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: 10152649
• 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/10152649
• 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 肾脏移植为患有末期肾脏疾病的患者提供了最大的生存优势，IS 比透析更具成本效益。肾脏移植的长期生存尚未改善 几十年。抗体介导的排斥（AMR）已被确定为移植衰竭的主要原因。现在， AMR患者的管理在中心之间是不一致的，并且经常失败。我们假设 细胞类型和AMR独有的细胞状态可以通过活检的单细胞RNA测序（SCRNA-SEQ）解决 诊断时从患者中取出的样本。这种方法使用无监督的框架 解剖复杂组织（例如肾脏）内的转录异质性。这允许 使用公正的聚类方法对细胞态和亚群的询问，该方法独立于 以前的知识，可以提供前所未有的解决方案。为了检验我们的假设，我们提出以下内容 目的：在AIM 1中，我们将执行40个研究活检核心（20 AMR和20个非AMR）的SCRNA-SEQ。由此 我们将确定在定义AMR特异性的内皮细胞和抗体分泌细胞中表达的基因 表型。我们通过从人体活检中产生单细胞数据来证明这种方法的可行性 如研究计划中概述的样品。对于AIM 2，我们将使用免疫组织化学来验证这些AMR 一组独立组织样品上的特定标记。对于AIM 3，我们将使用公开可用的Affymetrix 来自具有相关结果数据的肾脏移植活检中的微阵列数据集，以确定哪些细胞类型 与同种异体结果有关。该建议从逻辑上讲是基于首席研究员以前的 研究经验和临床培训。迄今为止，他一直在全职临床移植和 继续他的研究努力在“超过小时”的基础上。尽管他的研究产出和经验 继续增长，他最近发布了一份报告，有关该技术首次成功应用于 人类肾脏活检组织（联合第一作者）。现在，该提案专注于扩大他的科学技能 在单细胞方法，生物信息学和 免疫学。职业发展目标将通过涉及多方面的方法来实现 Benjamin Humphreys博士和由Drs组成的咨询委员会的指导。芭芭拉·墨菲（Barbara Murphy）（移植） 基因组学），菲尔·佩恩（Phil Payne）（生物医学信息和翻译科学），罗布·米特拉（Rob Mitra）（单细胞应用） 保罗·艾伦（Paul Allen）（翻译免疫学），教学课程，科学研究和科学培训 沟通和研究道德。这项工作将在华盛顿大学举行，历史悠久 心理成功的身体科学家。成功完成此职业发展奖将导致 为了更好地了解AMR，导致首席研究者向独立医师的过渡 - 科学家，并提供了坚实的基础，他将向他申请RO1级资金。