Genetics of LAM

LAM 遗传学

• 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
• 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

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.

摘要 淋巴管肌瘤病是一种低级别肿瘤，可导致进行性肺破坏、肺囊肿。 队形和呼吸衰竭。TSC2(或不太常见的TSC1)的双等位基因突变 在患有TSC和散发性LAM的个体中被认为是LAM的主要基因驱动因素。它还 一直认为TSC-LAM和零星LAM之间的区别是明确的。然而，最近 Pi Kwiatkowski和合作者Darling的研究表明，TSC1/TSC2的嵌合体很常见 在患有TSC-LAM的成年人中，并与一些明显的可能被遗漏的较轻微的临床表型有关 散发性LAM患者。此外，对LAM肺部病变的详细分析已经能够确定TSC1或 仅在一小部分散发性LAM患者中存在TSC2突变，提示其他基因参与其中。 此外，由PI领导的LAM GWA已经在15号染色体上靠近转录因子的位置发现了SNPs NR2F2具有与散发性LAM相关的等位基因。在这份提案中，我们检查了所有三个 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)和一个新的 我们开发的技术，多重高敏PCR分析(MHPA)，能够高度 在TSC2中检测到敏感的变异，等位基因频率降至0.05%，比之前的低10倍 靶向捕获试验。在目标1中，我们将确定其他mTOR途径基因和/或 MITF家族成员易位或扩增导致100例LAM患者中的散发性LAM。在目标2中， 我们将确定无细胞DNA中TSC2突变的存在是否为LAM的生物标志物；以及 检查在明显的散发性LAM患者中选择的亚群中的遗传嵌合体频率； 同时，也有100例LAM患者。我们将丰富针对单胎TSC患者的研究。 病变，如黑素性黄斑(HMM)或面部血管纤维瘤，或双侧血管肌脂肪瘤。我们将使用 我们新的MHPA分析方法。在目标3中，我们将研究NR2F2在LAM发展中的作用，通过 检查H3K27ac芯片序列数据中的等位基因不平衡，执行NR2F2芯片序列，使用绑定和 表达靶点分析，以推断最有可能由NR2F2驱动表达的基因，确定是否 NR2F2是血管肌脂肪瘤核心转录调控电路(CRC)的一部分，并评估 NR2F2在人血管平滑肌脂肪瘤细胞中的表达调控及激活剂和抑制剂的作用 621-101线。