1005405] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 12/28/2015] [Indexed: 11/19/2022] Open
Abstract
The Epstein-Barr virus (EBV) infects and transforms B-lymphocytes with high efficiency. This process requires expression of the viral latent proteins and of the 3 miR-BHRF1 microRNAs. Here we show that B-cells infected by a virus that lacks these non-coding RNAs (Δ123) grew more slowly between day 5 and day 20, relative to wild type controls. This effect could be ascribed to a reduced S phase entry combined with a moderately increased apoptosis rate. Whilst the first phenotypic trait was consistent with an enhanced PTEN expression in B-cells infected with Δ123, the second could be explained by very low BHRF1 protein and RNA levels in the same cells. Indeed, B-cells infected either by a recombinant virus that lacks the BHRF1 protein, a viral bcl-2 homolog, or by Δ123 underwent a similar degree of apoptosis, whereas knockouts of both BHRF1 microRNAs and protein proved transformation-incompetent. We find that that the miR-BHRF1-3 seed regions, and to a lesser extent those of miR-BHRF1-2 mediate these stimulatory effects. After this critical period, B-cells infected with the Δ123 mutant recovered a normal growth rate and became more resistant to provoked apoptosis. This resulted from an enhanced BHRF1 protein expression relative to cells infected with wild type viruses and correlated with decreased p27 expression, two pro-oncogenic events. The upregulation of BHRF1 can be explained by the observation that large BHRF1 mRNAs are the source of BHRF1 protein but are destroyed following BHRF1 microRNA processing, in particular of miR-BHRF1-2. The BHRF1 microRNAs are unlikely to directly target p27 but their absence may facilitate the selection of B-cells that express low levels of this protein. Thus, the BHRF1 microRNAs allowed a time-restricted expression of the BHRF1 protein to innocuously expand the virus B-cell reservoir during the first weeks post-infection without increasing long-term immune pressure.
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Affiliation(s)
- Katharina Bernhardt
- Pathogenesis of Virus Associated Tumors, German Cancer Research Center, Heidelberg, Germany
- Inserm unit U1074, Heidelberg, Germany
| | - Janina Haar
- Pathogenesis of Virus Associated Tumors, German Cancer Research Center, Heidelberg, Germany
- Inserm unit U1074, Heidelberg, Germany
| | - Ming-Han Tsai
- Pathogenesis of Virus Associated Tumors, German Cancer Research Center, Heidelberg, Germany
- Inserm unit U1074, Heidelberg, Germany
| | - Remy Poirey
- Pathogenesis of Virus Associated Tumors, German Cancer Research Center, Heidelberg, Germany
- Inserm unit U1074, Heidelberg, Germany
| | - Regina Feederle
- Pathogenesis of Virus Associated Tumors, German Cancer Research Center, Heidelberg, Germany
- Inserm unit U1074, Heidelberg, Germany
| | - Henri-Jacques Delecluse
- Pathogenesis of Virus Associated Tumors, German Cancer Research Center, Heidelberg, Germany
- Inserm unit U1074, Heidelberg, Germany
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Host Gene Expression Is Regulated by Two Types of Noncoding RNAs Transcribed from the Epstein-Barr Virus BamHI A Rightward Transcript Region. J Virol 2015; 89:11256-68. [PMID: 26311882 DOI: 10.1128/jvi.01492-15] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 08/21/2015] [Indexed: 12/22/2022] Open
Abstract
UNLABELLED In Epstein-Barr virus-infected epithelial cancers, the alternatively spliced BamHI A rightward transcripts (BARTs) are the most abundant viral polyadenylated RNA. The BART introns form the template for the production of 44 microRNAs (miRNAs), and the spliced and polyadenylated exons form nuclear non-protein-coding RNAs. Analysis of host cell transcription by RNA-seq during latency in AGS cells identified a large number of reproducibly changed genes. Genes that were downregulated were enriched for BART miRNA targets. Bioinformatics analysis predicted activation of the myc pathway and downregulation of XBP1 as likely mediators of the host transcriptional changes. Effects on XBP1 activity were not detected in these cells; however, myc activation was confirmed through use of a myc-responsive luciferase reporter. To identify potential regulatory properties of the spliced, polyadenylated BART RNAs, a full-length cDNA clone of one of the BART isoforms was obtained and expressed in the Epstein-Barr virus (EBV)-negative AGS cells. The BART cDNA transcript remained primarily nuclear yet induced considerable and consistent changes in cellular transcription, as profiled by RNA-seq. These transcriptional changes significantly overlapped the transcriptional changes induced during latent EBV infection of these same cells, where the BARTs are exclusively nuclear and do not encode proteins. These data suggest that the nuclear BART RNAs are functional long noncoding RNAs (lncRNAs). The abundant expression of multiple forms of noncoding RNAs that contribute to growth regulation without expression of immunogenic proteins would be an important mechanism for viral oncogenesis in the presence of a functional immune system. IMPORTANCE Infection with Epstein-Barr virus (EBV) is nearly ubiquitous in the human population; however, it does contribute to the formation of multiple types of cancer. In immunocompromised patients, EBV causes multiple types of lymphomas by expressing viral oncogenes that promote growth and survival of infected B lymphocytes. EBV-positive gastric carcinoma does not require immune suppression, and the viral oncoproteins that are frequent targets for an immunological response are not expressed. This study demonstrates using transcriptional analysis that the expression of various classes of viral non-protein-coding RNAs likely contribute to the considerable changes in the host transcriptional profile in the AGS gastric cancer cell line. This is the first report to show that the highly expressed polyadenylated BamHI A rightward transcripts (BART) viral transcript in gastric carcinoma is in fact a functional viral long noncoding RNA. These studies provide new insight into how EBV can promote transformation in the absence of viral protein expression.
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Latent Expression of the Epstein-Barr Virus (EBV)-Encoded Major Histocompatibility Complex Class I TAP Inhibitor, BNLF2a, in EBV-Positive Gastric Carcinomas. J Virol 2015; 89:10110-4. [PMID: 26178981 DOI: 10.1128/jvi.01110-15] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 07/07/2015] [Indexed: 12/14/2022] Open
Abstract
The Epstein-Barr virus (EBV) BNLF2a gene product provides immune evasion properties to infected cells through inhibition of transporter associated with antigen processing (TAP)-mediated transport of antigen peptides. Although BNLF2a is considered to be a lytic gene, we demonstrate that it is expressed in nearly half of the EBV-associated gastric carcinomas analyzed. Further, we show that BNLF2a expression is dissociated from lytic gene expression. BNLF2a is therefore expressed in this latency setting, potentially helping protect the infected tumor cells from immunosurveillance.
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50
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Rojas M, Golovko G, Khanipov K, Albayrak L, Chumakov S, Pettitt BM, Strongin AY, Fofanov Y. Secondary Analysis of the NCI-60 Whole Exome Sequencing Data Indicates Significant Presence of Propionibacterium acnes Genomic Material in Leukemia (RPMI-8226) and Central Nervous System (SF-295, SF-539, and SNB-19) Cell Lines. PLoS One 2015; 10:e0127799. [PMID: 26039084 PMCID: PMC4454691 DOI: 10.1371/journal.pone.0127799] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2015] [Accepted: 04/18/2015] [Indexed: 11/25/2022] Open
Abstract
The NCI-60 human tumor cell line panel has been used in a broad range of cancer research over the last two decades. A landmark 2013 whole exome sequencing study of this panel added an exceptional new resource for cancer biologists. The complementary analysis of the sequencing data produced by this study suggests the presence of Propionibacterium acnes genomic sequences in almost half of the datasets, with the highest abundance in the leukemia (RPMI-8226) and central nervous system (SF-295, SF-539, and SNB-19) cell lines. While the origin of these contaminating bacterial sequences remains to be determined, observed results suggest that computational control for the presence of microbial genomic material is a necessary step in the analysis of the high throughput sequencing (HTS) data.
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Affiliation(s)
- Mark Rojas
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas, United States of America
- Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
- * E-mail:
| | - Georgiy Golovko
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas, United States of America
- Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Kamil Khanipov
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas, United States of America
- Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Levent Albayrak
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas, United States of America
- Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Sergei Chumakov
- Department of Physics, University of Guadalajara, Guadalajara, Jalisco, Mexico
| | - B. Montgomery Pettitt
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas, United States of America
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
- Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Alex Y. Strongin
- Inflammatory and Infectious Disease Center/Cancer Research Center, Sanford-Burnham Medical Research Institute, La Jolla, California, United States of America
| | - Yuriy Fofanov
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas, United States of America
- Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
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