# Binding of Epstein Barr Virus EBNA2 unifies multiple sclerosis genetic mechanisms

> **NIH NIH R01** · CINCINNATI CHILDRENS HOSP MED CTR · 2021 · $341,377

## Abstract

Project Summary
 Multiple sclerosis (MS) is likely caused by a combination of genetic and environmental factors; however, the
mechanisms contributing to these factors remain poorly understood. Epstein-Barr virus (EBV) in particular is a
well-established environmental risk factor for MS. We have created a computational algorithm that systematically
searches for common molecular mechanisms that might be impacted at multiple MS-associated loci. Using this
algorithm, we have discovered that over 40% of MS-associated loci contain MS genetic variants that fall
within regions of the human genome occupied by the EBV-encoded EBNA2 protein (44 out of 109, >4.6-
fold enrichment, P<10-25). Other top proteins include known EBNA2 human interacting proteins (RBPJ, RELA,
SPI1) and proteins recently shown to participate in “EBV super-enhancers”, which enable proliferation and
survival of EBV infected B cells. The same MS-associated variants also impact gene expression levels of MS-
associated genes in EBV-infected B cell lines. Our hypothesis is that allele-dependent binding of EBNA2 and
its co-factors explains the allele-dependent risk at many MS genetic loci. Importantly, this hypothesis links the
genetic associations of MS to the known molecular roles played by EBV and Notch signaling. In total, >40 of the
known MS associations might be explained by this common mechanism uniting the genetic and the
environmental risk components of MS. We propose the following Aims.
 Aim 1. Genome-wide experimental assessment of allele-dependent EBNA2 and human protein binding
to risk alleles at MS loci. We will examine allele-dependent protein binding in MS patient-derived EBV-
transformed B cell lines and in T cells using ChIP-seq. We will identify genome-wide allele-dependent co-binding
of EBNA2 with its partners using our new, innovative Split Dam ID-seq technique. Resulting data will be used to
create an improved model of MS genetic risk mechanism and results will be freely disseminated.
 Aim 2. Discover specific MS-associated loci where allele-dependent EBNA2 or human protein-DNA
interactions result in allele-dependent gene expression. We will assess allele-dependent binding of these
proteins at likely causal variants, and allele-dependent gene expression by multiple experimental approaches.
 Aim 3. Establish causality for intermediate phenotypes at selected MS-associated variants. We will
establish the causal effect of these variants by demonstrating the necessity and sufficiency of candidate risk
alleles in MS patient-derived cells through a novel dead Cas9 activation system, and by performing genome
editing with CRISPR/Cas9 followed by gene expression monitoring.
 The concept that disease might be influenced by allele-dependent assembly of protein complexes controlled
by a virus is highly innovative and has never before been experimentally demonstrated. Results from this
proposal would provide strong rationale to develop therapies that interfere with EBNA2 binding, or ...

## Key facts

- **NIH application ID:** 10076867
- **Project number:** 5R01NS099068-05
- **Recipient organization:** CINCINNATI CHILDRENS HOSP MED CTR
- **Principal Investigator:** Matthew Tyson Weirauch
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2021
- **Award amount:** $341,377
- **Award type:** 5
- **Project period:** 2017-04-01 → 2022-12-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10076867

## Citation

> US National Institutes of Health, RePORTER application 10076867, Binding of Epstein Barr Virus EBNA2 unifies multiple sclerosis genetic mechanisms (5R01NS099068-05). Retrieved via AI Analytics 2026-05-22 from https://api.ai-analytics.org/grant/nih/10076867. Licensed CC0.

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