Scleroderma Subtyping from Fresh and Archived Biopsies using NextGen Sequencing

使用 NextGen 测序从新鲜和存档的活检中进行硬皮病亚型分析

基本信息

批准号：
8200724
负责人：
MICHAEL W FANGER
金额：
$ 53.54万
依托单位：
CELDARA MEDICAL, LLC
依托单位国家：
美国
项目类别：
财政年份：
2011
资助国家：
美国
起止时间：
2011-09-06 至 2013-09-05
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/8200724
关键词：
Affect American Archives Autoimmune Diseases Biochemical Pathway Biological Markers Biopsy Biopsy Specimen Blood Vessels Boston Caregivers Clinical Clinical Data Clinical Markers Clinical Trials Collaborations Collection Complex Cost Analysis DNA Microarray Chip Data Data Collection Databases Diagnosis Diagnostic Disease Drug Design Fibrosis Formalin Freezing Gene Expression Gene Expression Profile Gene Expression Profiling Genes Genomics Goals Heterogeneity Immune System and Related Disorders Institution Lead Measurement Measures Medical Methods Microarray Analysis Molecular Profiling Outcome Outcome Measure Paraffin Embedding Patients Pharmaceutical Preparations Phase Phenotype Preparation Process Protocols documentation RNA RNA Degradation Rare Diseases Reading Sample Size Sampling Scleroderma Sequence Analysis Services Severity of illness Skin Solutions Systemic Scleroderma Techniques Technology Testing Therapeutic Time Tissues Training Universities Validation Work base clinical phenotype clinical research site cost disorder subtype drug development effectiveness trial genetic analysis improved insight killings method development non-compliance novel outcome forecast patient population sample collection skin disorder trend

项目摘要

DESCRIPTION (provided by applicant): Systemic sclerosis (SSc) is an autoimmune disease that presents with a heterogeneous and complex phenotype. Major manifestations of the disease are skin fibrosis, vascular dysfunction, and immune system activation. There are no validated diagnostic markers. There are no curative treatments. One in three patients dies within 10 years of diagnosis. Some drugs (developed for other indications) are currently in clinical trials however, outcome measures such as the modified Rodnan skin score are inadequate, and heterogeneity in patient populations hinders trial effectiveness since only a subset of patients is likely to respond to any given drug. Celdara Medical is segmenting this heterogeneity or "subtyping" SSc by associating gene signatures with clinical phenotypes to provide a quantitative measure for patient prognosis, assessment of efficacy during clinical trials, and insight into disease mechanisms which will lead to drugs designed for each SSc subtype. Because SSc is a rare disease, skin biopsies are in high demand and longitudinal accrual of fresh biopsy samples for DNA microarray analysis is slow, which severely hampers clinical validation of the test. A retrospective analysis of archived formalin fixed paraffin embedded (FFPE) tissue blocks from a single clinical site is one solution to this problem, however, the degree of RNA degradation in these samples (vis- `-vis fresh frozen (FF) samples) makes them unsuitable for DNA microarray analysis. We therefore propose to develop a robust SSc subsetting method using measurement of gene expression by short read ultra high-throughput (UHTP) sequencing from FFPE and FF skin biopsies to predict SSc subtype. In Phase I we will accomplish the following Aims: Aim 1. Compare the utility of UHTS to NanoString technology for the measurement of gene expression profiles from FFPE and FF samples. Aim 2. Increase the quality and sample size of clinical longitudinal data using either UHTS or Nanostring and analyze the clinical covariates associated with the intrinsic subsets. Successful completion of the work described herein will: 1. allow for clinical validation, 2. simplify clinical implementation, 3. reduce the cost of patient subtyping, and 4. dramatically and quickly expand the gene expression sample database through inclusion of archived samples, potentially leading to novel genomics- based insights into this terrible and complex disease. PUBLIC HEALTH RELEVANCE: Scleroderma is a poorly-understood disease which affects 300,000 Americans, and kills 1/3 of those afflicted within 10 years of diagnosis. Genetic analyses of patient samples have revealed subtypes of the disease, each with different prognoses, and each suggesting different potential therapeutics. The goal of this project is to simplify the currently complex sample preparation protocol while improving the robustness and decreasing the cost of the genetic analyses.

描述（由申请人提供）：系统性硬化症（SSc）是一种自身免疫性疾病，具有异质性和复杂的表型。该疾病的主要表现是皮肤纤维化、血管功能障碍和免疫系统激活。没有经过验证的诊断标记物。没有治愈方法。三分之一的患者在诊断后 10 年内死亡。一些药物（为其他适应症开发）目前正在进行临床试验，然而，结果测量（例如改良的罗德南皮肤评分）不足，并且患者群体的异质性阻碍了试验的有效性，因为只有一小部分患者可能对任何给定药物有反应。 Celdara Medical 正在通过将基因特征与临床表型相关联来细分这种异质性或“亚型”SSc，从而为患者预后提供定量测量、临床试验期间的疗效评估以及深入了解疾病机制，从而为每种 SSc 亚型设计药物。由于 SSc 是一种罕见疾病，因此对皮肤活检的需求量很大，而且用于 DNA 微阵列分析的新鲜活检样本的纵向积累速度很慢，这严重阻碍了该测试的临床验证。对单个临床站点存档的福尔马林固定石蜡包埋 (FFPE) 组织块进行回顾性分析是解决此问题的一种方法，但是，这些样本中 RNA 降解的程度（相对于新鲜冷冻 (FF) 样本）使得它们不适合 DNA 微阵列分析。因此，我们建议开发一种稳健的 SSc 子集方法，通过对 FFPE 和 FF 皮肤活检进行短读超高通量 (UHTP) 测序来测量基因表达，以预测 SSc 亚型。在第一阶段，我们将实现以下目标：目标 1. 比较 UHTS 与 NanoString 技术在测量 FFPE 和 FF 样品的基因表达谱方面的效用。目标 2. 使用 UHTS 或 Nanostring 提高临床纵向数据的质量和样本量，并分析与内在子集相关的临床协变量。成功完成本文所述的工作将： 1. 允许临床验证， 2. 简化临床实施， 3. 降低患者亚型分型的成本，以及 4. 通过纳入存档样本，显着且快速地扩展基因表达样本数据库。从而对这种可怕而复杂的疾病产生基于基因组学的新见解。公共健康相关性：硬皮病是一种人们知之甚少的疾病，影响着 300,000 名美国人，并在诊断后 10 年内导致 1/3 的患者死亡。对患者样本的遗传分析揭示了该疾病的亚型，每种亚型都有不同的预后，并且每种亚型都表明了不同的潜在治疗方法。该项目的目标是简化当前复杂的样品制备方案，同时提高稳健性并降低遗传分析的成本。