Systematic identification of minor histocompatibility antigens to address GVHD

总结 异基因造血干细胞移植（allo-HSCT）是治疗多种血液病的有效方法 但常常并发移植物抗宿主病（GvHD）。尽管在治疗策略方面取得了重大进展， GvHD相关的发病率和死亡率仍然很高，迫切需要更好的工具来预测GvHD风险。 GvHD的免疫学基础是供体T细胞对次要组织相容性抗原（mHAg）的识别， 由供体和受体之间的非同义单核苷酸多态性（SNP）差异引起。 然而，到目前为止，只报告了大约50个mHAg。目前的进展，在表征 通过下一代测序在编码外显子组内的种系和体细胞事件， HLA I类和II类表位预测的改进，提供了前所未有的机会， 在个体化基础上鉴定候选mHAg。我们假设组织特异性mHAg的鉴定， 通过对患者和供体DNA的基线分析预测，可以实现个性化的基因组信息 GvHD的风险评估，有可能帮助完善当前的供体选择算法， 移植后免疫抑制的个性化定制。因此，我们的目标是：（1）构建表位 预测管道，以系统地识别mHAg，结合最先进的SNP发现工具 来自WES，通过对单细胞RNA-seq和蛋白质组学的综合分析设计的表达过滤器 一组通常靶向的GvHD组织（即皮肤、肝、结肠和肺）的概况分析，炎症特征， 和Y染色体特异性表达（在雌性和雄性移植的情况下）。这将与 HLA I类和II类预测。表位预测将通过直接检测HLA结合的 通过基于免疫肽组的GvHD影响的靶组织的评价，(2)定义并跟踪T GvHD患者对预测mHAg的细胞应答。将mHAg靶点预测与功能性 T细胞应答，我们将通过在三个区域测试mHAg特异性T细胞应答来建立概念验证。 临床相关背景：（i）经历器官特异性GvHD的患者，免疫蛋白质组学特征为 目的1;（ii）接受来自2个不同HLA相同供体的序贯allo-HSCT并经历 一种移植后GvHD，另一种移植后GvHD;以及（iii）接受移植后移植的患者 作为GvHD预防的一部分。(3)测试 mHAg预测产生预后GvHD风险评分的可行性。为了确定单个mHAg是否 负担与临床观察到的GvHD相关，我们将重点关注髓样肿瘤患者，并进行WES 分析来自DFCI治疗患者的约200个MRD患者-供体对的DNA发现集，然后 在来自URD HSCT的约200对的扩展集上， available.通过对来自CIBMTR的约600对其他对（也是髓样瘤）的计划验证分析，我们 将评估这种方法是否适用于跨机构和跨种族的患者。

Summary Allogeneic hematopoietic stem cell transplantation (allo-HSCT) is potentially curative for many blood disorders but is often complicated by graft-versus-host disease (GvHD). Despite major advances in therapeutic strategies, GvHD-related morbidity and mortality remain high, and better tools to predict the GvHD risk are urgently needed. The immunologic basis of GvHD is the recognition by donor T cells of minor histocompatibility antigens (mHAgs), arising from nonsynonymous single nucleotide polymorphism (SNP) differences between donor and recipient. However, only some 50 mHAgs have been reported thus far. Current advances in the characterization of germline and somatic events within coding exomes through next-generation sequencing, coupled with improvements in HLA class I and II epitope prediction, offer an unprecedented opportunity to systematically identify candidate mHAgs on an individualized basis. We hypothesize that identification of tissue-specific mHAgs, predicted through baseline analysis of patient and donor DNA, can enable a personalized genomics-informed risk assessment of GvHD, with the potential to help refine current donor selection algorithms and to enable personalized tailoring of post-transplant immunosuppression. Our aims are thus to: (1) Build an epitope prediction pipeline to systematically identify mHAgs, incorporating state-of-the-art tools for SNP discovery from WES, expression filters designed through comprehensive analysis of single-cell RNA-seq and proteomic profiling of a set of commonly targeted GvHD tissues (i.e. skin, liver, colon and lung), inflammation signatures, and Y-chromosome specific expression (in the case of female male transplants). This will be then coupled with HLA class I and II prediction. Epitope predictions will be confirmed through direct detection of HLA-bound peptides by immunopeptidome-based evaluations of GvHD-affected target tissues. (2) Define and track the T cell responses to predicted mHAgs in patients with GvHD. To link prediction of mHAg targets with functional T cell responses, we will establish proof-of-concept by testing for mHAg-specific T cell responses across three clinically relevant settings: (i) patients experiencing organ-specific GvHD, immunoproteomically characterized in Aim 1; (ii) patients who received sequential allo-HSCT from 2 distinct HLA-identical donors and experienced GvHD following one but not the other transplant; and (iii) patients who received post-transplant cyclophosphamide after matched related donor (MRD) HSCT as part of GvHD prophylaxis. (3) Test the feasibility of mHAg prediction to generate a prognostic GvHD risk score. To determine if individual mHAg burden relates to clinically observed GvHD, we will focus on patients with myeloid neoplasia, and perform WES analysis on a discovery set of DNA from ~200 MRD recipient-donor pairs from patients treated at DFCI, and then on an extension set of ~200 pairs from URD HSCT, from whom information regarding GvHD occurrence is available. Through a planned validation analysis of ~600 other pairs (also myeloid neoplasia) from CIBMTR, we will assess if this approach is applicable cross-institutionally, and for patients across ethnicities.