Phenome-wide genetic analysis of EBV EBNA1 and ZEBRA seroreactivity identifies divergent disease associations and candidate inflammatory pathways

Introduction Epstein–Barr virus (EBV) infects most adults worldwide, but the disease relevance of host responses to distinct EBV antigens remains incompletely characterized. We compared disease associations of seroreactivity to the latency-associated antigen EBNA1 and the immediate-early lytic antigen ZEBRA and explored candidate host pathways. Methods We performed phenome-wide genetic screening of 1,075 phenotypes using UK Biobank summary statistics from 408,961 participants, followed by two-sample Mendelian randomization using FinnGen R11 data. Literature mining analyzed SemRep-derived subject–predicate–object (SPO) triples from 42,392 PubMed abstracts to map EBV-related diseases, genes, and therapies. Host genes were prioritized through summary-data-based MR of anti-ZEBRA GWAS and GTEx v8 eQTL data, GeneCards disease-gene intersections, and protein interaction analysis. Experiments used an ovalbumin-induced mouse asthma model and B95-8 and Raji cells. Results Phenome-wide screening prioritized 40 antibody–phenotype pairs. Of the 34 pairs evaluated by Mendelian randomization, 21 reached nominal significance and 19 remained significant after false discovery rate correction. Genetically proxied anti-ZEBRA seroreactivity showed positive associations with type 1 diabetes, rheumatoid arthritis, psoriasis, nasal polyps, asthma, and hypothyroidism. In contrast, genetically proxied anti-EBNA1 seroreactivity showed inverse associations with several overlapping autoimmune phenotypes and a positive association with multiple sclerosis. Literature mining yielded 62,334 triples, with autoimmune disease concepts less frequent than malignancy or infection concepts. Frequently cited EBV-linked genes were enriched in inflammatory pathways, including NF-κB signaling. Integrative analyses identified 55 shared candidate genes, with NFKB1 showing the highest connectivity in the resulting interaction network. Lung tissues from the murine asthma model showed reduced cytoplasmic p105 and increased nuclear p50. BZLF1 overexpression in B95-8 and Raji cells was associated with reduced whole-cell p105 and increased nuclear p50. In B95-8 cells without BZLF1 overexpression, NFKB1-targeting siRNA reduced p105 abundance and was associated with higher EBV DNA levels. Discussion EBNA1 and ZEBRA seroreactivity exhibited distinct genetically supported disease-association patterns. Integrative analyses and experimental observations prioritize NFKB1 as a candidate hub within ZEBRA-associated inflammatory pathways, providing a basis for further mechanistic investigation.