Integrating human functional genomics and transcriptomics in highly phenotyped severe asthmatics

将人类功能基因组学和转录组学整合到高度表型的严重哮喘患者中

• 批准号: 2596378
• 金额: --
• 依托单位: University of Oxford
• 依托单位国家: 英国
• 项目类别: Studentship
• 财政年份: 2020
• 资助国家: 英国
• 起止时间: 2020 至 无数据
• 项目状态: 未结题
• 来源: https://gtr.ukri.org/projects?ref=studentship-2596378
• 关键词: Integrating; human; functional; genomics; transcriptomics

Asthma is the most common chronic lung disease, affecting 350 million people worldwide and causing 400,000 deaths annually. Up to 10% of asthmatics have severe, treatment-refractory disease, constituting a significant unmet clinical need due to exacerbations, healthcare costs and mortality. Asthma is pathobiologically and clinically heterogeneous. Identifying 'treatable traits', including type-2 cytokine-mediated ('T2-high') eosinophilic airway inflammation, has enabled highly-effective biomarker-directed approaches, targeting novel biologics according to blood and sputum eosinophilia, and fractional exhaled nitric oxide (FeNO). However other phenotypes and pathways remain to be defined and is widely recognised as an urgent research priority. In previous decades research has also been limited by the very small quantity of biological material which can be obtained from respiratory samples. Recent advances in single cell sequencing, multi-parameter flow cytometry and detailed clinical-and physiological phenotyping now make possible detailed transcriptional and functional analyses of human airway tissue in highly-characterised asthmatic subgroups.We set out to perform detailed transcriptomic analysis of samples from the airways of 60 selected participants who have also undergone WGS, performing paired single-cell RNAseq and single cell ATACseq using the 10X platform on bronchoscopically-obtained endobronchial brushes and scRNAseq on collagenase-dispersed bronchial biopsies. The main challenge will be to integrate the whole genome sequencing data with the transcriptomic gene expression data from airway samples obtained bronchoscopically from these patients and phenotypic data from the Oxford Airways Research Database and the NHS electronic patient record. Sample collection has progressed over the past 10 months. I undertook validation and optimisation steps and developed a sample processing pipeline. Preliminary RNAseq data are now available from 6 individuals which I begun analysing. Mulitiome libraries have been prepared but are yet to be sequenced. I undertook relevant training to develop my bioinformatics skills and knowledge of statistics, including Wellcome Sanger Single Cell Technologies and Analysis course and University of Washington Summer Institute in Statistical Genetics.We are aiming to collect at least 20 definitive bronchoscopy samples within the next 12 months. Subject recruitment is the rate limiting factor, but this depends on finding appropriate participants within the severe asthma clinic who are motivated to consent to this study. The clinicians review 528 new patients per year in the service and expect our accrual to continue at the current rate.

哮喘是最常见的慢性肺部疾病，影响全球3.5亿人，每年造成40万人死亡。高达10%的哮喘患者患有严重的难治性疾病，由于病情加重、医疗费用和死亡率，构成了显著的未满足的临床需求。哮喘在病理生物学和临床上是异质性的。鉴定“可治疗的特征”，包括2型烟碱介导的（“T2高”）嗜酸性气道炎症，已经实现了高效的生物标志物导向方法，根据血液和痰嗜酸性粒细胞增多和呼出一氧化氮分数（FeNO）靶向新型生物制剂。然而，其他表型和途径仍有待确定，并被广泛认为是一个紧迫的研究重点。在过去的几十年里，研究也受到了从呼吸道样本中获得的生物材料数量非常少的限制。单细胞测序、多参数流式细胞术和详细的临床和生理表型分析的最新进展，现在使得在高度特征化的哮喘亚组中对人类气道组织进行详细的转录和功能分析成为可能。使用10X平台在支气管镜获得的支气管内刷上进行配对的单细胞RNAseq和单细胞ATACseq，并在胶原酶分散的支气管活检组织上进行scRNAseq。主要的挑战是将全基因组测序数据与这些患者支气管镜下获得的气道样本的转录组基因表达数据以及来自牛津航空研究数据库和NHS电子病历的表型数据相结合。在过去10个月中，样本收集工作取得了进展。我进行了验证和优化步骤，并开发了一个样品处理管道。现在可以从我开始分析的6个个体获得初步的RNAseq数据。已经制备了多基因组文库，但尚未测序。我接受了相关培训，以发展我的生物信息学技能和统计学知识，包括Wellcome桑格单细胞技术和分析课程和华盛顿大学夏季统计遗传学研究所。我们的目标是在未来12个月内收集至少20个明确的支气管镜检查样本。受试者招募是速率限制因素，但这取决于在重度哮喘门诊中找到有动机同意本研究的适当受试者。临床医生每年审查528名新患者，并希望我们的应计费用继续以目前的速度增长。