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

慢性肾脏疾病（CKD）对医疗保健造成巨大负担， 美国人口。未经治疗的CKD导致纤维化和肾功能下降，直到患者需要生命- 维持肾脏替代疗法，因此迫切需要治疗方案来停止或逆转 疾病的进展。我的实验室已经鉴定出一种促炎细胞类型，起源于 损伤的近曲小管（FR-PT）细胞，与急性肾损伤（阿基）恢复失败相关， 随后转为CKD。成人肾脏样本的单细胞RNA和ATAC测序， 提供了这种细胞状态存在于未经历阿基的肾脏中的证据。因此，FR-PT 细胞可以代表急性和慢性肾损伤的汇合点， 炎症和纤维化信号持续存在，导致CKD进展。一种抑制或 逆转向修复失败状态的转变可以通过减少FR-PT细胞来改善CKD的结局。 负责持续促炎和促纤维化信号传导的群体。由于FR-PT细胞似乎 作为与健康近曲小管（PT）细胞不同的群体，基因调控机制可能是一种基因调控机制。 是FR-PT细胞形成的重要因素。该项目将揭示基因调控 通过分析FR-PT细胞群的网络和调控元件， 通过整合成年人的单细胞RNA-seq和ATAC-seq图谱生成的单细胞多组数据集 人类肾脏，特别是专注于表征转录和表观遗传差异之间 健康PT和FR-PT细胞。该数据集将用于训练参数基因调控网络模型， PT细胞，以鉴定参与健康和非健康之间转变的候选顺式和反式调节元件。 故障修复PT状态。随后将对鉴定的调控元件进行实验验证， 确认其预测的作用。该提案旨在确定针对FR-PT细胞的治疗候选药物，作为 CKD进展的驱动因素，解决了对更好的CKD治疗的突出需求。完成本 项目还将帮助我实现我的培训目标，以扩大我的科学知识，学会识别， 学习可翻译的研究问题，并获得生物信息学和单细胞技术的经验。博士 本杰明·汉弗莱斯是实现这些目标的模范物理学家兼科学家，他的实验室是一个最佳的实验室。 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， 实验室的优秀培训和协作氛围。该项目的成功完成将有助于 更好地了解CKD和可能的治疗策略，并将为我将来的职业生涯做好准备。 独立的物理学家和科学家

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.