Jul 31, 2018

Session 8B: Virus-Host Interactions II

Session Chairs: Britt Glaunsinger and Yasuaki Harabuchi (下屆EBV會議主辦人) (Play Circle)

Oral Talk #70
Role of KSHV in T cell Infiltration in Kaposi's Sarcoma
Microenvironment
Canrong Zhong1, Nannan Zhu1, Yuqing Li1, Yan Yuan1,2
1Sun Yat-sen University, 2University of Pennsylvania
Kaposi’s sarcoma-associated herpesvirus (KSHV), also termed human herpesvirus type 8 (HHV8), is an etiologic agent of Kaposi's Sarcoma (KS), primary effusion lymphoma (PEL), and multicentric Castleman’s disease (MCD). KS is a multifocal and oligoclonal malignancy. Tumors are comprised of proliferating spindle-shaped KS cells with abnormal neoangiogenesis and abundant inflammatory infiltrate. In many early KS lesions, inflammatory cells outnumber spindle cells. Various inflammatory cytokines promote KS cell proliferation and induce spindle cell morphology. Therefore, the immune cell infiltrate and cytokine-rich microenvironment apparently plays a significant role in the progression of KS. The goal of our study is to understand the role of KSHV in establishing the unique KS microenvironment, as well as the contribution of the microenvironment to KS pathogenesis. Recently we reported that KS might originate from KSHV-infected oral mesenchymal stem cells (Li et al., 2018 Cancer Res. 78: 230-245). KSHV infection of oral MSCs resulted in expression of a large spectrum of cytokines and chemokines, including IL-6, VEGF, CCL5, CCL8, and CXCL10, reminiscent of KS lesion. Using a Transwell assay with PBMC, we found that KSHV infection of oral MSCs dramatically enhances T cells chemotaxis, which can be blocked by anti-CCL5 or anti-CCL8 antibodies. Co-cultivation of KSHV-infected MSCs with naïve T cells promoted T cell differentiation to Treg and Th17. Furthermore, we compared KSHV-infected MSCs co-cultivated with and without T cells for tumor phenotypes in mice. Results show that after being exposed to T cells, KSHV-infected MSCs exhibit increased blood vessel formation on the Matrigel plug and invasion ability. Taken together, we established an MSC model to study KS microenvironment which demonstrates how KS precursor cells recruit T cells to inflamed sites and how T cells promote the progression of KS, thus shedding light on the formation of KS microenvironment and its role in KS progression. 

MSCs: Nestin+, CD31-, CD29+, CD34+, CD133+

  • neural crest cell contributions to the cranial facial development, neural crest cells migrate to form the craniofacial mesenchyme that differentiates into various cranial ganglia and craniofacial cartilages and bones
  • SJ Gao (kidney capsule implantation of KSHV-infected MSCs, PLLSC)

Evidence 2: KSHV infection leads to MEndT
Evidence 3: gene expression profiling reveals linagedistanc elf MSC to KS
Evidence 4: cytokines network in KSHV-MSCs: CCL8, bFGF, VEGF-A, VEGF-D, IL6, IGF1, TGFb, ANGPT2 (both by cytokines array in IHC)

Chemokine provided by KSHV-infected MSCs induces T cell chemotaxis (this is also true in KS lesion -> no B cell infiltration)

KSHV-PDLSCs promoter T cell differentiation to Th17 (and down-regulates Treg a little bit)

Activated T cell conditioned media (TCM) promotes MEndT of KSHV-infected PDLSCs Matrigel plug assay

KSHV-PDLSCs become more aggressive after co-cultivating with 

Oral Talk #71
Epstein-Barr Virus LMP1 Hijacks the Host ESCRT Machinery
for Exosomal Secretion
Dingani Nkosi1, Mujeeb Cheerathodi1, Mark A Rider1, David G Meckes1
1Florida State University College of Medicine, Department of Biomedical Sciences
Exosomes are endosomal-derived extracellular vesicles (EVs) that are important mediators of cell to cell communications in both normal and pathological conditions. Latent membrane protein 1 (LMP1), one of the major viral oncogenes expressed in most Epstein-Barr virus (EBV)-associated cancers is secreted from infected cells in EVs. LMP1-modified EVs have the ability to influence the tumor microenvironment. Despite the significance of LMP1- modified EVs in EBV malignancies, very little is known about how this viral protein hijacks the host EV pathways for secretion. ESCRT-dependent and -independent cellular machineries have shown to play a major role in biogenesis of EVs and cargo sorting. Using the BioID method, we identified LMP1 proximal interacting proteins that are known to play roles in exosome formation and protein trafficking including CD63, syntenin-1, Alix, Tsg101, Hrs, charged multivesicluar body proteins (CHMPs), and sorting nexins (Rider and Cheerathodi et al., Virology, 2018). To test the contributions of the identified ESCRT genes in LMP1 exosomal trafficking, cell lines expressing inducible short hairpin RNAs (shRNAs) were generated. Cell-derived EVs were collected from LMP1 expressing cells and levels of specific cargo were evaluated. Nanoparticle tracking and immunoblot analysis revealed reduced levels of LMP1 EV packaging and of vesicle production following knock-down of syntenin-1, Alix, Hrs and Tsg101. Furthermore, the levels of intracellular and exosomal CD63, a tetraspanin protein important for LMP1 EV incorporation and regulation of LMP1- mediated signaling, was reduced following knock-down of the individual genes. Importantly, the trafficking of LMP1 to lipid rafts, plasma membrane microdomains thought to be involved in signal transduction, EV biogenesis and cargo sorting remained intact despite syntenin-1 and Alix knock-down. These results suggest that the cellular ESCRT controls the incorporation of LMP1 into the host EV pathway for secretion and may also influence LMP1-mediated signaling due to alterations in the levels of intra- and extra-cellular CD63. 

Extracellular vesicles (EVs)

  • 40-120nm 
  • Diverted membrane enclosed particles
  • Classified according to sub-cellular origin and size
  • Fold I’m almost all nobody fluids
  • Transfer proteins, mRNAs, miRNAs, and lipid
  • Virus hijacks ENV host pathway

LMP1
  • Main EBV oncogene
  • Mimics CD40
EBV LMP1-modified EVs
  • EBV-infected cancer cells secrete EVs containing LMP1
  • Expression of LMP1 in cell causes enhancement IOC vehicle production
  • LMP1 expression increases the levels of EGFR and PI3K in EVs
The LMP1 interactive com trains proteins important for exosome trafficking and biogenesis
  • Cellular compartment 73% of origins identified were in vesiciepked 
  • TRAF2, STAT3, TDSG101, Syndin?, ITGB1, and HSC70
Hypothesis: LMP1 utilizes the ESCRT pathway to facilitate EV production

LMP1 expression increase mRNA and protein levels of EV biogenesis components
  • Alix, HRD, HSC70, TSG101, Syntenin-1, CD9, CD81
  • Knockdown of ESRT components reduces LMP1-mediated enhancement of vesicles
  • ESRT II complex is dispensable in LMP1 exosome sorting
  • SNAP  not required
  • VPS4A not required
  • LMP1 EV secretion requires upstream, but not downstream ESCRT components
  • The N-terminus and TM1 are sufficient to guide LMP1 EV sorting

Oral Talk #72
vIRF-1 Regulatesm Mitochondrial Content by Promoting
Mitophagy During HHV-8 Replication
Mai Tram Vo1, Young Bong Choi1
1Johns Hopkins School of Medicine
Human herpesvirus 8 (HHV-8) is known as an infectious agent that is causally related with AIDS-associated human malignancies including Kaposi sarcoma, primary effusion lymphoma (PEL), and multicentric Castleman's disease. HHV-8-encoded viral interferon regulatory factor 1 (vIRF-1) contributes to HHV-8 pathogenesis potentially by inhibiting antiviral responses such as innate immune signaling and apoptosis. We demonstrated previously that vIRF-1 localizes in part to mitochondria and inhibits associated antiviral responses, thereby promoting virus replication. However, the exact function of mitochondria-localized vIRF-1 is not fully understood. Here, we provide evidence of involvement of vIRF-1 in mitochondria quality control via mitophagy during virus replication. Firstly, we observed that cellular mitochondrial content, assessed by Cellometer image- based cytometry of mitochondria-encoded protein MTCO2, was reduced in lytic HHV-8- positive PEL cells, but this effect was reversed by vIRF-1 depletion and autophagy inhibitors, suggesting that vIRF-1 is likely to be involved in HHV-8 replication-induced mitophagy. Secondly, we found that mitophagy-related proteins including LC3-II, a lipidated form of LC3, and a mitophagy receptor, NIX, translocated to mitochondria upon virus replication. Importantly, their localization to mitochondria was significantly impaired in vIRF- 1-depleted PEL cells undergoing lytic replication, suggesting that vIRF-1 plays an essential role recruitment of the mitophagy machinery to mitochondria. Furthermore, we found that vIRF-1 could bind directly to NIX via a short linear motif in vIRF-1 containing the Asn8 and Phe10 residues. Co-transfection of vIRF-1 and NIX, but neither NIX nor vIRF-1 alone, resulted in a decrease in mitochondrial content of transfected HeLa cells, indicative of functional interaction between NIX and vIRF-1 to promote mitophagy. We also found that vIRF-1 interacts with the members of autophagy related protein 8 (ATG8) family upon mitochondria damage. Taken together, our results indicate that vIRF-1 is involved directly in mitochondrial quality control via interactions with key mitophagy proteins during HHV8 replication. 

Inhibitory interaction of vIRF1 with cellular proteins

  • IFN responses
  • TGFb?

VIRF1 localize on mitochondria (2 previous publications)

Mitochondrial content decreased during HHV8 lytic replication
iBCBL1 (TRex BCBL1)
  • MITCO2, MAVs, vIRF1, DAPY.
  • VIRF1/mtDNA/DAPI
Autophagy inhibitors rescued mitochondrial content during HHV8 lytic replication

Mitochondrial content is accumulated in vIRF1 depleted lytic cells

Mitochondrial-contains autophagosomes decreased in vIRF1-depleted lytic Ellis

Mitophagy, vIRF1 promotes mitophagy to eliminate the mictochondrial damage during HHV8 lytic replication

VIRF1 is essential for NOX targeting to and modification son mitochondria
NIX oligomers are reduced during vIRF expression

NIX(BNKIP3L) 
Function al interaction of vIRF1 and NIX for mitochondrial clearance
Detection f in trace lunar interaction of vIRF1 and NIX using NanoBiT system (luminescence) or by using PLA system

VIRF binding short linear motif containing ASN and PHE10 and interaction is required for NPC interaction

LC3 targets to mitochondria in a vIRF dependent way
VIRF1 binds indirectly to LC3 upon mitochondrial 

Oral Talk #73
Epstein-Barr Virus Activates F-Box Protein FBXO2 to Limit
Viral Infectivity by Targeting Glycoprotein B for Degradation
Hao-Jiong Zhang1, Jinxiu Tian1, Xue-Kang Qi1, Musheng Zeng1, Yi-Xin Zeng1, Lin Feng1
1Sun Yat-sen University Cancer Center
Epstein-Barr virus (EBV) is a human cancer-related virus closely associated with lymphoid and epithelial malignancies, and EBV glycoprotein B (gB) plays an essential role in viral entry into both B cells and epithelial cells by promoting cell-cell fusion. EBV gB is exclusively modified with high-mannose-linked N-glycans and primarily localizes to the endoplasmic reticulum (ER) with low levels on the plasma membrane (PM). However, the mechanism through which gB is regulated within host cells is largely unknown. Here, we report the identification of F-box only protein 2 (FBXO2), an SCF ubiquitin ligase substrate adaptor that preferentially binds high-mannose glycans and attenuates EBV infectivity by targeting N-glycosylated gB for degradation. gB possesses seven N-glycosylation sites, and FBXO2 directly binds to these high-mannose moieties through its sugar-binding domain. The interaction promotes the degradation of glycosylated gB via the ubiquitin- proteasome pathway. Depletion of FBXO2 not only stabilizes gB but also promotes its transport from the ER to the PM, resulting in enhanced membrane fusion and viral entry. FBXO2 is expressed in epithelial cells but not B cells, and EBV infection up-regulates FBXO2 levels. In summary, our findings highlight the significance of high-mannose modification of gB and reveal a novel anti-herpes mechanism involving glycoprotein homeostasis regulation. 



Oral Talk #74
Cell-Mediated Immune Responses to Persistent KSHV Infection
in Mice with Reconstituted Human Immune System
Components
Nicole Caduff1, Donal McHugh1, Patrick Rämer1, Christian Münz1
1Viral Immunobiology, Institute of Experimental Immunology
Cancers attributable to EBV and KSHV infection are more frequent in immunosuppressed individuals, indicating a crucial role of the immune system in controlling the respective malignancies. In contrast to EBV, the contribution of cellular immunosurveillance against KSHV is less well understood due to the lack of suitable in vitro and in vivo models for studying KSHV biology. In this project, we investigated the cellular immune control of KSHV in an in vivo model of persistent KSHV infection, recently developed in our laboratory, and based on EBV co-infection of NOD-scid γc-/- mice reconstituted with human immune system components (huNSG). In this model, EBV enables persistent KSHV infection beyond four weeks and both viruses seem to collaborate for increased PEL-like lymphomagenesis supported by lytic EBV activity. Interestingly, we observed significantly increased frequencies of unconventional CD56- CD16+ Natural Killer (NK) cells in KSHV co-infected mice compared to those solely infected with EBV, which positively correlated with the KSHV but not EBV burden in co-infected animals. This aberrant NK cell subset is associated with impaired effector functions and accordingly, KSHV loads and tumor frequencies were not affected by NK cell depletion prior to the double-infection of huNSG mice. Furthermore, we documented a significant expansion of central and effector memory T cells in KSHV co-infected compared to EBV-only infected mice, both in co-infection studies using EBV wildtype and lytically-compromised BZLF1-KO- EBV whose viral burden is not affected by KSHV co-infection. Hence, KSHV-specific T cells are likely expanding in our model. Future analysis will lead to a better understanding of how KSHV infections are controlled, which is pivotal for the development of immunotherapies. It will extend our knowledge on how these two prevalent herpesviruses shape the human immune cell landscape and further validate the potential and limitations of our newly developed in vivo co-infection model of KSHV persistence. 

KSHV persists more frequently in the presence of EBV in huNSG mice
EBV+KSHV confection (LANA and LMP +_
PEL like dusk iunfected B cells
EBV lytic gene expression leads to enhanced tumorigeneis in EBV nad KSHV dual infected huNSF mice
Do huNSG mice moist cellular immune responses to KSHV?

  • EBV infection is restricted to NK and T cells
  • NK cells mainly control EBV lyrically replicating cel;s (Cell Reports 201, Chijioke et al
  • EBV lytic replication 

KSHV co-infection results in a redistribution of NK cell subsets
Frequency of CD56neg CD17 po NL cells correlates with KSHV but not EBV burden
NK cells seem not to control KSHV in huNSG mice
KSHBV_EBVzko 
CD56negCD16pos NK cells ar associated with impaired effector functions
NK cells seem not to control KSHV during infection of huNSG mice

The cells expand significantly more in KSHV co-infected compared to EBV single-infected mice
  • Central and effector memory CD8+ T cells expand in KSHV/EBVzko dual infection
  • T cell depletion may lead to a higher KSHV burden and increased tumor formation (KSHV + EBV wt)
Outlook
  • +T cell repertoire
  • + Antigen specificuies
  • + Effector functions
  • + Analyze T an NK cell compartmentation of 
Already published?  check on 
  • "EBV infection on mice with reconstituted human immune system" in pdf 4759) 
  • Pdf 5272
  • pdf 5273

 2018 Feb 12;9:238. doi: 10.3389/fimmu.2018.00238. eCollection 2018.

Human γ-Herpesvirus Infection, Tumorigenesis, and Immune Control in Mice with Reconstituted Human Immune System Components.

Abstract

The human γ-herpesviruses Epstein-Barr virus (EBV or HHV4) and Kaposi sarcoma-associated herpesvirus (KSHV or HHV8) are each associated with around 2% of all tumors in humans worldwide. However, investigations into their infection, oncogenesis, and immune responses that protect from the associated tumors have been hampered by the exclusive tropism of these pathogens for humans. Mice with reconstituted human immune system components (HIS mice) provide the unique opportunity to study persistent infection, virus associated lymphoma formation, and cell-mediated immune control of EBV and KSHV. Moreover, since these pathogens are unique stimuli for cytotoxic human lymphocyte responses, they also allow us to characterize long-lasting cell-mediated immune control and the requirements for its initiation, which would also be desirable to achieve during antitumor vaccination in general. Thus, human γ-herpesvirus infection of HIS mice provides unique insights into the biology of these important human pathogens and human cell-mediated immune responses that are considered to be the main protective entity against tumors.(PDF 4759, 5272, 5273)


Oral Talk #75
Epstein-Barr Virus Infection Promotes Epithelial Cell Growth by
Attenuating Differentiation-Dependent Exit from Cell Cycle
Mark R. Eichelberg1, René Welch1, Ahmed Ali1, Kathleen Makielski1, Joseph T. Guidry2, Makoto Ohashi1, Shannon Kenney1, Sϋndϋz Keleş1, Rona Scott2, Eric Johannsen1
1University of Wisconsin-Madison, 2Louisiana State University
Latent infection of B lymphocytes and epithelial cells by Epstein-Barr virus (EBV) is causally linked to their transformation into lymphomas and carcinomas, respectively. Although carcinomas account for almost 90% of EBV associated cancers, progress had been limited due to lack of a physiologic in vitro model of EBV epithelial infection. Recently, EBV infection of normal oral keratinocytes (NOKs) has emerged as a model that recapitulates aspects of EBV infection in vivo, such as differentiation-associated viral replication. Using NOK and NOK-EBV cells we studied changes in gene expression due to EBV infection and differentiation. Although we observed that the effect of latent EBV infection in undifferentiated cells was subtle, the ability of NOK-EBV to differentiate was impaired. Keratinocytes undergoing differentiation exit the cell cycle and shut down most metabolic processes. However, RNA-seq data indicated that differentiated NOK-EBV maintained some expression of genes associated with these processes. Conversely, genes associated with differentiation were not as strongly induced in NOK-EBV. A possible mechanism for the inhibition of differentiation is expression of EBV lytic genes, since these genes are only expressed in differentiating NOK-EBV. To test this, we constructed an EBV mutant defective for lytic cycle entry by deletion of the R and Z immediate early genes (EBVΔRZ). RNA-seq analysis of NOK-EBVΔRZ suggests that lytic genes are at least partly responsible for the attenuated differentiation. In addition, we have grown NOKs, NOK-EBV, and NOK-EBVΔRZ in organotypic raft cultures. Consistent with our RNA-seq results, EBV partially disrupts the differentiation of NOK-EBV rafts, resulting in significant morphological changes and a reduction in differentiation-associated proteins in the suprabasal layers. Raft cultures of NOK-EBVΔRZ show at least partial restoration of differentiation capacity. Our results help define the mechanisms by which EBV infection alters keratinocyte differentiation and provide a basis for understanding the role of EBV in epithelial cancers. 

EBV establishes latency in B cells
hTert NOKs (Munger lab, Harvard)

NOK differentiation (methylcellulose MC)
IVL, Zta, Rta, EAD

Raft culture collagen base, cells at air interface

RNA-seq analysis NOK and NOK-EBV

  • Low LMP1 and LMP2A
  • High EBERs, BARTs, GFP/new

EBV has subtle effect on NOKs 45 up 88 down

However, in MC-induced differentiation many genes are altered, including ….
Pathways down regulated by the presence of EBV
EBV partially inhibits differentiation  (NOK, versus NOK-EBV)
KRT10 is quickly unregulated during differentiation in the absence of EBV
MCM7

Basal NOK-EBV are invasive

EBVdeltaRZ
  • This virus still strongly inhibits KRT10, ITGB1, IVL expression
Therefore, 
  • Latent EBV has subtle effect in ballad keratinocytesonce or more latent genes attenuated differentiation
  • EBERs, LMP1, LMP2A, BNLF2a/b possible mechanisms?

Oral Talk #76
INF-γ Responses in Peripheral Blood Lymphocytes of Patients
with KSHV-associated Diseases Treated with Pomalidomide
and Liposomal Doxorubicin
Romin Roshan1, Kathryn Lurain2, Nazzarena Labo1, Ramya Ramaswami2, Thomas Uldrick2, Priscila Goncalves2, Anna Widell2, Vickie Marshall1, Robert Yarchoan2, Denise Whitby1
1Viral Oncology Section, AIDS and Cancer Viral Program, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, 2HIV and AIDS Mailgnancy Branch, Center for Cancer Research, National Cancer Institute
Background: KSHV-specific T-cell responses are poorly understood, including how they vary among patients with different KSHV-associated diseases or are affected by treatment. We evaluated factors associated with cell-mediated IFN-ƴ responses to the entire KSHV proteome among patients with Kaposi sarcoma +/- other KSHV-associated diseases treated with pomalidomide and liposomal doxorubicin (LD).
Methods: 12 HIV+ male patients were studied: 7 with KS alone; and 5 with KS and primary effusion lymphoma (PEL), KSHV-associated multicentric Castleman disease (KSHV-MCD) or KSHV inflammatory cytokine syndrome (KICS) at baseline and after treatment with pomalidomide and LD. PBMCs were tested using a peptide-based ELISPOT assay measuring IFN-ƴ secretion in response to 82 KSHV-encoded proteins, an SIV peptide, and a peptide pool including EBV, CMV, and influenza. Breadth and intensity of T-cell responses were compared using nonparametric univariate analyses, while response levels to individual antigens were evaluated with nested random effect models.
Results: Median age was 43 (inter-quartile range [IQR] 41-56); median CD4+ cell count was 273 (IQR 90-408), HIV VL was undetectable in all patients but 3 who had KICS, PEL or KSHV-MCD (range 28-3318 copies/mL). While positive control responses were robust (median 2327 antigens; IQR 444-3213), patients generally responded to few KSHV antigens (median 4 antigens; IQR 2-11) with a moderate mean intensity (median 163 SFU/million PBMC, IQR 147-264). Baseline responses were not different among diseases. At a second timepoint, after a median of 161 days of treatment (IQR 102-172), CD4+ counts did not change significantly and the number and intensity of responses to KSHV antigens remained essentially stable in breadth (median 4.5, IQR 2.5-12) and mean intensity (median 195 SFU/million PBMC; IQR 160-466).
Conclusions: As previously observed, HIV+ patients had sparse, modest and heterogeneous IFN-ƴ response to KSHV antigens. Treatment with pomalidomide and LD did not result in changes in response levels or breadth. 

Association of KSHV with immunosuppressive suggests cellular immunity is a restriction 

KSHV whole proteome ELISPOT assay

  • 12 mer peptide pool ~7500 overlapping peptides 82 IRGFs in 84 pools

T cell responses to KSHV ORFs are variable

Treatment: pomalidomide (3rd generation immunomodulatory drug) angiogenesis inhibitor, T cell activation , NK cell activation and increase tumor surface marker down-regulated by virus + liposomal doxoreuicin

Antigen responses did not change over time
There no statistically (NO IMMUNODOMINANT ANTIGEN IDENTIFIED)

Some patients have good CD4 response

Oral Talk #77
Epstein-Barr Virus-Infected Tonsillar Marginal Zone B Cells in vivo as a Precursor for Immunosuppression-Related B-Cell
Lymphoma
Charles Torgbor1, Ann M. Moormann2, David A.Thorley-Lawson1
1Tufts University School of Medicine, 2University of Massachusetts Medical School
The germinal center model (GCM) of Epstein-Barr virus (EBV) persistence in humans proposes that, EBV infects and drives naïve B cells through the GC to establish a quiescent lifelong persistent infection in memory B cells. EBV causes several cancers and the normal in vivo counterparts of major EBV-associated cancers have been identified in the GCM. Yet, the normal in vivo counterparts of immunosuppression-related/ immunoblastic B-cell lymphoma (IL) which occurs in immunosuppressed transplant and HIV patients, and resembles lymphoblastoid cell lines (LCLs) remains elusive. We performed a comparative analysis of human tonsillar B cells to identify the closest normal in vivo counterparts of ILs/ LCLs. Here we show that EBV-infected tonsillar marginal zone (MZ) B cells which are GC-independent, are the closest in vivo correlates of ILs/ LCLs. Like LCLs, EBV-infected MZ B express the EBV growth program which includes high expression of the oncogenic LMP1, and the DNA mutating enzyme activation-induced cytidine deaminase (AID), in the absence of the transcription factor BCL6. Furthermore, these EBV-infected MZ B cells are proliferating extensively and are Ki67+. AID expression, rapid proliferation and LMP1 expression put these cells at high risk for tumor development. Of therapeutic importance, the high expression of the oncogenic LMP1 could prove the Achilles heel of EBV-infected MZ B cells, to be targeted. Consequently, we now propose that there are two pathways of EBV persistence in vivo: 1. the established GC model and 2. the alternate GC-independent MZ model.

GCM: germinal center model 

Search for immunologic lymphoma (IL-like B cells in human tonsils

EBV exploits normal B cell biology/differentiation route 2015 Curr top microbial Thorley-Lawson

EBV infected LCL give rise to lethal IL phenotype in immunodeficiency mice 
Cancer Cell 2014, Xang et al?

LCL: IgD+, CD27+, AID+,, CD10- Bcl6-

The only cell type detected in vivo expression the EBV growth is IgD+

None of the observed in vivo are LCL type

Phenotypically LCL resemble tonsil marginal zone (MZ) B cells

MZ (spleen, tonsils,lymph nodes)

EBV gene expression in marginal zone B cells

LCLs express the potent mutagenic enzyme AIF

EBV infected cells are in the AID+MZ cells and BCL6-

PROLIFERATIN OPROFILE OF MZ B CELLS AND NAIVE B CELLS
EBV+ M B CELLS HAV EUNDERGONE MULTIPLE CELL DIVISION

While naive B cell divide very infrequently
Extended edition proliferation and e

Session 8A: Latency

Session 8A Latency 10:30 AM – 12:00 PM
Session Chairs: Jennifer Totonchy & Maria Masucci


EBV Persistence without its EBNA3A and 3C Oncogenes in vivo Anita Murer

Oral Talk #62
EBV Persistence without its EBNA3A and 3C Oncogenes in
vivo
Anita Murer1, Donal McHugh1, Nicole Caduff1, Jens Kalchschmidt2, Mario Barros3, Andrea Zbinden4, Riccarda Capaul4, Gerald Niedobitek3, Martin Allday5, Obinna Chijioke1,6, Christian Münz1 1Viral Immunobiology, Institute of Experimental Immunology, University of Zürich, 2Genomics and Immunity, NIAMS, National Institutes of Health, 3Institute of Pathology, Unfallkrankenhaus Berlin, 4Institute of Medical Virology, University of Zürich, 5Molecular Virology, Department of Medicine, Imperial College London, 6Institute of Pathology and Molecular Pathology, University Hospital Zürich
The oncogenic Epstein Barr virus (EBV) infects the majority of the human population and usually persists within its host for life without symptoms. The EBV oncoproteins nuclear antigen 3A (EBNA3A) and 3C (EBNA3C) are required for B cell transformation in vitro and are expressed in EBV associated immunoblastic lymphomas in vivo. In order to address the necessity of EBNA3A and EBNA3C for persistent EBV infection in vivo, we infected NOD-scid γc null mice with reconstituted human immune system components (huNSG mice) with recombinant EBV mutants devoid of EBNA3A or EBNA3C expression. These EBV mutants established latent infection in secondary lymphoid organs of infected huNSG mice for at least 3 months, but did not cause tumor formation. Low level viral persistence in the absence of EBNA3A or EBNA3C seemed to be supported primarily by proliferation with the expression of early latent EBV gene products transitioning into absent viral protein expression without elevated lytic replication. In vitro, EBNA3A and EBNA3C deficient EBV infected B cells could be rescued from apoptosis through CD40 stimulation, mimicking T cell help in secondary lymphoid tissues. Thus, even in the absence of the oncogenes EBNA3A and 3C, EBV can access a latent gene expression pattern that is reminiscent of EBV persistence in healthy virus carriers without prior expression of its whole growth transforming program. 

G-quadruplexes Regulate mRNA Translation of LANA to Control Antigen Presentation during Latency Prerna Dabral

ral Talk #63
G-Quadruplexes Regulate mRNA Translation of LANA to
Control Antigen Presentation during Latency
Prerna Dabral1, Subhash C. Verma1
1Department of Microbiology and Immunology, University of Nevada, Reno School of Medicine
Kaposi’s sarcoma associated herpesvirus, like other herpesviruses establishes life-long latent infection in the B- and endothelial cells. During latency, only a handful viral genes are expressed, which play important roles in maintaining latency and escaping the infected cells from the host immune surveillance system. Latency Associated Nuclear Antigen (LANA) is one of the predominantly expressed proteins, which is critical for viral genome replication and persistence of the episomes during cell division. LANA self-regulates its synthesis and maintains the protein levels sufficient for persistence below a threshold triggering host’s immune recognition. However, the mechanism of how LANA regulates its synthesis is not fully understood. We previously showed that G-quadruplex in nucleic acid sequences affects biological process including DNA replication fork progression. Sequence analysis of LANA mRNA showed the presence of GC-rich regions that are required for formation of G-quadruplex structures. Various biophysical and biochemical assays including CD spectrometry and gel mobility shift assay of oligonucleotides with GC-rich region of LANA mRNA identified G-quadruplex. Furthermore, Crosslinking and Immunoprecipitation (CLIP) assay with G-quadruplex binding antibody confirmed the presence of G-quadruplex structures in LANA mRNA. Our experiments with LANA sequence (forming G-quadruplex) and full-length LANA treated with G-quadruplex stabilizing compounds showed a reduction in LANA translation and reduced activation of CD8+T cells owing to a lesser antigen presentation on the Antigen Presenting cells. Mass spectrometry of proteins interacting with G-quadruplex forming sequence of LANA mRNA revealed the binding of heterologous ribonucleoproteins (HNRNPs), which we propose to play critical role in destabilizing those G-quadruplexes for controlled expression of LANA. These data confirmed the importance of G-quadruplex in regulated LANA expression and evasion from host immune surveillance system. 

LMP2A Regulates BART miRNAs Transcription by Translational Activation of ETS Family Genes Hyoji Kim

Oral Talk #64
LMP2A Regulates BART miRNAs Transcription by
Translational Activation of ETS Family Genes
Hyoji Kim1, Hisashi Iizasa1, Yuichi Kanehiro1, Hironori Yoshiyama1
1Shimane University, Faculty of Medicine
BamHI A rightward transcript microRNAs (BART miRNAs) are expressed more abundantly in EBV-infected epithelial tumors than in EBV-infected B lymphomas. It is considered that BART miRNAs are important for maintenance of viral latency in EBV-infected epithelial cells. However, the mechanism of their transcriptional regulation is not fully understood. To clarify detailed regulation of BART miRNAs transcription in epithelial cells, BART promoter region was cloned to the luciferase vector.
The promoter activity was higher in EBV-infected epithelial cells than uninfected cells. Mutagenesis assay revealed 4 important regions for BART promoter activity, which were ETS family binding sites. The qPCR analysis showed 4 out of 28 ETS family genes were strongly expressed in EBV-infected epithelial cells. The siRNA inhibition clarified 3 out of 4 ETS family genes enhanced BART transcription. The most functional gene (ETS A) was deleted using CRISPR-Cas9 system. ETS A deletion resulted dramatic reduction in BART miRNAs transcription and induction of EBV lytic infection. Since EBV-infected cells showed higher ETS A expression than uninfected cells, ETS A expression was examined in epithelial cells transfected with different EBV latent gene plasmids. Cells expressing LMP2A showed upregulation of ETS A expression. Finally, epithelial cells infected with EBV mutant lacking LMP2A showed reduced ETS A expression as well as BART miRNAs transcription.
Suggesting, LMP2A enhances BART miRNAs transcription through upregulation of ETS family genes in epithelial cells showing latent EBV infection. 

EBV Latency IIb is Phenotypically Distinct from Latency III Independent of LMP1 Expression
Joshua E. Messinger

Oral Talk #65
EBV Latency IIb is Phenotypically Distinct from Latency III
Independent of LMP1 Expression
Joshua E Messinger1, Joanne Dai1, Lyla J Stanland1, Alexander M Price1, Micah A Luftig1
1Duke University
EBV infection of primary B cells in vitro generates immortalized lymphoblastoid cell lines (LCLs) expressing the full repertoire of latency proteins (latency III). However, we recently demonstrated that early after infection, LMP1 and LMP2A are expressed at reduced levels until ~2-3 weeks post-infection. This period of EBNA-positive, LMP-low gene expression is termed latency IIb.
Previous work has demonstrated that LCLs display a wide distribution of LMP1 expression. We found that LMP1low expressing cells within an LCL population overlap with LMP1 expression in latency IIb. Immuno-histochemical staining of EBV-associated lymphomas indicates heterogeneity in EBV latent gene expression with many cells expressing EBNA2, but lacking LMP1. Due to the similar expression levels of LMP1 in LMP1low LCLs and early infected latency IIb cells, it is difficult to discern these two molecular phenotypes in vivo. A better understanding of what defines these latency stages is needed to understand EBV-associated tumor composition in vivo and how this influences disease progression and response to therapy.
To address these questions, we performed total mRNA sequencing of sorted latency IIb cells and donor-matched LCLs stratified by LMP1 expression using ICAM-1 as a proxy for LMP1. Hierarchical clustering revealed that latency IIb is phenotypically distinct from LCLs independent of donor and LMP1 expression. Gene Set Enrichment Analysis identified DNA replication as a hallmark of latency IIb. We also identified and validated host biomarkers of latency IIb distinct from LMP1low latency III including CCR6 and FcRL4. Conversely, CCR7 and PLOD2 were confirmed to be host markers of latency III. These data demonstrate that latency IIb is a unique stage from latency III independent of LMP1 and provides host markers of these stages. This research will allow for a better understanding of the heterogeneity of EBV+ tumors and its role in pathogenesis, immunity, and therapeutic responses. 

Uracil DNA Glycosylase of Gammaherpesvirus and Mammals Differentially Support Mutational Outcomes Kevin McBride

Oral Talk #66
Uracil DNA Glycosylase of Gammaherpesvirus and Mammals
Differentially Support Mutational Outcomes
Yunxiang Mu1, Qiwen Dong2, Monika Zelazowska1, Joshua Plummer1, Laurie Krug2, Kevin Mcbride1
1University of Texas MD Anderson Cancer Center, 2Stony Brook University
All herpesviruses encode a viral homolog of the mammalian Uracil DNA-glycosylase (UNG) gene. Host UNG removes mutagenic uracils from genomic DNA and normally triggers high- fidelity base excision repair (BER). An exception is in B cells, where host UNG triggers mutagenic repair of U:G lesions created by activation-induced cytidine deaminase (AID) during class-switch recombination (CSR) and somatic hypermutation (SHM). The mechanism that shifts high-fidelity UNG/BER to error-prone repair is not understood. Gammaherpesvirus infect many B cell subsets including germinal center cells. Using murine gammaherpesvirus 68 infections in mice we find that germinal center cells are the major viral targets during acute infection. Analysis of infected cells demonstrates overlapping expression of both vUNG and AID. Neither the viral influence on CSR and SHM nor the effect of the mutagenic germinal center environment on the virus has not been well-characterized. Here, we investigated the consequences of the vUNG encoded by ORF46 of murine gammaherpesvirus (MHV68) on UNG-dependent processes of the host. Using an in vitro class switch recombination assay we find that vUNG from gammaherpesviruses can process genomic uracils during CSR. We analyzed the effect of vUNG on AID induced mutations in a fibroblast cell line with an indicator gene. We find that compared to mUNG, ORF46 dramatically suppressed AID induced mutations abating both transition and transversion mutations. Biochemical analysis revealed differences in the UNGs including abasic site binding and efficiency in catalyzing single stranded versus double stranded uracil containing substrates. Analysis of domain swaps between host and vUNG revealed domains that differentially supported catalytic activity, abasic site binding and support for mutational repair. These results demonstrate a divergence of UNG structure and function in supporting high-fidelity repair and demonstrate that biochemical properties of UNG influence repair outcome of AID lesions. 

Successful Short Term Infection of Humanized Mice with EBV Lacking EBNA3 Genes Contrasts Their Essential Role in B Cell Transformation In Vitro and Their Role in Favouring Latency in Memory B Cells  Christine T. Styles

Oral Talk #67
Successful Short Term Infection of Humanized Mice with EBV Lacking EBNA3 Genes Contrasts Their Essential Role in B Cell Transformation In Vitro and Their Role in Favouring Latency in
Memory B Cells
Christine T. Styles1, Quentin Bazot1, Gillian Parker1, Robert E. White1, Kostas Paschos1, Paul J. Farrell1, Martin J. Allday1
1Section of Virology, Imperial College Department of Medicine
Following infection of mature human B cells, EBV induces proliferation and differentiation, and the EBNA3 proteins are central to this process. The relationship between in vitro B cell transformation and in vivo persistent infection can be investigated in humanized mice, whose immune system has been reconstituted from human haematopoietic stem cells. In vitro infection of primary B cells with recombinant EBVs where the EBNA3 locus is deleted, or where EBNA3A and EBNA3C are conditionally inactivated leads to cell death/arrest around 15-20 days post infection. We have previously shown the EBNA3 proteins support B cell transformation and establishment of LCLs through repression of tumour suppressors including p16INK4a and BIM. However, we have established an additional function for the oncogenic EBNA3 proteins, whereby EBNA3A and EBNA3C epigenetically suppress the plasma cell differentiation factors p18INK4c and BLIMP-1. We speculate that this favours memory B cell differentiation and subsequent viral persistence. Western blotting and qPCR indicates EBNA3A and EBNA3C repress transcription of p18INK4a and BLIMP-1. Chromatin immunopreciptation shows that EBNA3A and EBNA3C bind within regulatory elements of these differentiation factors (suggesting direct regulation) and that EBNA3- mediated regulation involves PRC2 and the repressive histone mark H3K27me3. Concurrently, 20 days post infection EBNA3A/EBNA3C-null cells develop a plasma cell-like phenotype, characterised by elevated CD138 and CD38 levels alongside increased immunoglobulin production. Although EBNA3A is important and EBNA3C essential for in vitro B cell transformation and likely favour memory B cell differentiation and latency in vivo, in humanised mice we have identified splenic tumour development and persistence of virus-infected cells 6 weeks post infection with recombinant EBVs, both with single deletions of EBNA3A or EBNA3C, and with a deletion of the entire EBNA3 locus. Interestingly, splenic lymphocytes derived from these infections did not lead to LCL expansion ex vivo, in contrast to cells where all EBNA3s were expressed. 

Enhancement of in vivo Latency by Substitution of the KSHV LANA DNA Binding Domain with that of MHV68 in Chimeric Virus Kenneth M. Kaye

Oral Talk #68
Enhancement of in vivo Latency by Substitution of the KSHV
Lana DNA Binding Domain with that of MHV68 in Chimeric
Virus
Marta Pires de Miranda1, Ana Quendera1, Aline C. Habison2, Chantal Beauchemin2, Min Tan2, Sofia A. Cerqueira, Bruno Correia3, Rajesh Ponnusamy3, Edward J. Usherood4, Colin E. McVoy3, J. Pedro Simas, Kenneth M. Kaye2
1Instituto de Microbiologia e Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, 2Brigham and Women's Hospital, Harvard Medical School, 3Instituto de Tecnologia Quimica e Biologica, Universidade Nova de Lisboa, 4Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth
Kaposi’s sarcoma-associated herpesvirus (KSHV) LANA (kLANA) and murine gammaherpesvirus 68 (MHV68) LANA (mLANA) mediate episome persistence for their respective viruses. In order to persist during latent infection in proliferating cells, viral episomal genomes replicate and then partition to progeny cell nuclei following mitosis. C- terminal LANA is the DNA binding domain (DBD) and binds its recognition element in terminal repeat (TR) DNA. This binding is essential for LANA mediated DNA replication and episome persistence. N-terminal kLANA binds histones H2A/H2B on the nucleosome surface to attach to mitotic chromosomes. LANA simultaneously binds TR DNA and mitotic chromosomes to serve as a molecular tether to segregate viral genomes to progeny cell nuclei following mitosis. kLANA (1162 residues) and mLANA (314 residues) have substantial size and sequence differences. For instance, mLANA lacks the large internal repeat region present in kLANA. The KSHV TR (0.8kb) and MHV68 TR (1.2kb) elements also differ in size, and although both are GC rich, they lack sequence homology. Despite these differences, we recently found that kLANA can substitute for mLANA in recombinant MHV68 and that this chimeric virus is capable of establishing latent infection in mice. The mLANA and kLANA DBDs share sequence and structural homology. We now find that substitution of the kLANA DBD with the mLANA DBD enhances the ability of kLANA chimeric virus to establish latency in vivo. 

Identification of ARKL1 as a Jun-interacting Factor that Negatively Regulates EBV Reactivation Umama Zia Siddiqi

Oral Talk #69
Identification of ARKL1 as a Jun-interacting Factor that
Negatively Regulates EBV Reactivation
Umama Zia Siddiqi1, Anup Vaidya1, Xinliu Li1, Lori Frappier1 1Department of Molecular Genetics, University of Toronto
EBV reactivation from the latent to the lytic cycle starts with activation of the Zp promoter controlling expression of the EBV BZLF1 transcription factor. Zp includes a binding site for c-Jun which was previously shown to be an important activator of Zp. Through proteomic approaches, we identified an uncharacterized cellular protein, Arkadia-like 1 (ARKL1), as a protein that binds the cellular CK2 kinase regulatory subunit (β) through the same binding pocket as EBNA1. Investigation of the effect of ARKL1 on EBV infection showed that silencing ARKL1 in EBV-positive gastric carcinoma (AGS-EBV), nasopharyngeal carcinoma (NPC43) or B cells (containing M81 EBV) resulted in BZLF1 expression and EBV reactivation, while overexpression of ARKL1 decreased EBV reactivation. To gain insight into the mechanism of action of ARKL1, we purified FLAG-tagged ARKL1 from human cells and identified interacting proteins by tandem mass spectrometry. This confirmed the interaction of ARKL1 with CK2 and also revealed an interaction with Jun, suggesting that ARKL1 might suppress BZLF1 expression by inhibiting Jun function at Zp. Consistent with this hypothesis, overexpression of ARKL1 decreased Zp activity in a Zp reporter assay, while ARKL1 silencing increased Zp activity, and ARKL1 overexpression decreased Jun activity in a Jun reporter assay. In addition, chromatin-immunoprecipitation assays showed that ARKL1 localized to Zp within the EBV genome. The ARKL1 sequence that binds Jun was mapped and shown to be the same sequence that binds CK2β, suggesting that ARKL1 might bind Jun indirectly through CK2β. In keeping with this model, silencing of CK2β abrogated the ability of ARKL1 to immunoprecipitate endogenous Jun and mimicked the effect of ARKL1 silencing on causing EBV reactivation. Together these findings suggest that ARKL1 binds Jun indirectly through CK2β, and that this interaction inhibits Jun activity at Zp, turning off BZLF1 expression and subsequent reactivation.

Session 7: Non-Coding RNAs

Session Chairs: Scott Tibbetts & Erik Flemington

Oral Talk #54
Misprocessing of Cellular Noncoding RNAs as a Pathway for
Cell-Intrinsic Immune Activation
Yang Zhao1, Xiang Ye1, William Dunker1, Yu Song1, John Karijolich1
1Vanderbilt University School of Medicine
The RIG-I like receptors (RLRs) RIG-I and MDA5 are cytosolic RNA helicases best characterized as restriction factors for RNA viruses. However, evidence suggests RLRs participate in innate immune recognition of other pathogens, including DNA viruses. Kaposi's sarcoma-associated herpesvirus (KSHV) is an oncogenic human gammaherpesvirus and the etiological agent of Kaposi's sarcoma and primary effusion lymphoma (PEL). Here, we demonstrate that RIG-I and MDA5 restrict KSHV lytic reactivation in PEL. Furthermore, we define the in vivo RLR substrates and demonstrate that RIG-I and MDA5-mediated restriction is facilitated exclusively by the recognition of host derived RNAs. Misprocessed noncoding RNAs are prominent RIG-I bound RNAs, and biochemical characterizations reveal that an infection-dependent reduction in a key RNA processing enzyme results in an accumulation of triphosphorylated noncoding RNAs, enabling their recognition by RIG-I. These finds reveal an intricate relationship between RNA processing and innate immunity, and demonstrate that an antiviral innate immune response can be elicited by the sensing of misprocessed cellular RNAs. 


Oral Talk #55
Identifying EBV microRNA Targets in B-cell Lymphoma and
Gastric Cancer Using CLASH
Nathan Ungerleider1, Whitney Bullard2, Mehmet Kara2, Scott Tibbetts2, Erik Flemington1
1Tulane University, 2University of Florida
MicroRNAs are 20-25 base noncoding RNAs that post-transcriptionally regulate expression of target mRNAs. The Epstein Barr Virus genome codes for up to 25 microRNAs from two loci (BART1-22 and BHRF1-3), each of which targets a distinct subset of host transcripts. To comprehensively map EBV microRNAs to their host targets with high specificity, we performed crosslinking, ligation, and sequencing of hybrids (CLASH) in Akata (B-cell lymphoma; latent and reactivated conditions) and SNU719 (gastric cancer) cells. With this approach, we found a total of 4,643 unique human mRNA targets of EBV microRNAs (87, 148, and 4,627 from latent Akata, reactivated Akata, and SNU719, respectively.) Of these, 52 target transcripts were found in all three samples, including those coding for pro- apoptotic proteins, nuclear import proteins, and proteins involved in translation. Interestingly, 9.7% of EBV microRNA interactions with human mRNA were non-canonical and occurred in the absence of a seed match. By utilizing CLASH to explore the EBV microRNA interactome, we have uncovered and quantified interactions that are difficult or impossible to detect using prediction based methods. 

Nearly 10% of gastric tumor are EBV +
In EBV+gastric gastric tumors EBV miRNAs are most abundant
CLASH: crosslinkingm, ligation, ans sequencing of hybrid
EBV-miR targets in SNU719 cells
EBV-miR targets in Akata cells -> mostly about the same as those in SNU719

  • EBV miRs have similar targets in BL (Akata) and gastric cancer (SNU719)
Example seed matches
  • BAT3::IPO7
  • BART7::GFPT1
  • BART2::DAZAP2
EBV miRs have higher affinity for human transcripts than human miRs
Supplementary (3‘ of seed) complementarity can increase ternary AGO-miR-mRNA complex formation
miRNa affinity for targets and GO analysis

  1. viral carcinogenesis 
  2. cell cycle 
  3. protein procesing in ER 
  4. adherent junction 

Oral Talk #56
Transcriptional Regulation of Viral ncRNAs
Ashley N. Knox1, Eva Medina1, Lauren Oko1, Linda F.van Dyk1
1Department of Immunology & Microbiology, University of Colorado Denver | Anschutz Medical Campus
While viral RNA is known to play vital roles in viral infection and replication, the regulation of viral RNA polymerase III (pol III)-transcribed non-coding RNAs (ncRNAs) remains unclear. The gammaherpesviruses (γHVs) contain multiple ncRNAs that are highly expressed during infection. To study the contribution of pol III ncRNAs to viral infection, we have used a murine model of γHV (MHV68) that expresses pol III ncRNAs. Transcription by pol III imparts specific characteristics such as a 5’-triphosphate and 3’-oligouridylate sequence, which can be recognized and bound by host RNA-binding proteins. These RBP- RNA interactions may trigger innate immune signaling pathways that drive pathogenesis. Therefore, detailing how these viral ncRNAs are expressed is integral to understanding their role in pathogenesis. To compare the transcriptional regulation of pol III ncRNAs, we cloned several types of pol III promoters into a newly generated luciferase reporter we have optimized to measure pol III promoter activity during infection. Promoters include those of host ncRNAs (5S rRNA, tRNA, U6 snRNA), and of the MHV68 TMERs, the EBV EBERs, and the adenovirus VA RNAs. Infection with MHV68 drives differential expression of pol III transcription machinery, resulting in simultaneous repression of U6 promoter activity and stimulation of the MHV68 TMER promoters. This TMER promoter induction was prevented by inhibitors of viral replication and protein synthesis, indicating that these aspects of infection are vital for driving transcriptional regulation. This analysis of pol III promoter activity indicates shared and unique regulation patterns and identifies the critical promoter and polymerase features for preferential expression during infection. 

viral ncRNAs=highly abundant transcripts in infected cells
rHV infection alters pol III activity
EBV infection upregulates TFIIIC, increased expression of EBERs and the transcripts from type 1a and 2 pol III promoters
EBV and KSHV upregulate host vault RNA expression increased apoptotic resistance and cell proliferation enhanced EBV establishment

Structure of pol III promoters
type 2 of Pol III promoters are used for viral ncRNA

Activity of pol III promoters can be measured using a luciferase reporter
  • luciferase assay to measure promoter activity of both gene internal and external pol III promoters
  • allow direct comparison of pol III promoters outside
  • pol III transcription is stopped by TTTTTT stretch

Experimental design: measuring pol III promoter activiyt during rHV68 infection

infection with rHV68 differentially alters pol III promoter activity
  • TMER 1 is the only one cellular promoters upregulated during rHV68 infection
  • EBV is upregulated by rHV68 infection
  • pol III opromoters respond differently to infection (using PAA or CHX
  • inhibition of viral early gene expression attenuates changes in pol III promoter activity
What is the mechanism behind changes in pol III promtoer ctivity during infection?
  • CHX 
  • inhibition of viral life cycle attenuates changes in pol III promoter activity 
Next questions:
are differences among pol III type 2 promoters due to minimal promoters or require upstream regions?
Do diferences ... to specific pol III subunits, transcription


Oral Talk #57
EBV Encoded miR-BART10-3p and miR-BART22 Promote
Invasion and Metastasis by Activating Canonical Wnt/β-catenin
Signaling Pathway in EBV-Associated Gastric Carcinoma
Min Dong1, Li-ping Gong2, Jian-ning Chen2, Xiao-fang Zhang2, Yi-wang Zhang2, Chun-kui Shao2
1Department of Medical Oncology, The Third Affiliated Hospital, Sun Yat-sen University, 2Department of Pathology, The Third Affiliated Hospital, Sun Yat-sen University
Epstein-Barr virus (EBV)-associated gastric carcinoma (EBVaGC) accounts for approximately 10% of gastric carcinoma worldwide. Compared with other subtypes of gastric carcinoma, EBVaGC has distinct clinicopathological features and molecular abnormality, but the mechanisms of tumorigenesis and progression of EBVaGC are largely unknown. In recent years, an increasing number of studies have demonstrated that EBV- encoded microRNAs (EBV miRNAs) play important roles in the development and progression of EBV-associated tumors, including nasopharyngeal carcinoma and EBV- associated lymphoma. However, little has been reported about the expression and roles of EBV miRNAs in EBVaGC. In this study, we constructed a comprehensive profiling of EBV miRNAs expressed in EBVaGC by deep sequencing, and found ebv-miR-BART10-3p (BART10-3p) and ebv-miR-BART22 (BART22) were abundantly expressed. qRT-PCR analysis in 71 EBVaGC samples suggested that high expression of BART10-3p or BART22 was significantly associated with lymph node metastasis and worse 5-year overall survival. Furthermore, transwell assays demonstrated that both BART10-3p and BART22 enhanced cell migration and invasion. Bioinformatics analysis and luciferase reporter assay demonstrated that BART10-3p and BART22 directly target adenomatous polyposis coli (APC) and Dickkopf1 (DKK1). Forced expression of BART10-3p or BART22 in EBV- negative AGS and BGC823 cells upregulated the protein level of β-catenin and facilitated its transition from cytoplasm to nucleus thus activating the Wnt/β-catenin signaling pathway, and consequently upregulated the expression of Twist and downregulated the expression of E-cadherin. Reversely, reduced expression of endogenous BART10-3p or BART22 in EBV-positive SNU719 cells led to downregulation of β-catenin and Twist and upregulation of E-cadherin. These findings suggest that BART10-3p and BART22 play a vital role in promoting invasion and metastasis of EBVaGC by targeting APC and DKK1 and activating Wnt/β-catenin signaling pathway, providing novel prognostic biomarkers and therapeutic targets. 

EBV associated gastric carcinoma, EBaGC has..
EBV miRNAs: 44 EBV-encoded miRNAs (ebv-miR-BARTs)
relateive expression levels of EBV miRNAs in SNU-719 and YCCEL1 cell lines

  • BART10-3p and BART22 are highly expressed in EBVaGC
  • Expressionof BART10-3p and BART22 in 71 EBVaGC cases
  • forced expression of BART10 and BART22 increases EBaGC cell lines proliferation, invasion,migration

Enrichment analysis of predicated BART10-3p and BART22 targets in KEGG signaling pathway database

  • APC and DKK1 inhibitors of WNT signaling are potential targets of BAR10-3p and BART22



Oral Talk #58
A Herpesvirus Utilizes a Sm-class Non-Coding RNAs as a
miRNA Adaptor to Modulate Host Gene Expression
Carlos Gorbea1, Tim Mosbruger2, Demian Cazalla1
1University of Utah, 2Children’s Hospital of Philadelphia
Herpesvirus saimiri (HVS) is an oncogenic γ-herpesvirus that infects T cells and causes aggressive lymphomas and leukemias in New World primates. HVS expresses seven Sm- class RNAs called HSURs (Herpesvirus saimiri U-rich RNAs). We have recently shown that one of these ncRNAs, HSUR 2, functions as a miRNA adaptor that base-pairs with host mRNAs and recruits host miR-142-3p and miR-16 to repress target mRNA expression1. Using this mechanism, HSUR 2 modulates the expression of several transcripts that encode proteins with roles in different cellular processes including apoptosis, regulation of cell cycle, and innate immune response1. It is currently not clear how HSUR 2 specifically targets this diverse group of mRNAs. Psoralen crosslinking experiments showed that interactions between HSUR 2 and target mRNAs involve direct base-pairing, strongly suggesting that complementarity between sequences present in HSUR 2 and target mRNAs may dictate target mRNA recognition and specificity.
We had previously developed a method termed RNA-RNA interaction identification by crosslinking and capture (RICC), which combines in vivo psoralen crosslinking and specific HSUR 2 capture using biotinylated probe hybridization, with high-throughput sequencing (seq) to identify crosslinked RNAs1. We have now successfully modified RICC-seq (iRICC- seq) to determine sequences involved in the interactions between HSUR 2 and its target mRNAs with individual nucleotide resolution. HSUR 2 binds primarily to the 3' UTRs of target mRNAs at unique positions in some targets, but it can also bind some other targets at more than one position in their 3' UTR. The data obtained with iRICC-seq also showed that HSUR 2 binds some of its targets using the same sequence that is used for binding miR-16, partially explaining why HSUR 2 does not require miR-16 activity to repress some of its targets1.
2018 International Conference on EBV & KSHV
1Gorbea, c. et al. Nature 550(7675):275-279 (2017). 

HVS U-rich, Sm-class RBAs (HSURs)  超時太久!

Oral Talk #59
Impact of Demethylating Agents on Nasopharyngeal
Carcinoma Xenografts: De Novo Expression of Cp/Wp
Transcripts and BHRF1 microRNAs
Pierre Busson1, Nikifroros Kapetanakis1, Aaron Nguyen2
1UMR 8126 CNRS - Gustave Roussy, 2Celgene
Demethylating agents are expected to increase the immunogenicity of malignant cells by changing their protein profile; for example by increasing the expression of endogenous retroviral sequences. Inspired by this approach, we undertook to use 5 azacitidine (5 aza) and 5-aza-2’-deoxycytidine (Decitabine) for increasing the range and the abundance of EBV products in nasopharyngeal carcinoma (NPC) cells. We used the C666-1 NPC cell line which was initially derived from a primary tumor and which is propagated either in vitro or into nude mice as a cell-derived xenograft. We also used 3 patient-derived xenografts propagated into nude mice: C15, C17 and C18 which were derived from a primary tumor and two metastatic lesions, respectively. A tumor growth delay was recorded for all tumor lines with a much greater response for the C15 and C666-1, indicating that both agents have a cell-intrinsic inhibitory effect, especially in cells derived from primary tumors. Regarding viral protein expression, the most remarkable observation was a dose- dependent increase in EBNA1 and BZLF1 expression in the C666-1 and C18 tumors. Regarding viral microRNAs, we noted a de novo dose-dependent expression of the BHRF1 microRNAs with maximal levels in the C15 and C666-1 tumors, the most responsive in terms of tumor growth reduction. Plasma abundance of these microRNAs was correlated to their levels in the tumor. Simultaneously large transcripts originating from the Cp/Wp promoter were detected in the tumors. We also found some evidence of concomitant expression of the EBNA-LP protein in treated C666-1 cells (a point currently under verification). In conclusion, 5 Aza and decitabine have multiple effects on viral expression in malignant NPC cells including enhanced expression of immunogenic proteins and de novo expression of the BHRF1 microRNAs. Additional work will be required to investigate similar possible responses in malignant NPC cells in clinical specimens. 

NPC: Epigenetic contribution to the oncogenesis

EBV+ epithelial (type II latency)
Robust expression of BARTs, absence of BHRF1

EBV+ LCL (type III latency)
Abundant BHRFI, moderate BARTs

Demethylating agents 

  • 5-azacytidine
  • 5-aza deoxy cytidine

Hypothesis:
variation in the profile of plasma viral muRNAs = surrogate markers of anti=tumor activity

Biological resources : EBV positive NPC models
C666-1 NPC cell line (propagated in vitro, also used a a xenografts (CDX)

NPC PDX C15, C17, C18

Impact of demethylating agents on the growth of NPC xenografts

5-Aza DAC: significant regression of tumor

Changes in EBV protein expression in xenogrageted NPC cells treated by 5-Aza

  • C666-1 and C18, Zta and ___ are affected

MiRNAs

  • Profiling of viral mIRNAs in the 4 NPC tumor models at baseline
    • Changes in viral miRNA abundance in xenografts tumors and mouse plasma under treatment with 5-aka
    • Consistent de nova detection of BHRF1 in tumors and mouse plasma samples
    • De novo expression of transcripts reminiscent of latency III
    • No concomitant detection f the BHRF1 protein 
    • Same sickle gin mechanism as in LCL? (Xiang and Keiff,m 20011)
    • Possible detection of EBNA-LP
  • Conclusions
    • 5-aza induces de novo expression of miR BHRF1 in NPC cell line and PDX
    • Concomitant BHRF1 expression
    • Suggesting that epigenetic agents in NPC cells can modify that paternity of latent gene expression (not only the expression of lytic genes
    • Detection of miR BHRF1 in cinical specimens requires further investigation


Oral Talk #60
The Secondary Structure of the MHV68 Noncoding RNA TMER4 is Essential for Function at a Critical in vivo Dissemination
Bottleneck
Brett A. Hoffman1, Emily R. Feldman1, Yiping Wang1, Scott A.Tibbetts1
1University of Florida
The ability of EBV and KSHV to establish lifelong latency is a critical factor in their ability to cause pathogenesis; however, the precise determinants that mediate in vivo latency remain unclear due to the strict species specificity of these viruses. Murine gammaherpesvirus 68 (MHV68) infection of laboratory mice is a robust system to model natural in vivo gammaherpesvirus infection. Like EBV and KSHV, MHV68 establishes lifelong latency in B cells and is associated with the development of lymphoproliferative disorders and lymphomas. Using this system we have previously demonstrated a crucial in vivo role for the viral noncoding RNA TMER4 in MHV68 dissemination and establishment of peripheral latency. TMER4 is a 203 nt RNA that is comprised of a tRNA-like element plus two pre-miRNA stem-loops, encoding up to four mature miRNAs. We sought to define the component of TMER4 required for this critical in vivo function. As expected, in infected cells both full-length TMER4 and TMER4-derived mature miRNAs were both readily detectable. However, an approximately 145 nt species corresponding to the size of the vtRNA plus a single stem-loop was the most stable form of TMER4 present in infected cells. Interestingly, mutation of either of the miRNA seed sequences had no effect on TMER4 activity in vivo, demonstrating that it functions independent of miRNA targeting. Additional mutagenesis of the TMER4 structure in the context of the virus revealed that stem-loop secondary structure is essential for activity, but that full-length stem-loop is not required. These findings are now aiding in additional mechanistic studies to determine the specific molecular function of TMER4 at this critical in vivo bottleneck. 
MHV68: TMERs tRNA -miRNA-encoding RNAs)

8 TMERAS in MHV68 N terminus

TMER4 is required for heamato- dissemination

  • Dramatic attenuation in the blood samples, suggesting TMER4 is involved in virus egress from eh lymph node
  • TMER4 function is independent of miRNAs (change stem loop TMER4 still work fine)
  • Stem-loop II is required for function
  • Stem-loop size not critical

Is TMER4 function conserved among gammaherpesivruese?

  • ~150 Nat TMER4 species is predominantly expressed and functional
  • Function is 
  • EBERs!
  • Both TMER4 and EBERs are highly abundant
  • Can EBER1 expression rescue TMER4 in vivo function, yes! Strongly suggests a conserved in vivo function for MHV68 TMER4 and EBV EBER1
Questions:
In vivo B memory cells dropped, T cells not analyzed yet


Oral Talk #61
Epstein Barr Virus CircRNAome
Nathan Ungerleider1, Monica Concha1, Zhen Lin1, Claire Roberts1, Xia Wang1, Subing Cao1, Walter Moss3, Yi Yu1, Scott Tibbetts2, Rolf Renne2, Yan Dong1, Erik Flemington1
1Tulane University, 2University of Florida, 3Iowa State University
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 more recent findings of over a hundred newly discovered polyadenylated lytic transcripts. Here, we used RNase R-sequencing to elucidate the EBV circular RNAome (circRNAome). By performing RNase R-sequencing in cell models representing type I, II, and III latency and during reactivation, we identified EBV encoded circular RNAs expressed from latency Cp driven transcription, from latency expression of the long non- coding RPMS1 locus, from within the LMP2 gene, and we identified a highly expressed circular RNA derived from intragenic back-splicing of the BHLF1 gene. While expression of most of these circular RNAs correlate with the expression of the respective linear transcripts, circLMP2 is uniquely expressed during reactivation. Here we present the exonic structures and the nuclear/cytoplasmic localization of EBV encoded circular RNAs and show initial insights into phenotypic alterations mediated by one of these circular RNAs.
Transcriptome resukltion throughinterartion f multi platform data TRIMD - O’Grady et al NAR 2016

Global EBV polyA lytic Transcriptome analysis (found new transcripts!)

Virus non-coding RNAs effector of hose cell remodeling with minimal immunological impact

  • EBERs I and 2
  • RPMS2 (lncRNA)
  • MiRNAs
  • circRNA?

RNAase R-seq EBV middles
Cell type I )Akata, Mutu I, Sav I)
B cell (type III) Mutu III IB4, Jijoye, JY
Type II (SNU719 and. YCCEL1)

Importance of RNase R seq versus Ribo-depletion  R-seq

Backsplice read enrichment distribution by using RNase R-seq

EBV circRNA candidates
Type III latency

  • W1_C1
  • LMP2 E8_E2 identified only in reactivation
  • BHRF1 also abundant


Viral CircRNA similar to cellular circRNAs

Latency