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Egan KM, Kim Y, Bender N, Hodge JM, Coghill AE, Smith-Warner SA, Rollison DE, Teras LR, Grimsrud TK, Waterboer T. Prospective investigation of polyomavirus infection and the risk of adult glioma. Sci Rep 2021; 11:9642. [PMID: 33953301 PMCID: PMC8100283 DOI: 10.1038/s41598-021-89133-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 04/16/2021] [Indexed: 12/23/2022] Open
Abstract
Glioma is an aggressive primary tumor of the brain with a poorly understood etiology. We studied the association of 4 human polyomaviruses (HPyV)—JC virus (JCV), BK virus (BKV), human polyomavirus 6 (HPyV6), and Merkel cell polyomavirus (MCPyV) with glioma risk within the Cancer Prevention Study II in the US (CPS-II) and the Janus Serum Bank in Norway. Cohort participants subsequently diagnosed with glioma from the CPS-II (n = 37) and Janus Serum Bank (n = 323), a median of 6.9 and 15.4 years after blood collection, respectively, were matched to individual controls on age, sex, and date of blood draw. Serum antibodies to the major viral capsid protein (VP1) were used to establish infection history for each polyomavirus. Odds ratios (ORs) and 95% confidence intervals (CIs) were estimated using conditional logistic regression. In the Janus Serum Bank, MCPyV infection was associated with a higher risk of glioma overall (OR: 1.56; 95% CI 1.10, 2.19). A modest, nonsignificant positive association with MCPyV infection was also observed in CPS-II (OR: 1.29; 95% CI 0.54, 3.08). In both cohorts, glioma risk was not significantly related to infection with JCV, BKV or HPyV6. The present study suggests that MCPyV infection may increase glioma risk.
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Affiliation(s)
- Kathleen M Egan
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL, 33612, USA.
| | - Youngchul Kim
- Department of Biostatistics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA
| | - Noemi Bender
- Infections and Cancer Epidemiology, German Cancer Research Center (Deutsches Krebsforschungszentrum, DKFZ), 69120, Heidelberg, Germany
| | - James M Hodge
- Department of Population Science, American Cancer Society, Atlanta, GA, 30303, USA
| | - Anna E Coghill
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL, 33612, USA
| | - Stephanie A Smith-Warner
- Departments of Nutrition and Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Dana E Rollison
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL, 33612, USA
| | - Lauren R Teras
- Department of Population Science, American Cancer Society, Atlanta, GA, 30303, USA
| | - Tom K Grimsrud
- Department of Research, Cancer Registry of Norway, 0379, Oslo, Norway
| | - Tim Waterboer
- Infections and Cancer Epidemiology, German Cancer Research Center (Deutsches Krebsforschungszentrum, DKFZ), 69120, Heidelberg, Germany
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Yuan Z, Ye X, Zhu L, Zhang N, An Z, Zheng WJ. Virome assembly and annotation in brain tissue based on next-generation sequencing. Cancer Med 2020; 9:6776-6790. [PMID: 32738030 PMCID: PMC7520322 DOI: 10.1002/cam4.3325] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 06/20/2020] [Accepted: 07/01/2020] [Indexed: 12/15/2022] Open
Abstract
The glioblastoma multiforme (GBM) is one of the deadliest tumors. It has been speculated that virus plays a role in GBM but the evidences are controversy. Published researches are mainly limited to studies on the presence of human cytomegalovirus (HCMV) in GBM. No comprehensive assessment of the brain virome, the collection of viral material in the brain, based on recently sequenced data has been performed. Here, we characterized the virome from 111 GBM samples and 57 normal brain samples from eight projects in the SRA database by a tested and comprehensive assembly approach. The annotation of the assembled contigs showed that most viral sequences in the brain belong to the viral family Retroviridae. In some GBM samples, we also detected full genome sequence of a novel picornavirus recently discovered in invertebrates. Unlike previous reports, our study did not detect herpes virus such as HCMV in GBM from the data we used. However, some contigs that cannot be annotated with any known genes exhibited antibody epitopes in their sequences. These findings provide several avenues for potential cancer therapy: the newly discovered picornavirus could be a starting point to engineer novel oncolytic virus; and the exhibited antibody epitopes could be a source to explore potential drug targets for immune cancer therapy. By characterizing the virosphere in GBM and normal brain at a global level, the results from this study strengthen the link between GBM and viral infection which warrants the further investigation.
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Affiliation(s)
- Zihao Yuan
- School of Biomedical InformaticsUniversity of Texas Health Science Center at HoustonHoustonTXUSA
- Texas Therapeutics InstituteInstitute of Molecular MedicineMcGovern Medical SchoolUniversity of Texas Health Science Center at HoustonHoustonTXUSA
| | - Xiaohua Ye
- Texas Therapeutics InstituteInstitute of Molecular MedicineMcGovern Medical SchoolUniversity of Texas Health Science Center at HoustonHoustonTXUSA
| | - Lisha Zhu
- School of Biomedical InformaticsUniversity of Texas Health Science Center at HoustonHoustonTXUSA
| | - Ningyan Zhang
- Texas Therapeutics InstituteInstitute of Molecular MedicineMcGovern Medical SchoolUniversity of Texas Health Science Center at HoustonHoustonTXUSA
| | - Zhiqiang An
- Texas Therapeutics InstituteInstitute of Molecular MedicineMcGovern Medical SchoolUniversity of Texas Health Science Center at HoustonHoustonTXUSA
| | - W. Jim Zheng
- School of Biomedical InformaticsUniversity of Texas Health Science Center at HoustonHoustonTXUSA
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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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Wittekindt C, Wagner S, Sharma SJ, Würdemann N, Knuth J, Reder H, Klußmann JP. [HPV - A different view on Head and Neck Cancer]. Laryngorhinootologie 2018; 97:S48-S113. [PMID: 29905354 PMCID: PMC6540966 DOI: 10.1055/s-0043-121596] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Head and neck cancer is the sixth most common cancer with over 500000 annually reported incident cases worldwide. Besides major risk factors tobacco and alcohol, oropharyngeal squamous cell carcinomas (OSCC) show increased association with human papillomavirus (HPV). HPV-associated and HPV-negative OSCC are 2 different entities regarding biological characteristics, therapeutic response, and patient prognosis. In HPV OSCC, viral oncoprotein activity, as well as genetic (mutations and chromosomal aberrations) and epigenetic alterations plays a key role during carcinogenesis. Based on improved treatment response, the introduction of therapy de-intensification and targeted therapy is discussed for patients with HPV OSCC. A promising targeted therapy concept is immunotherapy. The use of checkpoint inhibitors (e.g. anti-PD1) is currently investigated. By means of liquid biopsies, biomarkers such as viral DNA or tumor mutations in the will soon be available for disease monitoring, as well as detection of treatment failure. By now, primary prophylaxis of HPV OSCC can be achieved by vaccination of girls and boys.
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Affiliation(s)
- Claus Wittekindt
- Klinik für HNO-Heilkunde, Kopf-/Halschirurgie, Plastische Operationen, Universitätsklinikum Gießen und Marburg GmbH, Standort Gießen
| | - Steffen Wagner
- Klinik für HNO-Heilkunde, Kopf-/Halschirurgie, Plastische Operationen, Universitätsklinikum Gießen und Marburg GmbH, Standort Gießen
| | - Shachi Jenny Sharma
- Klinik für HNO-Heilkunde, Kopf-/Halschirurgie, Plastische Operationen, Universitätsklinikum Gießen und Marburg GmbH, Standort Gießen
| | - Nora Würdemann
- Klinik für HNO-Heilkunde, Kopf-/Halschirurgie, Plastische Operationen, Universitätsklinikum Gießen und Marburg GmbH, Standort Gießen
| | - Jennifer Knuth
- Klinik für HNO-Heilkunde, Kopf-/Halschirurgie, Plastische Operationen, Universitätsklinikum Gießen und Marburg GmbH, Standort Gießen
| | - Henrike Reder
- Klinik für HNO-Heilkunde, Kopf-/Halschirurgie, Plastische Operationen, Universitätsklinikum Gießen und Marburg GmbH, Standort Gießen
| | - Jens Peter Klußmann
- Klinik für HNO-Heilkunde, Kopf-/Halschirurgie, Plastische Operationen, Universitätsklinikum Gießen und Marburg GmbH, Standort Gießen
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5
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Cantalupo PG, Katz JP, Pipas JM. Viral sequences in human cancer. Virology 2017; 513:208-216. [PMID: 29107929 DOI: 10.1016/j.virol.2017.10.017] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Revised: 10/10/2017] [Accepted: 10/19/2017] [Indexed: 01/14/2023]
Abstract
We have developed a virus detection and discovery computational pipeline, Pickaxe, and applied it to NGS databases provided by The Cancer Genome Atlas (TCGA). We analyzed a collection of whole genome (WGS), exome (WXS), and RNA (RNA-Seq) sequencing libraries from 3052 participants across 22 different cancers. NGS data from nearly all tumor and normal tissues examined contained contaminating viral sequences. Intensive computational and manual efforts are required to remove these artifacts. We found that several different types of cancers harbored Herpesviruses including EBV, CMV, HHV1, HHV2, HHV6 and HHV7. In addition to the reported associations of Hepatitis B and C virus (HBV & HCV) with liver cancer, and Human papillomaviruses (HPV) with cervical cancer and a subset of head and neck cancers, we found additional cases of HPV integrated in a small number of bladder cancers. Gene expression and mutational profiles suggest that HPV drives tumorigenesis in these cases.
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Affiliation(s)
- Paul G Cantalupo
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Joshua P Katz
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - James M Pipas
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA.
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Lack of human cytomegalovirus expression in single cells from glioblastoma tumors and cell lines. J Neurovirol 2017; 23:671-678. [PMID: 28695489 DOI: 10.1007/s13365-017-0543-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 05/23/2017] [Accepted: 06/08/2017] [Indexed: 12/21/2022]
Abstract
The relationship between human cytomegalovirus (HCMV) and glioblastoma (GBM) is an ongoing debate with extensive evidence supporting or refuting its existence through molecular assays, pre-clinical studies, and clinical trials. We focus primarily on the crux of the debate, detection of HCMV in GBM samples using molecular assays. We propose that these differences in detection could be affected by cellular heterogeneity. To take this into account, we align the single-cell RNA sequencing (scRNA-seq) reads from five GBM tumors and two cell lines to HCMV and analyze the alignments for evidence of (i) complete viral transcripts and (ii) low-abundance viral reads. We found that neither tumor nor cell line samples showed conclusive evidence of full HCMV viral transcripts. We also identified low-abundance reads aligned across all tumors, with two tumors having higher alignment rates than the rest of the tumor samples. This work is meant to rigorously test for HCMV RNA expression at a single cell level in GBM samples and examine the possible utility of single cell data in tumor virology.
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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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Beck TN, Chikwem AJ, Solanki NR, Golemis EA. Bioinformatic approaches to augment study of epithelial-to-mesenchymal transition in lung cancer. Physiol Genomics 2014; 46:699-724. [PMID: 25096367 PMCID: PMC4187119 DOI: 10.1152/physiolgenomics.00062.2014] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Accepted: 08/04/2014] [Indexed: 12/22/2022] Open
Abstract
Bioinformatic approaches are intended to provide systems level insight into the complex biological processes that underlie serious diseases such as cancer. In this review we describe current bioinformatic resources, and illustrate how they have been used to study a clinically important example: epithelial-to-mesenchymal transition (EMT) in lung cancer. Lung cancer is the leading cause of cancer-related deaths and is often diagnosed at advanced stages, leading to limited therapeutic success. While EMT is essential during development and wound healing, pathological reactivation of this program by cancer cells contributes to metastasis and drug resistance, both major causes of death from lung cancer. Challenges of studying EMT include its transient nature, its molecular and phenotypic heterogeneity, and the complicated networks of rewired signaling cascades. Given the biology of lung cancer and the role of EMT, it is critical to better align the two in order to advance the impact of precision oncology. This task relies heavily on the application of bioinformatic resources. Besides summarizing recent work in this area, we use four EMT-associated genes, TGF-β (TGFB1), NEDD9/HEF1, β-catenin (CTNNB1) and E-cadherin (CDH1), as exemplars to demonstrate the current capacities and limitations of probing bioinformatic resources to inform hypothesis-driven studies with therapeutic goals.
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Affiliation(s)
- Tim N Beck
- Developmental Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania; Program in Molecular and Cell Biology and Genetics, Drexel University College of Medicine, Philadelphia, Pennsylvania; and
| | - Adaeze J Chikwem
- Developmental Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania; Temple University School of Medicine, Philadelphia, Pennsylvania; and
| | - Nehal R Solanki
- Immune Cell Development and Host Defense Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania; Program in Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania
| | - Erica A Golemis
- Developmental Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania; Temple University School of Medicine, Philadelphia, Pennsylvania; and Program in Molecular and Cell Biology and Genetics, Drexel University College of Medicine, Philadelphia, Pennsylvania; and
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