Unraveling the molecular pathophysiological landscape in primary immunodeficiencies to improve personalized medicine approaches.

先天性免疫缺陷(IEI)是一组免疫系统对外部病原体或内部自身抗原的反应受损的异质性疾病。这种免疫动态平衡的丧失可能存在于高达0.2%的人中，并不是所有人都同样明显。一些人可能会发展成轻度、中度和一些非常严重的表型，从感染易感性增加到危及生命的感染，经常合并不同类型和程度的自身免疫、自体炎症和恶性肿瘤。在少数IEI患者中，单基因缺陷可以完全解释疾病，而在其他患者中，罕见的基因变异部分导致了疾病的发病(风险等位基因)。在过去的几年里，我们在弗莱堡和慕尼黑的大学医院对5000多名IEI患者进行了基因分型。在大多数患者(约3,500例)中，基因组的所有蛋白质编码基因都被筛选出致病突变，而在一些(约1,500例)患者中，只有50-150个基因的子集被靶向基因小组筛选。基因诊断的得率在20%-40%之间，这取决于所采用的方法、功能表征的可能性以及是否有更多的家庭成员。基因诊断对患者管理具有重要影响，因为患者受益于显著改善疾病预后和生活质量的有针对性的治疗。因此，该项目的第一个目标是继续我们的基因分型工作，通过分析尚未进行基因分型或目标基因小组分析后结果为阴性的患者的整个外显子组。这也可能导致新的基因缺陷的发现，这有助于IEI诊断产量的全面和持续增加。然而，在这些基因定义的疾病中，分子病理生理学并不完全清楚；因此，其他解释目前正在探索中。例如，基因调控/表达的差异--由表观遗传因素控制--或肠道微生物区系组成的差异可能会影响疾病的外显性和严重性。第二个目的是探索具有明显单基因缺陷的IEI患者关键免疫相关细胞的转录图谱。更深入地了解不同影响的细胞群体和改变的细胞路径将有助于开发更好的小分子药物或生物制品的靶向治疗。第三个目标是解决肠道微生物群作为疾病修正因子在选定的IEI患者队列中的作用，这些患者具有不同的表达能力和/或不完全外显。更好地了解肠道微生物群如何调节IEI的病程和严重程度，将有助于开发更有效的治疗方案，并超越目前现有治疗的限制。这笔测序拨款还得到了八个已获资助的研究项目的补充。

Inborn errors of immunity (IEI) are a group of heterogeneous disorders in which the immune system’s response to external pathogens or to internal self-antigens is impaired. This loss of immune homeostasis may be present in up to 0.2% of people and does not manifest equally in all individuals. Some may develop mild, some moderate and some very severe phenotypes ranging from an increased infection susceptibility to life-threatening infections, often combined with different types and degrees of autoimmunity, auto-inflammation and malignancy. In the minority of patients with IEI, a monogenic defect can fully explain the disease, while in other patients, rare genetic variants partially contribute to the pathogenesis of the disorder (risk alleles). Over the last years we genotyped more than 5,000 individuals with IEI at the University Hospitals of Freiburg and Munich. In most of these patients (~3,500), all protein-coding genes of the genome were screened for disease-causing mutations, whereas in some (~1,500), only a subset of 50-150 genes was screened by a targeted gene panel. The yield of a genetic diagnosis varied between 20-40%, depending on the method employed, the possibility of functionally characterization, and the availability of additional family members. A genetic diagnosis has an important impact on patient management, as patients benefit from a targeted treatment that significantly improves disease prognosis and quality of life. Therefore, the first aim of this project is to continue our genotyping efforts by analysing the entire exome in patients who have not been genotyped yet or who had a negative result after a targeted gene panel analysis. This could also lead to the discovery of novel gene defects, which contributes to the overall and continuous increase in diagnostic yield in IEI. However, in some of these genetically defined conditions, the molecular pathophysiology is not entirely understood; thus, additional explanations are currently being explored. For instance, differences in gene regulation/expression -controlled by epigenetic factors- or differences in gut microbiota composition could influence disease penetrance and severity. The second aim is to explore the transcriptomic profiles of key immune-related cells in IEI patients with distinct monogenic defects. A deeper understanding of the differentially affected cell populations and altered cellular pathways will help to develop better targeted therapies with small molecule drugs or biologicals. The third aim is to address the role of the gut microbiome as a disease modifying factor in selected cohorts of IEI patients with variable expressivity and/or incomplete penetrance. A better understanding of how the gut microbiome modulates the disease course and severity in IEI will help to develop more effective therapeutic options and to override the limitation of currently existing treatments. This sequencing grant is complemented by eight already funded research projects.