Single-cell analysis to promote kidney repair

单细胞分析促进肾脏修复

• 批准号: 10053595
• 负责人: BENJAMIN D. HUMPHREYS
• 金额: $ 73.55万
• 依托单位: WASHINGTON UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-09-01 至 2025-05-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10053595
• 关键词: 3-Dimensional; Ablation; Acute; Acute Renal Failure with Renal Papillary Necrosis; Adopted; Atlases; Attenuated; Automobile Driving; Bioinformatics; California; Candidate Disease Gene; Cell Nucleus; Cells; Chromatin; Chronic Disease; Chronic Kidney Failure; Communities; Data; Data Set; Databases; Development; Diagnosis; Epigenetic Process; Epithelial Cells; Excision; Female; Fibrosis; Gene Deletion; Gene Expression; Genes; Genetic; Genetic Transcription; Hospitalization; Human; Immunohistochemistry; Impairment; In Situ Hybridization; Inflammation; Inflammatory; Injury; Injury to Kidney; Intervention; Kidney; Kidney Diseases; Knock-out; Knowledge; Laboratories; Logic; MAP4K4 gene; Maps; Medicare; Modeling; Modification; Molecular; Mus; NF-kappa B; Nephrons; Nuclear; Nuclear RNA; Online Systems; Outcome; Pathway interactions; Patient-Focused Outcomes; Patients; Persons; Population; Predisposition; Probability; Process; Property; Recovery; Recurrence; Regulator Genes; Renal function; Renal tubule structure; Research; Resources; Risk; Role; Route; Sampling; Sex Differences; Signal Transduction; Small Nuclear RNA; Surveys; TNF Receptor-Associated Factors; TRAF2 gene; Technology; Testing; Therapeutic Intervention; Time; Transgenic Mice; Tubular formation; Universities; Visualization software; Washington; adverse outcome; aged; cell type; cytokine; data mining; epigenome; epithelial injury; experience; genetic approach; high risk; improved; improved outcome; injured; injury and repair; kidney biopsy; kidney repair; male; member; men; mouse model; multimodal data; multimodality; multiple omics; novel; novel strategies; novel therapeutic intervention; prevent; repaired; response; response to injury; sex; single cell analysis; single molecule; single-cell RNA sequencing; therapeutic development; therapeutic target; transcriptome; transcriptome sequencing; transcriptomics

Summary Acute kidney injury (AKI) has a wide spectrum of outcomes from recovery to a long-term transition to chronic kidney disease (CKD). Between 2000 and 2014, AKI hospitalizations have increased from 3.5 to 11.7 per 1000 persons. Medicare patients aged 66 years and older hospitalized for AKI have a 35% cumulative probability of a recurrent AKI hospitalization within one year and 28% will be diagnosed with CKD in the same time frame. Men have a higher risk of AKI, and of developing progressive CKD, although the mechanisms are poorly understood. In the mouse, males also show a heightened vulnerability to AKI. Recent single cell RNA-seq studies from the McMahon and Kim groups have highlighted marked differences in gene expression between the sexes in proximal tubule segments, the region of the nephron most susceptible to AKI. Preliminary studies in the Humphreys and McMahon laboratories using single nuclear sequencing identified a cell type resulting from failed repair of proximal tubule cells (FR-PTC) following mild to severe AKI with a pro-inflammatory, pro- fibrotic signature. FR-PTCs are hypothesized to drive progressive kidney disease following AKI. This proposal centers on the postulates that an understanding of sex differences in response to AKI, and the application of genetic approaches to target proinflammatory properties of FR-PTCs and to eliminate FR-PTCs following renal repair, will be effective routes to ultimately benefit patient outcomes post AKI. To this end, we have assembled a complementary team, with prior collaborative experience: Humphreys (Washington University), Kim (University of Pennsylvannia) and McMahon (University of Southern California). All team members have participated in the ReBuilding a Kidney Consortium. In Specific Aim 1: we will characterize successful versus failed proximal tubule repair with single nucleus transcriptomics (snRNA-seq) and single nuclear chromatin accessibility studies (scATAC-seq) in male and female mouse models examining key findings in human kidney biopsies. In Specific Aim 2: we will harmonize multimodal datasets generated in Specific Aim1 to facilitate viewing and interrogation of these data by the broad research community. Mining of these data by the group will focus on defining the regulatory logic of repair strategies and outcomes in the male and female kidney. In Specific Aim 3: we will examine the hypothesis that adverse outcomes in the male kidney following AKI are driven by NF-kB pathway components Nfkb1 and TNIK in FR-PTCs, genetically eliminating the action of these genes. We will generate and validate a new transgenic mouse resource for the community, enabling genetic modification and elimination of FR-PTCs. We will determine whether FR-PTC removal has a favorable outcome, as we predict, on progressive kidney disease following AKI.

总结 急性肾损伤（阿基）具有从恢复到长期过渡到慢性的广泛结局 肾病（CKD）。2000年至2014年，阿基住院率从每1000人3.5人增加到11.7人 人士66岁及以上因阿基住院的医疗保险患者的累积概率为35%， 在一年内复发阿基住院治疗，28%将在同一时间范围内诊断为CKD。 男性患阿基和进展性CKD的风险更高，尽管其机制很差。 明白在小鼠中，雄性也表现出对阿基的高度脆弱性。最新单细胞RNA-seq 来自McMahon和Kim小组的研究强调了基因表达的显著差异， 近端小管段的性别，肾单位的区域最容易受到阿基。初步研究 在Humphreys和McMahon实验室，使用单核测序确定了一种细胞类型， 从轻度至重度阿基后近端小管细胞（FR-PTC）修复失败， 纤维化特征FR-PTC被假设为在阿基后驱动进行性肾脏疾病。这项建议 中心的假设，即对阿基反应的性别差异的理解，以及 靶向FR-PTC的促炎特性并消除肾移植后FR-PTC的遗传方法 修复将是最终使阿基后患者结局受益的有效途径。为此，我们召集了 一个互补的团队，具有先前的合作经验：汉弗莱斯（华盛顿大学），金 （宾夕法尼亚大学）和麦克马洪（南加州大学）。所有工作组成员都可以 参加了重建肾脏联盟。在具体目标1中：我们将描述成功与 单核转录组学（snRNA-seq）和单核染色质的近端小管修复失败 在雄性和雌性小鼠模型中进行的可及性研究（scATAC-seq），检查了人类肾脏中的关键发现 活组织检查在具体目标2中：我们将协调具体目标1中生成的多模式数据集，以促进 广泛的研究界对这些数据的观察和询问。集团对这些数据的挖掘 将集中于定义男性和女性肾脏修复策略和结果的调节逻辑。在 具体目标3：我们将检验以下假设：阿基后男性肾脏的不良结局是 由FR-PTC中的NF-kB通路组分Nfkb 1和TNIK驱动，在遗传上消除了这些组分的作用， 基因.我们将为社区产生并验证新的转基因小鼠资源，使遗传 FR-PTC的修饰和消除。我们将确定FR-PTC去除是否具有有利的 正如我们预测的那样，阿基后进行性肾脏疾病的结局。