ImMiGeNe - Interplay of immune parameters, microbiota and host genetics during childhood stem cell transplantation

肠道微生物区系被认为强烈影响人类健康，并受先天性(例如，通过识别微生物相关分子模式而介导的模式识别受体(PRRs))和适应性(由抗原和可溶性IgA介导)免疫识别和效应机制的调节。然而，微生物区系、宿主免疫系统和宿主遗传学之间的相互作用并没有得到系统和纵向的研究。由于人类的微生物组研究通常是非干预性的，出于伦理原因，迄今为止建立的关系主要是基于对小鼠模型的观察，或者是纯粹的相关，而没有确定因果关系。干细胞移植(SCT)患者在他们的微生物区系、免疫系统和宿主遗传学方面接受了重要的干预，这为评估强有力的干预对人类受试者的微生物区系和免疫系统的影响提供了独特的机会。但供体免疫遗传学如何影响SCT受者体内的匹配，就经典人类白细胞抗原以外的宿主因素(例如，包括所谓的次要组织相容性抗原，MIHAS，例如编码SNP和非典型HLA)而言，尚不完全清楚，也不清楚供体免疫系统是否由于受体的微生物区系被受体免疫系统印记而遇到匹配问题。在ImMiGeNe研究(NCT02940093)中，20对供受者SCT的纵向(9个时间点)粪便、尿液和血液样本以及完整的临床文件已经获得，粪便样本已经接受了宏基因组猎枪微生物组分析。为了将微生物组的变化与宿主遗传学和免疫系统的变化联系起来，我们建议通过Tübingen NGS中枢对SCT供体和受体进行全外显子测序(WES)和转录组学。使用我们开发的新的生物信息学工具，我们将探索供体和受体在PRR方面的差异是否会在微生物区系水平上影响MAMP丰度和突变。这些数据还将用于探索经典的HLA-A、-B、-C、DRB1和DQB1以外的匹配，包括MIHAS。此外，我们将研究微生物群的鸟枪式元基因组学序列，以寻找接受者免疫系统‘印记’的证据，以及某些分类群的免疫原性改变是否会导致SCT后微生物组组成的变化。所有这三个问题都将与移植物抗宿主病(GvHD)和长期并发症(如腹泻和吸收不良)方面的详细临床数据有关。将我们在免疫学和生物信息学方面的专家聚集在一起，我们的共同目标是发现宿主和微生物生物标记物，用于预测和随后减少/预防SCT相关的不良反应，并通过这种无偏见的多组学方法获得关于微生物区系和宿主之间相互作用的有价值的见解。

The gut microbiota are thought to strongly influence human health and are regulated by innate (mediated, for example, by pattern recognition receptors (PRRs) via recognition of microbe-associated molecular patterns, MAMPs) and adaptive (mediated by antigens and soluble IgA) immune recognition and effector mechanisms. However, the interplay of microbiota, host immune system and host genetics have not always been studied systematically and longitudinally. Since microbiome studies in humans are usually non-interventional for ethical reasons, the relationships established so far have, for the major part, been based on observations in mouse models or purely correlative without establishing causalities. Stem cell transplantation (SCT) patients undergo significant interventions in terms of their microbiota, immune system, and host genetics, providing the unique opportunity to assess the impact of strong interventions on both the microbiota and the immune system in human subjects. But how donor immuno-genetics affect matching within a SCT recipient in terms of host factors beyond classical HLA (e.g. including so-called minor histocompatibility antigens, miHAs, e.g. coding SNPs, and non-typical HLAs) is not fully understood, and whether the donor immune system encounters ‘matching issues’ due to the recipient’s microbiota having been imprinted by the recipient immune system is unclear. Within the ImMiGeNe study (NCT02940093) longitudinal (nine time points) stool, urine, and blood samples as well as full clinical documentation have been acquired for 20 donor-recipient SCT pairs and fecal samples have already been subjected to metagenomics shotgun microbiome analysis. In order to correlate changes in the microbiome to changes in host genetics and immune system, we here propose to conduct whole-exome sequencing (WES) and transcriptomics of SCT donor and recipients via the Tübingen NGS hub. Using novel bioinformatics tools developed by us, we will explore whether differences between donor and recipient in terms of PRRs affect MAMP abundance and mutations at the level of the microbiota. The data will also be used to explore matching beyond classical HLA-A, -B, -C, DRB1 and DQB1 and include miHAs. Additionally, we will investigate microbiota shotgun metagenomics sequences for evidence of ‘imprinting’ by the recipient’s immune system, and whether changed immunogenicity of certain taxa leads to a change in microbiome composition post-SCT. All three questions will be related to well-documented and detailed clinical data in terms of graft versus host disease (GvHD) and long-term complications like diarrhea and malabsorption. Bringing our expertises in immunology and bioinformatics together, our joint aim is to discover host and microbial biomarkers for the prediction and subsequent reduction/prevention of SCT-associated adverse effects and to gain valuable insights into the interplay between microbiota and host via this unbiased multi-omics approach.