Single Cell Analysis of Kidney Transplant Antibody Mediated Rejection

肾移植抗体介导的排斥反应的单细胞分析

• 批准号: 10399506
• 负责人: ANDREW FRANCIS MALONE
• 金额: $ 16.43万
• 依托单位: WASHINGTON UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-07-01 至 2024-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10399506
• 关键词: Advisory Committees; Allografting; Archives; Arteritis; B-Cell Activation; B-Lymphocytes; Bayesian Method; Binding; Bioinformatics; Biopsy; Biopsy Specimen; Candidate Disease Gene; Cell Survival; Cells; Clinical; Communication Research; Complex; Core Biopsy; Data; Data Set; Diagnosis; Diagnostic; Dialysis procedure; Disease; Disease Marker; End stage renal failure; Endothelial Cells; Endothelium; Event; Excision; FYN gene; Failure; Foundations; Functional disorder; Funding; Future; Gene Expression; Gene Expression Profile; Genes; Genetic Transcription; Genomics; Goals; Heterogeneity; Histologic; Hour; Human; IGFBP3 gene; Immune response; Immunoglobulin-Secreting Cells; Immunohistochemistry; Immunology; Inflammatory; Investigation; K-Series Research Career Programs; Kidney; Kidney Transplantation; Knowledge; Link; Machine Learning; Masks; Measurement; Mentors; Methods; Microfluidics; Outcome; Output; Patient-Focused Outcomes; Patients; Phenotype; Physicians; Pilot Projects; Plasma Cells; Population; Principal Investigator; Publishing; Recording of previous events; Reporting; Reproducibility; Research; Research Ethics; Research Personnel; Resolution; Retrieval; Sampling; Scientist; Solid; Source; Specimen; Stains; TNFRSF17 gene; Technology; Testing; Thromboplastin; Time; Tissue Sample; Tissues; Training; Translational Research; Transplantation; Universities; Washington; Work; XBP1 gene; antibody-mediated rejection; base; belimumab; biomedical informatics; career; career development; cell type; cost effective; diagnostic accuracy; donor-specific antibody; experience; experimental study; human data; improved; in vivo; kidney biopsy; novel; novel diagnostics; novel marker; prediction algorithm; predictive modeling; prognostic; protein expression; random forest; single cell analysis; single-cell RNA sequencing; skills; tool; transcriptomics; treatment strategy

PROJECT SUMMARY/ABSTRACT Kidney transplantation offers the greatest survival advantage to patients with end stage kidney disease and is vastly more cost effective than dialysis. Long-term survival of kidney transplants has not improved in recent decades. Antibody mediated rejection (AMR) has been identified as a major cause of transplant failure. Currently, management of patients with AMR is inconsistent among centers and frequently fails. We hypothesize that the cell types and cell states unique to AMR can be resolved by single cell RNA sequencing (scRNA-seq) of biopsy samples taken from patients at the time of diagnosis. This approach uses an unsupervised framework for dissecting transcriptional heterogeneity within complex tissues such as the kidney. This allows for the interrogation of cell states and subpopulations using an unbiased clustering approach that is independent of previous knowledge and can provide unprecedented resolution. To test our hypothesis we propose the following aims: In Aim 1, we will perform scRNA-seq of 40 research biopsy cores (20 AMR and 20 non-AMR). From this data we will identify genes expressed in endothelial cells and antibody secreting cells that define AMR specific phenotypes. We have demonstrated feasibility of this approach by generating single cell data from human biopsy samples as outlined in the research plan. For Aim 2, we will use immunohistochemistry to validate these AMR specific markers on a set of independent tissue samples. For Aim 3, we will use publicly available Affymetrix microarray datasets from kidney transplant biopsies with associated outcomes data to determine which cell types are associated with allograft outcome. This proposal logically builds on the principal investigator’s previous research experience and clinical training. To date he has been working full time in clinical transplantation and continuing his research endeavors on an ‘out of hours’ basis. Despite this his research output and experience continue to grow and he has recently published a report on the first successful application of this technology to human kidney biopsy tissue (co-first author). This proposal now focuses on expanding his scientific skills by attaining additional knowledge and practical research experience in single cell methods, bioinformatics and immunology. The career development goals will be achieved through a multi-faceted approach involving mentoring by Dr. Benjamin Humphreys and an advisory committee consisting of Drs. Barbara Murphy (transplant genomics), Phil Payne (biomedical informatics and translational science), Rob Mitra (single cell applications) and Paul Allen (translational immunology), didactic coursework, scientific investigation, and training in scientific communication and research ethics. This work will take place in Washington University which has a rich history of mentoring successful physician-scientists. Successful completion of this career development award will result in a better understanding of AMR, result in the principal investigator’s transition to an independent physician- scientist, and provide a solid foundation from which he will apply for RO1-level funding.

项目摘要/摘要 肾移植为终末期肾病患者提供了最大的生存优势。 比透析划算得多。近年来，肾移植的长期存活率没有改善。 几十年。抗体介导的排斥反应(AMR)已被认为是移植失败的主要原因。目前， AMR患者的管理在各中心之间不一致，经常失败。我们假设 AMR特有的细胞类型和细胞状态可以通过活检的单细胞RNA测序(scRNA-seq)来分辨 诊断时从患者身上采集的样本。此方法使用无人监督的框架 解剖复杂组织中的转录异质性，如肾脏。这允许 使用独立于以下各项的无偏聚类方法询问细胞状态和子群体 以前的知识，可以提供前所未有的解决方案。为了验证我们的假设，我们提出了以下建议 目的：在目标1中，我们将对40个研究活检核心(20个AMR和20个非AMR)进行scRNA-seq。由此 数据我们将确定在内皮细胞和抗体分泌细胞中表达的定义AMR特异性的基因 表型。我们已经通过从人类活体组织中产生单细胞数据来证明这种方法的可行性 研究计划中概述的样本。对于目标2，我们将使用免疫组织化学来验证这些AMR 一组独立组织样本上的特定标记。对于目标3，我们将使用公开可用的Affymetrix 来自肾移植活检的微阵列数据集和相关的结果数据，以确定哪些细胞类型 与同种异体移植的结果有关。这项建议从逻辑上讲是建立在首席调查员之前的 研究经验和临床培训。到目前为止，他一直全职从事临床移植和 在“下班”的基础上继续他的研究工作。尽管如此，他的研究成果和经验 继续增长，他最近发表了一份报告，首次成功地将这项技术应用于 人肾活检组织(合著者)。这项提议现在专注于通过以下方式扩大他的科学技能 获得单细胞方法、生物信息学和 免疫学。职业发展目标将通过多方面的方法实现，包括 由本杰明·汉弗莱斯博士和由芭芭拉·墨菲博士组成的咨询委员会(移植 基因组学)，Phil Payne(生物医学信息学和翻译科学)，Rob Mitra(单细胞应用) 保罗·艾伦(翻译免疫学)，教学课程，科学研究和科学培训 沟通和研究伦理。这项工作将在历史悠久的华盛顿大学进行 指导成功的内科科学家。成功完成这项职业发展奖的结果是 为了更好地了解AMR，导致首席研究员转变为独立的医生- 科学家，并提供坚实的基础，他将申请RO1级的资金。