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 vaccines that prevent EBV infection, offering the prospect of eliminating MS.

Public Health Relevance

The proposed research is relevant to human health because it will establish a new important molecular mechanism linking genetic and environmental factors to disease risk. This project is relevant to the NIH's mission, and the mission of NINDS in particular, because it will provide fundamental insights into the role of the Epstein Barr virus in the etiology of multiple sclerosis, leading to better diagnostics and treatments.

National Institute of Health (NIH)
National Institute of Neurological Disorders and Stroke (NINDS)
Research Project (R01)
Project #
Application #
Study Section
Genetics of Health and Disease Study Section (GHD)
Program Officer
Utz, Ursula
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
Cincinnati Children's Hospital Medical Center
United States
Zip Code
Zhang, Xue; Biagini Myers, Jocelyn M; Burleson, J D et al. (2018) Nasal DNA methylation is associated with childhood asthma. Epigenomics 10:629-641
Valanejad, Leila; Cast, Ashley; Wright, Mary et al. (2018) PARP1 activation increases expression of modified tumor suppressors and pathways underlying development of aggressive hepatoblastoma. Commun Biol 1:67
Harley, John B; Chen, Xiaoting; Pujato, Mario et al. (2018) Transcription factors operate across disease loci, with EBNA2 implicated in autoimmunity. Nat Genet 50:699-707
Patel, Zubin; Lu, Xiaoming; Miller, Daniel et al. (2018) A plausibly causal functional lupus-associated risk variant in the STAT1-STAT4 locus. Hum Mol Genet :
Tillo, Desiree; Ray, Sreejana; Syed, Khund-Sayeed et al. (2017) The Epstein-Barr Virus B-ZIP Protein Zta Recognizes Specific DNA Sequences Containing 5-Methylcytosine and 5-Hydroxymethylcytosine. Biochemistry 56:6200-6210
Gu, Zirong; Kalambogias, John; Yoshioka, Shin et al. (2017) Control of species-dependent cortico-motoneuronal connections underlying manual dexterity. Science 357:400-404
Zhang, Xue; Biagini Myers, Jocelyn M; Yadagiri, Veda K et al. (2017) Nasal DNA methylation differentiates corticosteroid treatment response in pediatric asthma: A pilot study. PLoS One 12:e0186150