Single-cell analysis to promote kidney repair

单细胞分析促进肾脏修复

基本信息

批准号：
10646473
负责人：
BENJAMIN D. HUMPHREYS
金额：
$ 73.22万
依托单位：
WASHINGTON UNIVERSITY
依托单位国家：
美国
项目类别：
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/10646473
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 Profibrotic signal Property Recovery Recurrence Regulator Genes Renal function Renal tubule structure Research Resources Risk Role Route Sampling Sex Differences Signal Transduction Surveys TNF Receptor-Associated Factors Technology Testing Therapeutic Intervention Time Transgenic Mice Tubular formation Universities Visualization software Washington adverse outcome aged cell type data mining epigenome epithelial injury experience genetic approach high risk improved improved outcome injured kidney biopsy kidney repair male member men mouse model multimodal data multimodality multiple omics novel novel strategies novel therapeutic intervention prevent profibrotic cytokine repair strategy repaired response response to injury sex single cell analysis single molecule single nucleus RNA-sequencing single-cell RNA sequencing therapeutic development therapeutic target transcriptome transcriptome sequencing transcriptomics

项目摘要

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.

概括急性肾损伤 (AKI) 具有广泛的后果，从恢复到长期转变为慢性肾脏疾病（CKD）。 2000 年至 2014 年间，AKI 住院人数从每 1000 人 3.5 人增加到 11.7 人人。因 AKI 住院的 66 岁及以上医疗保险患者有 35% 的累积概率一年内反复 AKI 住院，28% 将在同一时间范围内被诊断为 CKD。男性发生 AKI 和进展性 CKD 的风险较高，尽管其机制尚不明确明白了。在小鼠中，雄性小鼠也表现出对 AKI 的高度脆弱性。最近的单细胞RNA-seq 麦克马洪和金小组的研究强调了基因表达的显着差异近端小管段（肾单位最容易发生 AKI 的区域）中的性别。初步研究汉弗莱斯和麦克马洪实验室使用单核测序确定了一种细胞类型轻度至重度 AKI 后近端小管细胞修复失败 (FR-PTC) 纤维化特征。据推测，FR-PTC 会导致 AKI 后进行性肾病。这个提议中心假设是理解 AKI 反应中的性别差异，以及应用遗传方法可靶向 FR-PTC 的促炎特性并消除肾病后的 FR-PTC 修复，将是最终有利于 AKI 后患者预后的有效途径。为此，我们集合了具有先前合作经验的互补团队：Humphreys（华盛顿大学）、Kim （宾夕法尼亚大学）和麦克马洪（南加州大学）。所有团队成员都有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) 和单核染色质修复近端小管失败在雄性和雌性小鼠模型中进行的可及性研究 (scATAC-seq) 检查人类肾脏的关键发现活检。在特定目标 2 中：我们将协调特定目标 1 中生成的多模式数据集，以促进广大研究界查看和询问这些数据。小组对这些数据的挖掘将重点关注确定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：AKI 后男性肾脏的不良后果是由 FR-PTC 中的 NF-kB 通路成分 Nfkb1 和 TNIK 驱动，从基因上消除这些成分的作用基因。我们将为社区生成并验证一种新的转基因小鼠资源，使遗传 FR-PTC 的修改和消除。我们将确定 FR-PTC 去除是否有利正如我们预测的那样，AKI 后进行性肾脏疾病的结果。

项目成果

期刊论文数量（21）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

Kidney and organoid single-cell transcriptomics: the end of the beginning.

肾脏和类器官单细胞转录组学：开始的结束。

DOI：
发表时间：
2020-02
期刊：
影响因子：
0
作者：
Wilson, Parker C;Humphreys, Benjamin D
通讯作者：
Humphreys, Benjamin D

Multi-omics integration in the age of million single-cell data.

百万单细胞数据时代的多组学整合。

DOI：
发表时间：
2021-11
期刊：
影响因子：
0
作者：
Miao, Zhen;Humphreys, Benjamin D;McMahon, Andrew P;Kim, Junhyong
通讯作者：
Kim, Junhyong

Tubular Epithelial Cell HMGB1 Promotes AKI-CKD Transition by Sensitizing Cycling Tubular Cells to Oxidative Stress: A Rationale for Targeting HMGB1 during AKI Recovery.

管状上皮细胞 HMGB1 通过使循环管状细胞对氧化应激敏感来促进 AKI-CKD 转变：AKI 恢复期间靶向 HMGB1 的基本原理。

DOI：
发表时间：
2023-03-01
期刊：
影响因子：
0
作者：
Zhao, Zhi Bo;Marschner, Julian A;Iwakura, Takamasa;Li, Chenyu;Motrapu, Manga;Kuang, Meisi;Popper, Bastian;Linkermann, Andreas;Klocke, Jan;Enghard, Philipp;Muto, Yoshiharu;Humphreys, Benjamin D;Harris, Helena Erlandsson;Romagnani, Paola;Ander
通讯作者：
Ander

The 25th Anniversary of the American Society of Clinical Investigation's Korsmeyer Award.

美国临床研究学会科斯梅尔奖颁发 25 周年。

DOI：
发表时间：
2023-02-15
期刊：
影响因子：
0
作者：
Humphreys; Benjamin D
通讯作者：
Benjamin D

Lineage Tracing and Single-Nucleus Multiomics Reveal Novel Features of Adaptive and Maladaptive Repair after Acute Kidney Injury.

谱系追踪和单核多组学揭示了急性肾损伤后适应性和适应不良修复的新特征。

DOI：
发表时间：
2023-04-01
期刊：
影响因子：
0
作者：
Gerhardt, Louisa M S;Koppitch, Kari;van Gestel, Jordi;Guo, Jinjin;Cho, Sam;Wu, Haojia;Kirita, Yuhei;Humphreys, Benjamin D;McMahon, Andrew P
通讯作者：
McMahon, Andrew P