The gene regulatory landscape of healthy and failed repair proximal tubule subpopulations in kidney disease

肾脏疾病中健康和修复失败的近端小管亚群的基因调控景观

• 批准号: 10599152
• 负责人: Nicolas Hyun Ledru
• 金额: $ 5.16万
• 依托单位: WASHINGTON UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-04-01 至 2025-03-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10599152
• 关键词: ATAC-seq; Acute; Acute Renal Failure with Renal Papillary Necrosis; Address; Adult; Affect; Aging; American; Area; Back; Binding; Bioinformatics; Black, Indigenous, People of Color; Cell Culture Techniques; Cell Nucleus; Cells; Characteristics; Chromatin; Chronic; Chronic Kidney Failure; Clinical; Data Set; Development; Dialysis procedure; Disease; Disease Outcome; Disease Progression; End stage renal failure; Environment; Epigenetic Process; Fibrosis; Financial Hardship; Gene Expression Profile; Generations; Genetic; Genetic Transcription; Goals; Health; Healthcare; Heterogeneity; Human; In Vitro; Incentives; Individual; Inflammatory; Injury to Kidney; Kidney; Kidney Diseases; Kidney Transplantation; Knowledge; Laboratories; Learning; Libraries; Life; Maintenance; Mediating; Medical; Modeling; Multiomic Data; Nucleic Acid Regulatory Sequences; Organ; Outcome; Patients; Persons; Phenotype; Physicians; Population; Prevalence; Profibrotic signal; Recovery; Regulator Genes; Regulatory Element; Renal Replacement Therapy; Renal function; Research; Resolution; Role; Sampling; Scientist; Signal Transduction; Techniques; Therapeutic; Therapeutically Targetable; Training; Update; Validation; Work; burden of illness; candidate identification; career; cell type; collaborative environment; computerized tools; educational atmosphere; effective therapy; experience; gene regulatory network; health disparity; improved; injury and repair; insight; multimodality; multiple omics; network models; patient population; repaired; risk variant; single cell sequencing; single nucleus RNA-sequencing; single-cell RNA sequencing; therapeutic candidate; transcription factor; transcriptome; transcriptomics; treatment strategy

Chronic kidney disease (CKD) has an immense burden on healthcare, with a prevalence of 37 million in the American population. Untreated CKD leads to fibrosis and declining renal function until a patient requires life- sustaining renal replacement therapy, so there is a critical need for treatment options to halt or reverse the progression of disease. My lab has characterized a pro-inflammatory cell type, originating from the failed repair of injured proximal tubule (FR-PT) cells, that correlates with failed recovery from acute kidney injury (AKI) and subsequent transition to CKD. Single cell RNA and ATAC sequencing of human adult kidney samples has provided evidence for this cell state’s presence in kidneys that have not experienced AKI. As such the FR-PT cell could represent a convergence point for acute and chronic renal injury through which progressive inflammatory and fibrotic signals are perpetuated, leading to CKD progression. A treatment that inhibits or reverses transition to a failed repair state could ameliorate CKD outcomes by reducing the FR-PT cell population responsible for continued pro-inflammatory and pro-fibrotic signaling. Since FR-PT cells appear to be a distinct population from healthy proximal tubule (PT) cells, gene regulatory mechanisms may be an important contributing factor to the formation of FR-PT cells. This project will reveal the gene regulatory networks and regulatory elements underpinning development of the FR-PT cell population through analysis of a single cell multiomic dataset generated by integrating single cell RNA-seq and ATAC-seq profiles of adult human kidney, specifically focusing on characterizing transcriptional and epigenetic differences between healthy PT and FR-PT cells. This dataset will be used to train a parametric gene regulatory network model for PT cells to identify candidate cis- and trans-regulatory elements involved in the transition between healthy and failed repair PT states. This will be followed by experimental validation of the identified regulatory elements to confirm their predicted role. This proposal aims to identify therapeutic candidates targeting FR-PT cells as a driver of CKD progression, addressing an outstanding need for better CKD therapies. Completion of this project will also help me achieve my training goals to expand my scientific knowledge, learn to identify and study translatable research questions, and gain experience with bioinformatics and single cell techniques. Dr. Benjamin Humphreys is a model physician-scientist for these goals, and his laboratory is an optimal environment for this project and my training goals, because of his research group’s single cell expertise and the lab’s excellent training and collaborative atmosphere. Successful completion of this project will contribute a better understanding of CKD and possible treatment strategies and will prepare me to pursue a career as an independent physician-scientist.

慢性肾病 (CKD) 对医疗保健造成巨大负担，该病的患病率高达 3700 万 美国人口中，未经治疗的 CKD 会导致纤维化和肾功能下降，直到患者需要生命。 维持肾脏替代治疗，因此迫切需要治疗方案来停止或逆转 我的实验室已鉴定出一种促炎细胞类型，源自失败的修复 受损的近端小管 (FR-PT) 细胞，这与急性肾损伤 (AKI) 恢复失败相关 随后转向对成人肾脏样本进行单细胞 RNA 和 ATAC 测序。 为未经历过 AKI 的肾脏中存在这种细胞状态提供了证据。 细胞可能代表急性和慢性肾损伤的交汇点，通过该交汇点进行进展 炎症和纤维化信号持续存在，导致 CKD 进展。 逆转向失败修复状态的转变可以通过减少 FR-PT 细胞来改善 CKD 结局 FR-PT 细胞似乎负责持续的促炎症和促纤维化信号传导。 与健康的近端小管（PT）细胞不同，基因调控机制可能是 该项目将揭示FR-PT细胞形成的重要影响因素。 通过分析支持 FR-PT 细胞群发育的网络和调控元件 通过整合成人单细胞 RNA-seq 和 ATAC-seq 配置文件生成的单细胞多组学数据集 人类肾脏，特别关注表征之间的转录和表观遗传差异 该数据集将用于训练健康的 PT 和 FR-PT 细胞的非参数参数基因调控网络模型。 PT 细胞可识别参与健康和健康之间过渡的候选顺式和反式调节元件 失败的修复 PT 状态随后将通过实验验证已确定的调节元件。 该提案旨在确定以 FR-PT 细胞为靶点的治疗候选药物。 CKD 进展的驱动因素，解决了对更好的 CKD 治疗的突出需求。 项目还将帮助我实现培训目标，扩展我的科学知识，学会识别和 研究可翻译的研究问题，并获得生物信息学和单细胞技术的经验。 本杰明·汉弗莱斯（Benjamin Humphreys）是实现这些目标的模范医师科学家，他的实验室是最佳的 这个项目的环境和我的培训目标，因为他的研究小组的单细胞专业知识和 该实验室出色的培训和协作氛围将有助于该项目的成功完成。 更好地了解 CKD 和可能的治疗策略，将使我为从事职业生涯做好准备 独立医师科学家。