Integrated pan-cancer map of EBV-associated neoplasms reveals functional host–virus interactions

Srishti Chakravorty, Bingyu Yan, Chong Wang, Luopin Wang, Joseph Taylor Quaid, Chin Fang Lin, Scott D. Briggs, Joydeb Majumder, D. Alejandro Canaria, Daniel Chauss, Gaurav Chopra, Matthew R. Olson, Bo Zhao, Behdad Afzali, Majid Kazemian

Research output: Contribution to journalArticlepeer-review

41 Scopus citations

Abstract

Epstein–Barr virus (EBV) is a complex oncogenic symbiont. The molecular mechanisms governing EBV carcinogenesis remain elusive and the functional interactions between virus and host cells are incompletely defined. Here we present a comprehensive map of the host cell–pathogen interactome in EBV-associated cancers. We systematically analyzed RNA sequencing from >1,000 patients with 15 different cancer types, comparing virus and host factors of EBVþ to EBV tissues. EBV preferentially integrated at highly accessible regions of the cancer genome, with significant enrichment in super-enhancer architecture. Twelve EBV transcripts, including LMP1 and LMP2, correlated inversely with EBV reactivation signature. Overexpression of these genes significantly suppressed viral reactivation, consistent with a "virostatic" function. In cancer samples, hundreds of novel frequent missense and nonsense variations in virostatic genes were identified, and variant genes failed to regulate their viral and cellular targets in cancer. For example, one-third of patients with EBVþ NK/T-cell lymphoma carried two novel nonsense variants (Q322X, G342X) of LMP1 and both variant proteins failed to restrict viral reactivation, confirming loss of virostatic function. Host cell transcriptional changes in response to EBV infection classified tumors into two molecular subtypes based on patterns of IFN signature genes and immune checkpoint markers, such as PD-L1 and IDO1. Overall, these findings uncover novel points of interaction between a common oncovirus and the human genome and identify novel regulatory nodes and druggable targets for individualized EBV and cancer-specific therapies. Significance: This study provides a comprehensive map of the host cell-pathogen interactome in EBVþ malignancies. See related commentary by Mbulaiteye and Prokunina-Olsson, p. 5917.

Original languageEnglish (US)
Pages (from-to)6010-6023
Number of pages14
JournalCancer Research
Volume79
Issue number23
DOIs
StatePublished - Dec 1 2019
Externally publishedYes

Bibliographical note

Funding Information:
We thank Drs. Fred P. Davis (NIH, Bethesda, MD), Claudia Kemper (NIH, Bethesda, MD), Ourania Andrisani (Purdue University, West Lafayette, IN), and Jeffrey Cohen (NIH, Bethesda, MD) for invaluable comments on the manuscript. This work was supported by Purdue Cancer Center (startup fund to M. Kazemian), National Heart, Lung, and Blood Institute (NIH grant 5K22HL125593 to M. Kazemian), Showalter Trust (research award to M. Kazemian and G. Chopra), and the Wellcome Trust (grant 097261/Z/ 11/Z to B. Afzali). This work was supported (in part) by the Intramural Research Program of the NIH, The National Institutes of Diabetes and Digestive and Kidney Diseases (NIDDK). The authors thank patients who donated tissue samples and investigators that carried out the RNA-sequencing.

Publisher Copyright:
© 2019 American Association for Cancer Research.

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