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

基本信息

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
项目类别：
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

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

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项目摘要

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.

慢性肾脏疾病（CKD）在医疗保健上遭受了巨大烧伤，患病率为3700万美国人口。未经处理的CKD导致纤维化和肾功能下降，直到患者需要生命为止维持肾脏替代疗法，因此需要治疗选择以停止或逆转疾病的进展。我的实验室表征了促炎细胞类型，源自失败的维修受伤的近端管（FR-PT）细胞，与急性肾损伤（AKI）恢复失败相关，并且随后过渡到CKD。人类成人肾脏样品的单细胞RNA和ATAC测序具有提供了这种细胞状态在没有经历过AKI的肾脏中存在的证据。这样fr-pt 细胞可能代表急性和慢性肾损伤的收敛点炎症和纤维化信号已永久存在，导致CKD进展。抑制或逆转过渡到失败的维修状态可以通过减少FR-PT细胞来改善CKD结果负责持续促炎和促纤维化信号传导的人群。由于Fr-Pt-PT细胞似乎与健康的近端小管（PT）细胞是一个不同的人群，基因调节机制可能是一种引起FR-PT细胞形成的重要促成因素。该项目将揭示基因调节性通过分析，网络和监管元素为FR-PT细胞种群开发而言通过整合成人的单细胞RNA-seq和ATAC-Seq曲线而生成的单细胞多组分数据集人类肾脏，特别着重于表征转录和表观遗传学差异健康的PT和FR-PT细胞。该数据集将用于训练一个参数基因调节网络模型 PT细胞以鉴定候选者顺式和反式调节元素，涉及健康和维修状态失败。随后将对已确定的调节元素进行实验验证确认他们的预测作用。该建议旨在确定针对FR-PT细胞的治疗候选者 CKD进展的驱动程序，满足了对更好CKD疗法的杰出需求。完成此操作项目还将帮助我实现培训目标，以扩大我的科学知识，学习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。博士本杰明·汉弗莱斯（Benjamin Humphreys）是这些目标的典范物理科学家，他的实验室是最佳的该项目的环境和我的培训目标，因为他的研究小组的单元专业知识和该实验室的出色培训和协作气氛。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，并将为我做好准备从事职业独立的物理科学家。