Table_4_Optimized Whole Genome Association Scanning for Discovery of HLA Class I-Restricted Minor Histocompatibility Antigens.xlsx

Patients undergoing allogeneic stem cell transplantation as treatment for hematological diseases face the risk of Graft-versus-Host Disease as well as relapse. Graft-versus-Host Disease and the favorable Graft-versus-Leukemia effect are mediated by donor T cells recognizing polymorphic peptides, which are presented on the cell surface by HLA molecules and result from single nucleotide polymorphism alleles that are disparate between patient and donor. Identification of polymorphic HLA-binding peptides, designated minor histocompatibility antigens, has been a laborious procedure, and the number and scope for broad clinical use of these antigens therefore remain limited. Here, we present an optimized whole genome association approach for discovery of HLA class I minor histocompatibility antigens. T cell clones isolated from patients who responded to donor lymphocyte infusions after HLA-matched allogeneic stem cell transplantation were tested against a panel of 191 EBV-transformed B cells, which have been sequenced by the 1000 Genomes Project and selected for expression of seven common HLA class I alleles (HLA-A∗01:01, A∗02:01, A∗03:01, B∗07:02, B∗08:01, C∗07:01, and C∗07:02). By including all polymorphisms with minor allele frequencies above 0.01, we demonstrated that the new approach allows direct discovery of minor histocompatibility antigens as exemplified by seven new antigens in eight different HLA class I alleles including one antigen in HLA-A∗24:02 and HLA-A∗23:01, for which the method has not been originally designed. Our new whole genome association strategy is expected to rapidly augment the repertoire of HLA class I-restricted minor histocompatibility antigens that will become available for donor selection and clinical use to predict, follow or manipulate Graft-versus-Leukemia effect and Graft-versus-Host Disease after allogeneic stem cell transplantation.

以异基因干细胞移植（allogeneic stem cell transplantation）治疗血液系统疾病的患者，面临移植物抗宿主病（Graft-versus-Host Disease）与疾病复发的风险。移植物抗宿主病与有益的移植物抗白血病（Graft-versus-Leukemia）效应均由供体T细胞介导：供体T细胞可识别由人类白细胞抗原（Human Leukocyte Antigen）分子呈递于细胞表面的多态性肽段，此类肽段源于供受体间存在差异的单核苷酸多态性（single nucleotide polymorphism）等位基因。鉴定这类被称为次要组织相容性抗原（minor histocompatibility antigens）的多态性HLA结合肽段，曾是一项极为繁琐的工作，因此可用于大规模临床应用的此类抗原的数量与范围仍十分有限。在此，我们提出一种优化的全基因组关联方法，用于发现HLA I类次要组织相容性抗原。我们从经HLA匹配的异基因干细胞移植后，对供体淋巴细胞输注（donor lymphocyte infusions）产生应答的患者体内分离出T细胞克隆，并针对由1000 Genomes Project测序、且经筛选表达7种常见HLA I类等位基因（HLA-A*01:01、A*02:01、A*03:01、B*07:02、B*08:01、C*07:01及C*07:02）的191株EBV-transformed B细胞开展了功能检测。通过纳入次要等位基因频率（minor allele frequencies）高于0.01的所有多态性位点，我们证实该新方法可直接发现次要组织相容性抗原：我们在8种不同HLA I类等位基因中发现了7种全新的抗原，其中包括针对原本未适配该方法的HLA-A*24:02与HLA-A*23:01各发现1种抗原。我们的新型全基因组关联策略有望快速扩充HLA I类限制性次要组织相容性抗原的储备库，这些抗原可用于供体筛选，以及临床预测、监测或调控异基因干细胞移植后的移植物抗白血病效应与移植物抗宿主病。