Genetics of LAM

LAM 遗传学

基本信息

批准号：
10524041
负责人：
DAVID J. KWIATKOWSKI
金额：
$ 44.97万
依托单位：
BRIGHAM AND WOMEN'S HOSPITAL
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：
2020-12-15 至 2024-11-30
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/10524041
关键词：
AKT1 gene AKT2 gene AKT3 gene Adult Affect Alleles Allelic Imbalance Angiofibroma Angiomyolipoma Bilateral Binding Biological Assay Biological Markers Biopsy Specimen Blood Cell Line Cells ChIP-seq Chromosome 15 Clinical Cyst DNA Data Detection Development Diagnosis Enhancers Epigenetic Process Event FRAP1 gene Face Family member Freezing Frequencies Gene Family Gene Frequency Genes Genetic Genetic Screening Genetic Transcription Growth Human Individual Lesion Lung Lung Lymphangioleiomyomatosis Lymphangioleiomyomatosis Massive Parallel Sequencing Mosaicism Mutation Mutation Analysis Mutation Detection Naphthalene Neoplasms Pathogenesis Pathologic Pathway interactions Patients Plasma Cells Population Prognosis Renal Angiomyolipoma Reporting Research Personnel Respiratory Failure Role Sampling Series Skin Manifestations Somatic Mutation Specimen Subgroup TFE3 gene TSC1 gene TSC1/2 gene TSC2 gene Testing Time Tretinoin United States National Institutes of Health analog apoAI regulatory protein-1 cell free DNA cell type clinical center clinical phenotype diagnostic criteria genome wide association study genome-wide high standard inhibitor lung lesion new technology new therapeutic target novel novel marker overexpression transcription factor transcriptome sequencing treatment response variant detection

项目摘要

Abstract Lymphangioleiomyomatosis is a low grade neoplasm that causes progressive lung destruction, lung cyst formation, and respiratory failure. Bi-allelic mutations in TSC2 (or much less commonly TSC1) have been known as the main genetic driver of LAM in both individuals with TSC as well as sporadic LAM. It has also been thought that the distinction between TSC-LAM and sporadic LAM was well-defined. However, recent studies by PI Kwiatkowski and co-investigator Darling have shown that mosaicism for TSC1/TSC2 is common in adults with TSC-LAM, and associated with a milder clinical phenotype that may be missed in some apparent sporadic LAM patients. In addition, detailed analyses of LAM lung lesions have been able to identify TSC1 or TSC2 mutations in only a fraction of sporadic LAM patients, suggesting the involvement of other genes. Furthermore, a LAM GWAS led by the PI has identified SNPs on chromosome 15 near the transcription factor NR2F2 as having alleles that show association with sporadic LAM. In this proposal, we examine all three of these issues in greater detail. Two of the Aims will use massively parallel sequencing (MPS) and a novel technology we have developed, Multiplex High-sensitivity PCR Assay (MHPA), that is capable of highly sensitive variant detection in TSC2, down to an allele frequency of 0.05%, 10-fold lower than our previous targeted capture assay. In Aim 1, we will determine whether mutations in other mTOR pathway genes and/or MITF family member translocation or amplification cause sporadic LAM in a set of 100 LAM patients. In Aim 2, we will determine whether the presence of TSC2 mutations in cell free (cf) DNA is a biomarker of LAM; and examine the frequency of genetic mosaicism in selected subsets of apparent sporadic LAM patients; simultaneously, also in 100 LAM patients. We will enrich the patients studied for those with singleton TSC lesions, such as hypomelanotic macule (HMM) or facial angiofibroma, or bilateral angiomyolipoma. We will use our new MHPA assay for this analysis. In Aim 3, we will examine the role of NR2F2 in LAM development, by examining allelic imbalance in the H3K27ac ChIP-Seq data, performing NR2F2 ChIP-Seq, using Binding and expression target analysis to infer the genes most likely to have their expression driven by NR2F2, determine if NR2F2 is part of the Core transcription Regulatory Circuitry (CRC) in angiomyolipoma, and assess effects of NR2F2 expression modulation, and treatment with activators and inhibitors in the human angiomyolipoma cell line 621-101.

抽象的淋巴管平滑肌瘤病是一种低度肿瘤，可导致进行性肺破坏、肺囊肿形成和呼吸衰竭。 TSC2（或更不常见的 TSC1）的双等位基因突变已被已知是 TSC 和散发性 LAM 个体中 LAM 的主要遗传驱动因素。它还具有人们认为 TSC-LAM 和零星 LAM 之间的区别是明确的。然而，最近 PI Kwiatkowski 和合作研究员 Darling 的研究表明，TSC1/TSC2 的嵌合现象很常见在患有 TSC-LAM 的成人中，并与较温和的临床表型相关，在一些明显的病例中可能会忽略这种临床表型。散发性 LAM 患者。此外，对 LAM 肺部病变的详细分析已经能够识别 TSC1 或仅一小部分散发性 LAM 患者出现 TSC2 突变，这表明其他基因也参与其中。此外，由 PI 领导的 LAM GWAS 已在转录因子附近的 15 号染色体上发现了 SNP NR2F2 具有与散发性 LAM 相关的等位基因。在本提案中，我们研究了所有三个这些问题更加详细。其中两个目标将使用大规模并行测序（MPS）和一种新颖的我们开发的多重高灵敏度 PCR 检测 (MHPA) 技术能够高度检测 TSC2 中的敏感变异检测，等位基因频率降至 0.05%，比我们之前的低 10 倍靶向捕获测定。在目标 1 中，我们将确定其他 mTOR 通路基因是否发生突变和/或 MITF 家族成员易位或扩增导致 100 名 LAM 患者出现散发性 LAM。在目标 2 中，我们将确定无细胞 (cf) DNA 中 TSC2 突变的存在是否是 LAM 的生物标志物；和检查明显散发的 LAM 患者的选定亚群中遗传嵌合的频率；同时，也在 100 名 LAM 患者中进行了研究。我们将丰富单例 TSC 患者的研究对象病变，如低黑色素斑 (HMM) 或面部血管纤维瘤，或双侧血管平滑肌脂肪瘤。我们将使用我们用于此分析的新 MHPA 测定法。在目标 3 中，我们将通过以下方式研究 NR2F2 在 LAM 开发中的作用：检查 H3K27ac ChIP-Seq 数据中的等位基因不平衡，执行 NR2F2 ChIP-Seq，使用 Binding 和表达目标分析以推断最有可能由 NR2F2 驱动表达的基因，确定是否 NR2F2 是血管平滑肌脂肪瘤核心转录调节电路 (CRC) 的一部分，可评估以下因素的影响人血管平滑肌脂肪瘤细胞中 NR2F2 表达调节以及激活剂和抑制剂的治疗 621-101 行。