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: 10015553
• 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/10015553
• 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; Population; Process; 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; neoplastic; new therapeutic target; novel; outcome forecast; 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， 尽管人们对这一机制知之甚少。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。肿瘤抑制基因通常被 CpG位点的超甲基化。癌症基因组也经常在全球范围内低甲基化。 基因调控元件的低甲基化，如转录因子结合位点和增强子， 导致谱系不适当的“异位”基因表达，以及致癌途径的激活。高度 表达的癌细胞特异性基因是有吸引力的阳性生物标志物， 测试或新的治疗目标。癌症中基因表达缺失导致的阴性生物标志物是 由于其间接性和非特异性而存在问题。与超甲基化在 在癌症中，低甲基化的影响是非常不足的。Sezary综合征（SS）是一种侵袭性白血病， 皮肤T细胞淋巴瘤（CTCL）的变异是一个很好的模型，研究癌症相关的 低甲基化，因为它是最严重的低甲基化癌症之一。SS，其具有6 - 8倍高 退伍军人群体的发病率以表观遗传调节因子的频繁突变为特征，包括 参与DNA甲基化和去甲基化的酶。我们最近发表了一个基因表达谱 使用高分辨率微阵列研究SS中的恶性T细胞，并确定了一些高度相关的T细胞。 过表达的SS T细胞特异性基因（SS-HEG）可作为阳性生物标志物发挥作用。我们有 还发表了我们的发现，即启动子低甲基化与PLS 3的过表达相关， GATA 6和TWIST 1基因在SS T细胞中的表达，DNA甲基化可以调节PLS 3基因的表达。到 为了更全面地探讨DNA甲基化变化对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。我们的初步数据显示， 另外的SS-HEG在SS T细胞中显著低甲基化，表明DNA低甲基化可能 导致这些基因的过度表达。额外的初步数据表明，DNA甲基化可能 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 例，但恶性T细胞MF仅限于皮肤。对于几个协调过表达和 在SS中，CpG低甲基化基因增加，从MF肿瘤洗脱的T细胞中CpG低甲基化也增加。 基于这些观察结果，我们假设DNA甲基化改变支持致病性和异位 早期和进展性MF/SS中的基因表达。这一问题将通过以下具体目标加以解决。 目标1.确定SS异位基因表达的关键表观遗传驱动因素。配对转录组测序和 全基因组DNA甲基化分析将绘制从1999年到2000年的SS T细胞中的差异甲基化和基因表达。 同一受试者来鉴定晚期疾病的生物标志物。目标2.识别有用的SS-HEG MF中疾病严重程度的生物标志物。SS和MF肿瘤洗脱的T细胞的DNA甲基化谱将被分析。 比较以鉴定两个谱系中差异甲基化的SS-HEG。选定的SS-HEG将在 从早期和晚期MF洗脱的损伤T细胞以鉴定阶段相关的生物标志物。目标3.鉴别SS-HEG 推动MF/SS进展。将在进展者和非进展者中纵向检查SS-HEG。一 我们方法的新方面将是对静息和活化的T细胞进行RNA测序，因此DNA 甲基化可能与基础基因表达和活化的容许性相关。的 本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的早期诊断。这可以防止多年的不适当的治疗， 患有CTCL的退伍军人。该研究计划还将产生对CTCL的机理性见解 发病机制，并产生用于研究皮肤来源的MF T细胞的实验模型。