Epigenetic Regulation of Differentially Expressed Genes in Cutaneous T Cell Lymphoma

皮肤T细胞淋巴瘤差异表达基因的表观遗传调控

• 批准号: 10467983
• 负责人: HENRY Keung WONG
• 金额: --
• 依托单位: CENTRAL ARKANSAS VETERANS HLTHCARE SYS
• 依托单位国家: 美国
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-04-01 至 2024-03-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10467983
• 关键词: Address; Affect; Benign; Binding Sites; Biological; Biological Assay; Biological Markers; Chemicals; Chronic; Clinical; Complex; Consequentialism; Cross-Sectional Studies; Cutaneous T-cell lymphoma; DNA; DNA Methylation; DNA analysis; Data; Databases; Development; Diagnosis; Diagnostic; Diagnostic Specificity; Diagnostic tests; Disease; Disease Progression; Early Diagnosis; Eczema; Enhancers; Enzymes; Epigenetic Process; Etiology; Evolution; Experimental Models; Exposure to; Gene Abnormality; Gene Expression; Gene Expression Profiling; General Population; Genes; Genetic; Genetic Heterogeneity; Genomic Instability; Genomics; Goals; Grant; Health; Hydrocarbons; Hypermethylation; Incidence; Indolent; Inflammation; Inflammatory; Informatics; Lead; Lesion; Life; Malignant - descriptor; Malignant Neoplasms; Maps; Methylation; Military Personnel; Monitor; Mutation; Mycosis Fungoides; Nature; Neoplastic Cell Transformation; Occupational; Oncogenic; Pain; Pathogenesis; Pathogenicity; Pathway interactions; Patients; Pesticides; Play; Process; Prognosis; Prognostic Marker; Pruritus; Psoriasis; Publishing; Quality of life; Regulator Genes; Regulatory Element; Reproducibility; Research; Resolution; Rest; Risk; Risk Factors; Role; Sensitivity Training Groups; Services; Severity of illness; Sezary Syndrome; Signal Transduction; Site; Skin; Sleep disturbances; Study models; T-Cell Lymphoma; T-Lymphocyte; TWIST1 gene; Technology; Training; Tumor Suppressor Genes; Variant; Veterans; advanced disease; base; cancer cell; cancer genome; cell growth; combat; demethylation; diagnostic biomarker; differential expression; effective therapy; emotional distress; epigenetic regulation; experimental study; genome-wide; improved; insight; leukemia; loss of function; mRNA Expression; methylation biomarker; methylome; military veteran; neoplastic; new therapeutic target; novel; overexpression; permissiveness; personalized medicine; prevent; promoter; skin lesion; transcription factor; transcriptome; transcriptome sequencing; treatment strategy; tumor; tumorigenesis

Genomic instability and dysregulated epigenetic control are now both recognized as hallmarks of cancer, although the mechanisms responsible are poorly understood. Both lead to abnormal gene expression, and gains and losses of function that can promote oncogenesis. Tumor suppressor genes are often repressed by hypermethylation of CpG sites. Cancer genomes are also frequently globally hypomethylated. Hypomethylation of gene-regulatory elements, such as transcription factor binding sites and enhancers, may cause lineage-inappropriate “ectopic” gene expression, and activation of oncogenic pathways. Highly expressed genes specific to cancer cells make attractive positive biomarkers that may be useful in diagnostic tests, or new targets for therapy. Negative biomarkers resulting from loss of gene expression in cancer are problematic due to their indirect nature and nonspecificity. In contrast to the role of hypermethylation in cancer, the impact of hypomethylation is very understudied. Sezary syndrome (SS), an aggressive, leukemic variant of cutaneous T cell lymphoma (CTCL) is a good model for studies of cancer-associated hypomethylation because it is one of the most heavily hypomethylated cancers. SS, which has 6-8 fold higher incidence in the Veteran population, is marked by frequent mutations in epigenetic modulators, including enzymes involved in methyation and demethylation of DNA. We recently published a gene expression profiling study of malignant T cells in SS using high resolution microarrays, and identified a number of highly overexpressed genes specific to SS T cells (SS-HEG), that could function as positive biomarkers. We have also published our discovery that promoter hypomethylation is associated with overexpression of PLS3, GATA6, and TWIST1 genes in SS T cells, and that DNA methylation can regulate PLS3 gene expression. To more fully explore the effect of DNA methylation changes that may drive ectopic gene expression in SS, we have recently obtained genome wide DNA methylation profiles for SS T cells. Our preliminary data shows that additional SS-HEG are significantly hypomethylated in SS T cells, suggesting that DNA hypomethylation may contribute to overexpression of these genes. Additional preliminary data indicates that DNA methylation may also contribute to ectopic gene expression in mycosis fungoides (MF). MF represents more than half of CTCL cases, but malignant T cells in MF are limited to the skin. For several coordinately overexpressed and hypomethylated genes in SS, CpG hypomethylation was also increased in T cells eluted from MF tumors. Based on these observations, we hypothesize that altered DNA methylation supports pathogenic and ectopic gene expression in early and progressing MF/SS. This will be addressed with the following specific aims. Aim 1. Identify key epigenetic drivers of ectopic gene expression in SS. Paired transcriptome sequencing and genome-wide DNA methylation assays will map differential methylation and gene expression in SS T cells from the same subject to identify biomarkers of advanced disease. Aim 2. Identify SS-HEG that are useful biomarkers of disease severity in MF. DNA methylation profiles of SS and MF tumor-eluted T cells will be compared to identify SS-HEG differentially methylated in both lineages. Selected SS-HEG will be examined in lesional T cells eluted from early and late MF to identify stage-associated biomarkers. Aim 3. Identify SS-HEG that drive MF/SS progression. SS-HEG will be examined longitudinally in progressors and non-progressors. A novel facet of our approach will be to conduct RNA sequencing on both resting and activated T cells, so DNA methylation may be correlated to both basal gene expression and the permissiveness of activation. The conclusion of the proposed experiments will yield useful gene expression and DNA methylation biomarkers that could enable earlier diagnosis of CTCL in Veterans. This could prevent years of inappropriate therapy for Veterans suffering from CTCL. The research plan will also produce mechanistic insight into CTCL pathogenesis, and generate an experimental model for studies of skin-derived MF T cells.

基因组不稳定性和失调的表观遗传控制现在都被认为是癌症的标志， 尽管负责的机制知之甚少。两者都导致异常基因表达，并且 可以促进肿瘤发生的功能的收益和损失。肿瘤抑制基因通常由 CpG位点的高甲基化。癌症基因组也经常是全球降低甲基化的。 基因调节元件的低甲基化，例如转录因子结合位点和增强子，可能 引起谱系不合适的“异位”基因表达，并激活致癌途径。高度 特异性的癌细胞的基因使可能有用的阳性生物标志物可用于诊断 测试或治疗的新目标。癌症基因表达丧失导致的负生物标志物是 由于其间接的性质和非特异性，有问题。与高甲基化在 癌症，低甲基化的影响是非常了解的。 SEZARY综合征（SS），一种侵略性的白血病 皮肤T细胞淋巴瘤（CTCL）的变异是研究癌症相关的良好模型 低甲基化是因为它是最严重的低甲基化癌症之一。 SS，高6-8倍 退伍军人人口的发病率是表观遗传调节剂中经常突变的特征，包括 参与DNA的甲基化和脱甲基化的酶。我们最近发表了一个基因表达分析 使用高分辨率微阵列研究SS中的恶性T细胞，并确定了许多高度 特异性的SS T细胞（SS-HEG）过表达的基因可以用作阳性生物标志物。我们有 我们的发现还发表了我们的发现，即启动子的甲基化与PLS3的过表达有关 SS T细胞中的GATA6和Twist1基因，DNA甲基化可以调节PLS3基因表达。到 更充分地探索DNA甲基化变化的作用，该变化可能驱动SS中的生态基因表达，我们 最近获得了SS T细胞的基因组宽DNA甲基化谱。我们的初步数据表明 在SS T细胞中，额外的SS-HEG显着降低了甲基化，表明DNA降压甲基化可能 有助于这些基因的过表达。其他初步数据表明DNA甲基化可能 也有助于真菌性真菌基因表达，在真菌病（MF）中。 MF代表CTCL的一半以上 病例，但是MF中的恶性T细胞仅限于皮肤。对于几个协调过表达的 从MF肿瘤洗脱的T细胞中，SS中的低甲基化基因也增加了CpG甲基化。 基于这些观察结果，我们假设改变的DNA甲基化支持致病性和生态 早期和进展的MF/SS中的基因表达。这将以以下特定目标解决。 目标1。确定SS中生态基因表达的关键表观遗传驱动因素。配对的转录组测序和 全基因组DNA甲基化测定将绘制从SS T细胞中的差异甲基化和基因表达 同一主题以识别晚期疾病的生物标志物。目标2。确定有用的SS-HEG MF中疾病严重程度的生物标志物。 SS和MF肿瘤洗脱T细胞的DNA甲基化轮廓将是 相比，在两个谱系中鉴定出不同的甲基化甲基化。选定的SS-HEG将在 病变的T细胞从早期和晚期洗脱，以鉴定与阶段相关的生物标志物。目标3。确定SS-HEG 驱动MF/SS进展。 SS-HEG将在进步者和非培训者中进行纵向检查。一个 我们方法的新方面是在静止和活化的T细胞上进行RNA测序，因此DNA 甲基化可能与碱性基因表达和激活的允许性相关。 提出的实验的结论将产生有用的基因表达和DNA甲基化生物标志物 这可以使退伍军人的CTCL早期诊断。这可以防止多年的不当疗法 患有CTCL的退伍军人。研究计划还将对CTCL产生机械洞察力 发病机理，并生成一个实验模型，用于研究皮肤衍生的MF T细胞。