BACKGROUND: To elucidate mechanisms involved in multiple sclerosis (MS), we 
studied genetic regulation of experimental autoimmune encephalomyelitis (EAE) in 
rats, assuming a conservation of pathogenic pathways. In this study, we focused 
on Eae23, originally identified to regulate EAE in a (LEW.1AV1xPVG.1AV1)F2 
cross. Our aim was to determine whether one or more genes within the 67 Mb 
region regulate EAE and to define candidate risk genes.
METHODOLOGY/PRINCIPAL FINDINGS: We used high resolution quantitative trait loci 
(QTL) analysis in the 10th generation (G10) of an advanced intercross line (AIL) 
to resolve Eae23 into two QTLs that independently regulate EAE, namely Eae23a 
and Eae23b. We established a congenic strain to validate the effect of this 
region on disease. PVG alleles in Eae23 resulted in significant protection from 
EAE and attenuated CNS inflammation/demyelination. Disease amelioration was 
accompanied with increased levels of Foxp3(+) cells in the CNS of the congenic 
strain compared to DA. We then focused on candidate gene investigation in 
Eae23b, a 9 Mb region linked to all clinical phenotypes. Affymetrix exon arrays 
were used to study expression of the genes in Eae23b in the parental strains, 
where none showed differential expression. However, we found lower expression of 
exon 4 of ZEB1, which is specific for splice-variant Zfhep1. ZEB1 is an 
interleukin 2 (IL2) repressor involved in T cell development. The 
splice-specific variance prompted us to next analyze the expression of ZEB1 and 
its two splice variants, Zfhep1 and Zfhep2, in both lymph node and spleen. We 
demonstrated that ZEB1 splice-variants are differentially expressed; severity of 
EAE and higher IL2 levels were associated with down-regulation of Zfhep1 and 
up-regulation of Zfhep2.
CONCLUSIONS/SIGNIFICANCE: We speculate that the balance between splice-variants 
of ZEB1 could influence the regulation of EAE. Further functional studies of 
ZEB1 and the splice-variants may unravel novel pathways contributing to MS 
pathogenesis and inflammation in general.