The role of gene enhancer elements in colon cancer

基因增强子元件在结肠癌中的作用

• 批准号: 10541884
• 负责人: Paul Joseph Tesar
• 金额: $ 36.16万
• 依托单位: CASE WESTERN RESERVE UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2012
• 资助国家: 美国
• 起止时间: 2012-04-01 至 2023-12-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10541884
• 关键词: Adult; American; Award; Binding; Biological Assay; Biological Process; CRISPR/Cas technology; Cancer Etiology; Carcinoma; Cell physiology; Cells; Cessation of life; ChIP-seq; Chromatin; Colon; Colon Carcinoma; Colonic Neoplasms; Colorectal Cancer; DNA Sequence Alteration; DNase I hypersensitive sites sequencing; Development; Disease Progression; Embryonic Development; Enhancers; Epigenetic Process; Event; Foundations; Gene Targeting; Genes; Genetic Enhancer Element; Genetic Transcription; Goals; Grant; Growth; Histones; Human; Individual; Intestines; KRAS2 gene; Knowledge; MADH4 gene; Maintenance; Malignant - descriptor; Malignant Neoplasms; Mediating; Messenger RNA; Microsatellite Instability; Mismatch Repair Deficiency; Modeling; Mus; Mutate; Mutation; Normal Cell; Oncogenes; Organoids; Patients; Pattern; Play; Preventive measure; Recurrence; Risk; Role; Sampling; Shapes; Signal Transduction; Site; Small Interfering RNA; Somatic Mutation; Specific qualifier value; Switch Genes; System; TP53 gene; Testing; Therapeutic; Transcriptional Activation; Tumor Suppressor Proteins; Tumorigenicity; Variant; Xenograft procedure; adenoma; colon cancer cell line; colon carcinogenesis; effective therapy; epigenetic regulation; epigenome; genome editing; insertion/deletion mutation; insight; knock-down; mutation correction; neoplastic cell; overexpression; programs; targeted treatment; therapeutic target; transcription factor; tumor; tumor growth; tumorigenesis

PROJECT(SUMMARY/ABSTRACT! Colorectal cancer (CRC) is associated with the deaths of over 50,000 adult Americans annually. In the previous award period, we showed that in addition to genetic mutation, disease progression is accompanied by epigenetic changes at gene enhancer elements that switch genes on and off. We term these Variant Enhancer Loci, or VELs. Remarkably, colon tumors from different individuals show a common pattern of enhancers that are recurrently activated across patient samples. These recurrently activated enhancers constitute a signature of CRC. In this competing renewal application, we will investigate three non-mutually exclusive hypotheses to uncover the mechanism by which these signature VELs form in CRC. Specific Aim 1 tests the hypothesis that the VELs are a direct consequence of mutations in canonical CRC oncogenes and tumor suppressors. This hypothesis will be tested through H3K27ac ChIP-seq analysis of the enhancer epigenome in human intestinal organoids in which each of known CRC driver genes were sequentially mutated via CRISPR/Cas9 to recapitulate the adenoma- carcinoma sequence predicted by the Vogelgram. Specific Aim 2 tests the hypothesis that transcription factors drive formation of the signature VELs. This hypothesis will be tested through knockdown and overexpression of transcription factors that bind to the signature VELs in CRC cell lines and intestinal organoid models, followed by analysis of chromatin at CRC signature VELs. Specific Aim 3 tests the hypothesis that somatic indel mutations in enhancer elements drive VEL formation. CRISPR-Cas9 genome editing strategies will be used to correct or introduce candidate enhancer-creating indel mutations in CRC cell lines, followed by functional analysis of enhancer activity. Lastly, we propose a fourth Aim to assess whether VELs are required for tumorigenicity of CRC. CRISPR-Cas9-based strategies will be used to disrupt signature VELs in CRC cell lines, followed by quantification of their growth in mouse xenografts relative to unedited control cells. We expect to gain fundamental insights to epigenetic enhancer dysregulation as a root cause of CRC tumorigenesis that could lay the foundation for targeted therapies for patients. !

项目（摘要/摘要！ 结直肠癌（CRC）每年与超过50，000名成年美国人的死亡相关。 在之前的颁奖期间，我们发现除了基因突变，疾病 进展伴随着基因增强子元件的表观遗传变化， 基因开关我们将这些变体增强子基因座称为VEL。值得注意的是，结肠肿瘤 显示出一种共同的增强子模式， 在病人样本中。这些反复激活的增强子构成CRC的特征。在 这个竞争性的更新应用程序，我们将调查三个不相互排斥的假设 揭示CRC中这些签名VEL形成的机制。具体目标1测试 VEL是典型CRC突变的直接结果的假设 癌基因和肿瘤抑制因子。该假设将通过H3 K27 ac ChIP-seq进行检验 分析人肠类器官中的增强子表观基因组，其中每种已知的CRC 驱动基因通过CRISPR/Cas9顺序突变以重现腺瘤- 由Vogelgram预测的癌序列。具体目标2检验假设， 转录因子驱动签名VEL的形成。这一假设将得到检验 通过敲低和过表达与标记VEL结合的转录因子 在CRC细胞系和肠类器官模型中，随后分析CRC中的染色质 签名VEL。具体目的3测试增强子中的体细胞插入缺失突变的假设。 元素驱动VEL形成。CRISPR-Cas9基因组编辑策略将用于纠正 或在CRC细胞系中引入候选增强子-产生indel突变，随后 增强子活性的功能分析。最后，我们提出了第四个目标，以评估是否 CRC的致瘤性需要VEL。基于CRISPR-Cas9的策略将用于 破坏CRC细胞系中的特征VEL，然后定量其在小鼠中的生长 相对于未编辑的对照细胞的异种移植物。我们希望获得基本的见解， 表观遗传增强子失调是CRC肿瘤发生的根本原因， 为患者提供靶向治疗的基础。 !

项目成果

Upregulation of Glucose-Regulated Protein 78 in Metastatic Cancer Cells Is Necessary for Lung Metastasis Progression.

• DOI: 10.1016/j.neo.2016.09.001
• 发表时间: 2016-11
• 期刊: NEOPLASIA
• 影响因子: 4.8
• 作者: Lizardo, Michael M.;Morrow, James J.;Miller, Tyler E.;Hong, Ellen S.;Ren, Ling;Mendoza, Arnulfo;Halsey, Charles H.;Scacheri, Peter C.;Helman, Lee J.;Khanna, Chand
• 通讯作者: Khanna, Chand

ZNF143 provides sequence specificity to secure chromatin interactions at gene promoters.

• DOI: 10.1038/ncomms7186
• 发表时间: 2015-02-03
• 期刊: NATURE COMMUNICATIONS
• 影响因子: 16.6
• 作者: Bailey, Swneke D.;Zhang, Xiaoyang;Desai, Kinjal;Aid, Malika;Corradin, Olivia;Iari, Richard Cowper-Sal;Akhtar-Zaidi, Batool;Scacheri, Peter C.;Haibe-Kains, Benjamin;Lupien, Mathieu
• 通讯作者: Lupien, Mathieu

H3K4me3 inversely correlates with DNA methylation at a large class of non-CpG-island-containing start sites.

• DOI: 10.1186/gm346
• 发表时间: 2012-05-28
• 期刊: Genome medicine
• 影响因子: 12.3
• 作者: Balasubramanian D;Akhtar-Zaidi B;Song L;Bartels CF;Veigl M;Beard L;Myeroff L;Guda K;Lutterbaugh J;Willis J;Crawford GE;Markowitz SD;Scacheri PC
• 通讯作者: Scacheri PC

12th International CHARGE syndrome conference proceedings.

第十二届国际 CHARGE 综合征会议论文集。

• DOI: 10.1002/ajmg.a.37544
• 发表时间: 2016
• 期刊: American journal of medical genetics. Part A
• 作者: Martin,DonnaM;Salem-Hartshorne,Nancy;Hartshorne,TimothyS;Scacheri,PeterC;Hefner,MargaretA
• 通讯作者: Hefner,MargaretA

Combinatorial effects of multiple enhancer variants in linkage disequilibrium dictate levels of gene expression to confer susceptibility to common traits.

• DOI: 10.1101/gr.164079.113
• 发表时间: 2014-01
• 期刊: Genome research
• 影响因子: 7
• 作者: Corradin O;Saiakhova A;Akhtar-Zaidi B;Myeroff L;Willis J;Cowper-Sal lari R;Lupien M;Markowitz S;Scacheri PC
• 通讯作者: Scacheri PC