Fine-Mapping of HLA Effects in Oral and Non-Oral Lichen Planus

Lichen planus (LP) is an inflammatory disease affecting squamous epithelia, typically manifesting in a cutaneous (non-OLP) and an oral mucosa (OLP) form, the latter conferring elevated risk of oral squamous cell carcinoma. Despite the presence of CD4+ and CD8+ T-cell infiltrates in LP lesions, specific autoantibodies or target T-cell antigens have not been identified. A recent genome-wide association study (GWAS) uncovered 27 genome-wide independent associations, with the strongest signal within HLA Class II, particularly involving DQB1*05:01. This association showed stronger effects in non-OLP (OR = 2.09) versus OLP (OR = 1.36). Here, we performed a high-resolution HLA fine-mapping analysis in FinnGen to dissect this strong Class II signal and clarify its relationship to LP subtypes. We find that most DQA1*01~DQB1*05:01 haplotypes confer increased susceptibility, with the highest risk conferred by DQA1*01:05~DQB1*05:01 followed by DQA1*01:01~DQB1*05:01. In subjects not carrying DQB1*05:01, DRB1*15:01~DQA1*01:02~DQB1*06:02 had a strong protective effect, more pronounced in non-OLP than OLP. Further associations were found with DRB1*09:01 and DQB1*02:02 as well as independent HLA Class I associations with A*03:01, B*08:01 and B*13:02, all stronger in OLP versus non-OLP. Conditioning SNP associations for these effects eliminated the HLA GWAS signal. These effects highlight that while the DQB1*05:01 association remains largely invariant to DQA1 polymorphisms across LP subtypes, the variable strength of HLA associations in non-OLP and OLP forms suggests distinct immunopathological mechanisms. The presence of strong trans-heterodimer effects in this disease illustrates the need to analyse HLA-DQ-associated diseases with methods beyond simple conditioning. The invariance to DQA1 polymorphisms in LP may facilitate the identification of potential pathological epitopes.