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

肠道微生物群被认为强烈影响人类健康，并受到先天（例如，通过识别微生物相关分子模式（MAMPs）的模式识别受体（PRRs）介导）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，微生物群与宿主免疫系统和宿主遗传之间的相互作用尚未得到系统和纵向的研究。由于人类微生物组研究出于伦理原因通常是非干预性的，迄今为止建立的关系主要是基于对小鼠模型的观察或纯粹的相关性，而没有建立因果关系。干细胞移植（SCT）患者在其微生物群、免疫系统和宿主遗传学方面经历了重大干预，为评估强干预对人类受试者微生物群和免疫系统的影响提供了独特的机会。但是，供体免疫遗传学如何影响SCT受者在经典HLA之外的宿主因子（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）内的匹配尚不完全清楚，并且供体免疫系统是否由于受者的微生物群被受体免疫系统印记而遇到“匹配问题”尚不清楚。在ImMiGeNe研究（NCT02940093）中，已经获得了20对供体-受体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，粪便样本已经进行了宏基因组学霰枪枪微生物组分析。为了将微生物组的变化与宿主遗传和免疫系统的变化联系起来，我们建议通过t<s:1>宾根NGS中心对SCT供体和受体进行全外显子组测序（WES）和转录组学。利用我们开发的新型生物信息学工具，我们将探索供体和受体之间在PRRs方面的差异是否会影响微生物群水平上的MAMP丰度和突变。这些数据还将用于探索经典HLA-A， -B, -C， DRB1和DQB1之外的匹配，包括miha。此外，我们将研究微生物群霰弹枪宏基因组序列，以寻找受体免疫系统“印记”的证据，以及某些分类群免疫原性的改变是否会导致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）的详细临床数据相关。结合我们在免疫学和生物信息学方面的专业知识，我们的共同目标是发现宿主和微生物生物标志物，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微生物群与宿主之间相互作用的宝贵见解。

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.