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.

基因组不稳定和表观遗传控制失调现在都被认为是癌症的标志， 尽管人们对这两种现象的机制知之甚少，但两者都会导致基因表达异常。 促进肿瘤发生的功能的获得和丧失通常受到抑癌基因的抑制。 CpG 位点的高甲基化也经常在全球范围内发生低甲基化。 基因调控元件（例如转录因子结合位点和增强子）的低甲基化可能 导致谱系不适当的“异位”基因表达，并激活致癌途径。 向癌细胞表达的特定基因可形成有吸引力的阳性生物标志物，可用于诊断 测试或治疗的新目标是由于癌症中基因表达缺失而产生的阴性生物标志物。 与高甲基化的作用相反，由于其间接性质和非特异性而存在问题。 塞扎里综合征 (SS) 是一种侵袭性白血病，其影响尚未得到充分研究。 皮肤 T 细胞淋巴瘤 (CTCL) 变异型是研究癌症相关性的良好模型 低甲基化，因为它是低甲基化最严重的 SS 癌症之一，其水平高出 6-8 倍。 退伍军人群体中的发病率，其特点是表观遗传调节剂的频繁突变，包括 我们最近发表了一份基因表达谱。 使用高分辨率微阵列对 SS 中的恶性 T 细胞进行研究，并鉴定了一些高度 过度表达 SS T 细胞 (SS-HEG) 特有的基因，可以作为阳性生物标志物。 还发表了我们的发现，即启动子低甲基化与 PLS3 的过度表达相关， SS T细胞中存在GATA6和TWIST1基因，并且DNA甲基化可以调节PLS3基因的表达。 为了更全面地探索 DNA 甲基化变化可能驱动 SS 异位基因表达的影响，我们 最近获得了 SS T 细胞的全基因组 DNA 甲基化谱，我们的初步数据表明 额外的 SS-HEG 在 SS T 细胞中显着低甲基化，表明 DNA 低甲基化可能 额外的初步数据表明 DNA 甲基化可能导致这些基因的过度表达。 也有助于蕈样肉芽肿 (MF) 的异位基因表达，MF 占 CTCL 的一半以上。 但 MF 中的恶性 T 细胞仅限于皮肤。 SS 中的低甲基化基因，从 MF 肿瘤洗脱的 T 细胞中 CpG 低甲基化也增加。 基于这些观察，我们发现改变的 DNA 甲基化支持致病性和异位性 早期和进展中的 MF/SS 中的基因表达 这将通过以下具体目标来解决。 目标 1. 确定 SS 中异位基因表达的关键表观遗传驱动因素。 全基因组 DNA 甲基化检测将绘制 SS T 细胞中差异甲基化和基因表达的图谱 目标 2. 识别有用的 SS-HEG。 SS 和 MF 肿瘤洗脱 T 细胞的 DNA 甲基化谱将是 MF 疾病严重程度的生物标志物。 比较以确定在两个谱系中差异甲基化的 SS-HEG 将在中进行检查。 从早期和晚期 MF 中洗脱病变 T 细胞，以识别阶段相关的生物标志物。目标 3. 识别 SS-HEG。 驱动 MF/SS 进展的因素将在进展者和非进展者 A 中进行纵向检查。 我们方法的一个新颖之处是对静息和激活的 T 细胞进行 RNA 测序，因此 DNA 甲基化可能与基础基因表达和激活的许可性相关。 拟议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 这可以使退伍军人能够更早地诊断出 CTCL，从而避免多年的不当治疗。 该研究计划还将深入了解 CTCL 的退伍军人。 发病机制，并生成用于研究皮肤源性 MF T 细胞的实验模型。