类风湿关节炎（RA）是以慢性关节炎症和骨破坏为主要特征的自身免疫性疾病，具有明显遗传倾向。MHC是迄今最为公认的RA遗传相关区域。本课题组近期通过对MHC全区域深度测序和进一步独立验证，新发现多个核苷酸插入或缺失片段(insertions-deletions, Indels)与ACPA阳性RA发病显著相关，其中绝大多数Indels为非编码DNA序列。通过系统生物信息学分析预测和功能注释，提示这些RA发病相关Indels所在区域包含多个转录因子结合域；并具有增强子序列所特有的表观遗传学特征；数个Indels具有潜在eQTL作用。为进一步证实这些Indels调控功能，课题组将通过一系列经典和现代分子生物技术，研究其转录调控功能并鉴定其关键靶基因。最后，我们将选择数个功能最显著的Indels构建条件性敲除或敲入鼠, 进一步在关节炎模型定向研究RA高风险Indels的致病作用和分子机制。

Rheumatoid arthritis (RA) is an autoimmune disease characterized by chronic joint inflammation leading to bone erosions and joint destruction. Genetic factors play important role in RA pathogenesis, many of them remain unidentified. Human leukocyte antigens (HLA) genes within major histocompatibility complex (MHC) region, were the first and still remain to be the best described genetic risk factors contributing to RA. However, due to the high linkage disequilibrium in MHC region, it is difficult to define the causal gene(s) or additional independent risks using the conventional HLA genotyping or chip-based methodology. Recently our group has performed a deep sequencing for entire MHC region and further Sanger sequencing for validation. By the targeted sequencing and bioinformatics analysis, we found a number of novel DNA insertion-deletion fragments (Indels) were strongly associated with ACPA-positive RA, and majority of the Indels are non-coding variants. From ENCODE, RegulomeDB, and rVarBase databases, there are abundant transcription factor binding and classic epigenetic signatures for an enhancer functions in this region, suggesting that they are active enhancers. In addition, several Indels displayed eQTLs effects from Blood eQTL databases. To further verify and functional characterize these genetic variants, varied molecular biology experiments in vitro will be carried out. To further understand the molecular mechanisms of these Indels contributed to RA susceptibility and pathogenesis, we will generate conditional knock-in or knock -out mice specific for the Indels with significant functional properties, and study the impact of these Indels in experimental arthritis models. We expect that the combination of functional study with MHC deep sequencing will lead to a better understanding in the role of non-coding DNA variants in RA pathogenesis.