Understanding Host Epigenetic changes to Salmonella Typhi Exposure and Infection in the context of a Human Challenge Model

由伤寒沙门氏菌和甲型副伤寒沙门氏菌引起的肠热是发病率和死亡率的重要原因。每年约有2100万人患肠热病，其中约22.2万人死亡，儿童面临的风险最大。大多数病例发生在中南亚和东南亚。在预防和管理伤寒感染方面存在若干关键挑战，包括：由于目前的检测方法敏感性差，在诊断肠热病方面存在困难；短期疫苗效力，没有两岁以下儿童的许可疫苗；以及抗生素耐药菌株的出现。因此，需要新的感染生物标志物、更有效的疫苗和新的抗伤寒疗法；实现这些目标需要更好地了解对伤寒的免疫反应，特别是先天和适应性细胞免疫的作用。牛津大学目前正在研究对这些沙门氏菌的免疫力，在这些研究中，成年人被一剂伤寒细菌攻击，无免疫力的参与者的攻击率为65%。初步数据显示，感染和疫苗接种改变了白细胞中的基因表达，这些变化与疾病期间的免疫反应和炎症反应有关。这种情况发生的方式和原因取决于表观遗传机制，包括DNA甲基化和miR表达。MicroRNAs是一种短的非编码RNA，可以对60%的基因进行转录后调控。它们是宿主对感染反应的重要介质。mir与免疫应答有关，例如miR-155通过抑制SOCS1（抑制细胞因子信号传导1）促进促炎细胞因子的白细胞分泌，从而促进抗菌反应。microrna调节b细胞、t细胞、单核细胞和树突状细胞的分化和活化，因此可能控制宿主对伤寒的易感性5-7。伤寒挑战研究提供了在一个独特的受控环境中，在表观遗传水平上描述对细菌病原体的免疫反应的机会。本研究将使用小RNA测序技术和甲基化芯片来表征伤寒暴露后和伤寒感染期间肠道热挑战研究中使用存储样本的参与者的pbmc中的microRNA和基因甲基化变化。将整合表观遗传学和预衍生转录组学数据，以提供暴露和感染期间基因表达的前所未有的详细水平。DNA甲基化模式和microrna的功能意义将通过体外研究来确定。该项目的数据可以鉴定出新的伤寒或细菌感染的microRNA生物标志物，并可能为促进或预防伤寒感染的蛋白质和途径提供生物学见解，这可能有助于设计新的伤寒疫苗或抗伤寒疗法。

Enteric fever caused by Salmonella enterica serovars Typhi and Paratyphi A is an important cause of morbidity and mortality. Around 21 million people per year develop enteric fever of which approximately 222,000 die, with children being most at risk. The majority of cases arise in South-Central and Southeast Asia. There are several key challenges in preventing and managing typhoid infection including: difficulties in diagnosing enteric fever as current tests have poor sensitivity; short term vaccine efficacy, with no licensed vaccine for children under two years old; and the emergence of antibiotic resistant strains. Novel biomarkers of infection, more efficacious vaccines and novel anti-typhoid therapies are therefore needed; achieving these goals requires a better understanding of immune response to typhoid and in particular the role of innate and adaptive cellular immunity.Enteric fever challenge studies, in which adults are challenged with a dose of typhoid bacteria with an attack rate of 65% in non-immune participants are currently being employed in Oxford to study immunity to these Salmonellae. Preliminary data show that infection, and vaccination alters gene expression in leukocytes and that these changes are associated with both immune responses and the inflammatory response during disease. How and why this occurs is governed by epigenetic mechanisms including DNA methylation and miR expression. MicroRNAs are a species of short non-coding RNA that post transcriptionally regulate 60% of genes. They are important mediators of host response to infection. MiRs are implicated in immune response e.g. miR-155 promotes an antimicrobial response by suppressing SOCS1 (suppression of cytokine signalling 1)to promote leukocyte secretion of pro-inflammatory cytokines4. MicroRNAs regulate differentiation and activation of B-cells, T-cells, monocytes and dendritic cells and therefore may govern host susceptibility to typhoid5-7. Typhoid challenge studies present the opportunity to delineate immune response to a bacterial pathogen, at an epigenetic level, in a uniquely controlled environment. This study will use small RNA sequencing techniques and methylation chips to characterise microRNA and gene methylation changes after typhoid exposure and during typhoid infection in the PBMCs of participants of an enteric fever challenge study using stored samples. Epigenetic and pre-derived transcriptomic data will be integrated to provide an unprecedented level of detail in gene expression during exposure and infection. The functional significance of DNA methylation patterns and microRNAs will be determined using in-vitro studies. Data from this project could identify novel microRNA biomarkers of typhoid or bacterial infection, and may provide biological insights into the proteins and pathways which promote or prevent typhoid infection which could be exploited to facilitate the design of novel typhoid vaccines or anti-typhoid therapeutics.