MHC and KIR Region Genomics in Psoriasis

 描述（由申请人提供）：银屑病是一种常见的免疫介导的炎性皮肤病，与关节炎和全身性炎症相关。银屑病的全基因组关联研究已经确定了40多个涉及先天和适应性免疫途径的易感基因座。表现出与银屑病最大关联的遗传位点是MHC，HLAC：06：02在多个种族群体中显示出非常强的关联。然而，在考虑HLAC：06：02的影响后，显著的残留遗传信号保留在MHC中，并且不清楚残留信号是否存在于其他HLA等位基因中， 额外的邻近基因或调节变体。也有证据表明银屑病易感性可能受到杀伤细胞免疫球蛋白样受体（KIR）与HLA I类配体相互作用的影响;然而，迄今为止，银屑病中HLA-KIR的研究通常受到HLA和KIR分型耗时和高成本的阻碍。最后，尽管已知HLAC：06：02与银屑病显著相关，并且与HLAC：06：02阴性银屑病患者相比，HLAC：06：02阳性银屑病患者在疾病发作、严重程度和对治疗的反应方面显示出差异，但HLAC：06：02导致银屑病的机制尚未得到充分研究。在这个应用程序中，我们利用各种创新的方法来解决这些问题。首先，我们在银屑病参考队列中对扩展MHC进行高保真下一代测序，并将鉴定的变体输入欧洲和亚洲GWAS队列，总计超过8，500例病例和17，000例对照。我们构建了一个全面的遗传模型，以最好地解释MHC内的遗传关联，使用多个模型输入，包括26个HLA/云母/MICB/TAP基因的4位数分辨率调用，SNP，indels和功能变量。其次，我们优化了一种新的KIR插补方法，该方法使用SNP阵列数据准确地调用KIR拷贝数，并应用该方法使用大型队列研究银屑病中的HLA-KIR关联。最后，我们利用一种新的流式细胞术方案从HLAC：06：02阳性和HLAC：06：02阴性银屑病患者的皮肤中分选银屑病相关细胞群，对单个细胞群进行全转录组RNA测序，并使用系统生物学分析方法更好地了解HLAC：06：02对银屑病发病机制的贡献。总之，拟议的工作将确定银屑病的因果变异，阐明功能机制，并可能确定新的治疗途径。这里开发的方法和工具将极大地促进其他免疫介导疾病的研究。

 DESCRIPTION (provided by applicant): Psoriasis is a common, immune-mediated, inflammatory skin disease associated with arthritis and systemic inflammation. Genome-wide association studies of psoriasis have identified over 40 susceptibility loci implicating both innat and adaptive immune pathways. The genetic locus exhibiting the greatest association with psoriasis is the MHC, with HLAC:06:02 showing very strong association in multiple ethnic groups. However, significant residual genetic signal remains in the MHC after accounting for the effects of HLAC:06:02 and it is not clear whether the residual signal resides in other HLA alleles, additional nearby genes, or regulatory variants. There is also evidence to suggest psoriasis susceptibility may be influenced by the interaction of killer cell immunoglobulin-like receptors (KIR) with HLA class I ligands; however, studies to date of HLA-KIR in psoriasis have generally been hampered by the time-consuming nature and high cost of HLA and KIR typing. Finally, although HLAC:06:02 is known to associate significantly with psoriasis and HLAC:06:02-positive psoriasis patients show differences in disease onset, severity, and response to therapy compared to HLAC:06:02-negative psoriasis patients, the mechanism by which HLAC:06:02 contributes to psoriasis has not been well studied. In this application, we utilize a variety of innovative approaches to address these questions. First, we perform high fidelity next-generation sequencing of the extended MHC in a psoriasis reference cohort and impute identified variants into European and Asian GWAS cohorts totaling over 8,500 cases and 17,000 controls. We construct a comprehensive genetic model to best explain the genetic association within the MHC using multiple model inputs including 4-digit resolution calls for 26 HLA/MICA/MICB/TAP genes, SNPs, indels, and functional variables. Second, we optimize a novel KIR imputation method that uses SNP array data to accurately call KIR copy number and apply this method to examine HLA-KIR associations in psoriasis using a large cohort. Finally, we utilize a novel flow cytometry protocol to sort psoriasis-relevant cell populations from the ski of HLAC:06:02-positive and HLAC:06:02- negative psoriasis patients, perform whole transcriptome RNA-sequencing on individual cell populations, and use systems biology analytical approaches to better understand the contribution of HLAC:06:02 to psoriasis pathogenesis. Together, the proposed work will identify causal variants in psoriasis, shed light on functional mechanisms, and potentially identify novel therapeutic pathways. The approaches and tools developed here will greatly facilitate the study of other immune-mediated diseases.