A Molecular Case Series: Deep Cellular and Spatial Epigenetic Characterization of Human Colorectal Cancer

分子案例系列：人类结直肠癌的深层细胞和空间表观遗传特征

• 批准号: 10677611
• 负责人: Nathan J. Spix
• 金额: $ 4.67万
• 依托单位: VAN ANDEL RESEARCH INSTITUTE
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-08-01 至 2026-07-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10677611
• 关键词: Aberrant DNA Methylation; Address; Awareness; Bioinformatics; Case Series; Cell division; Cells; Cellularity; Clinical; Clonal Expansion; Collaborations; Colon Carcinoma; Colorectal; Colorectal Cancer; Colorectal Neoplasms; Complex; DNA Methylation; DNA Modification Methylases; DNA Sequence Alteration; DNA mapping; Data; Data Set; Deposition; Development; Disease; Doctor of Philosophy; Early treatment; Environment; Epigenetic Process; Etiology; Event; Evolution; Exhibits; Frequencies; Gene Frequency; Gene Targeting; Genes; Genetic; Genetic Transcription; Goals; Growth; Heterogeneity; Histologic; Human; Hypermethylation; Immune; Individual; Intestinal Polyps; Joints; Knowledge; Laboratories; Large Intestine Carcinoma; Learning; Libraries; Link; Malignant - descriptor; Malignant Neoplasms; Measures; Mediating; Medicine; Mentorship; Methylation; Michigan; Modeling; Molecular; Mucous Membrane; Mutation; Normal tissue morphology; Pattern; Play; Polycomb; Recurrence; Research Training; Resolution; Resources; Role; Sampling; Scientist; Spatial Distribution; System; Techniques; Testing; The Cancer Genome Atlas; Time; Tissue Sample; Tissues; Training; Training Programs; Transcriptional Regulation; Tumor Expansion; Universities; WNT Signaling Pathway; Work; age related; base; bisulfite sequencing; cancer genome; cancer initiation; college; colorectal cancer progression; colorectal cancer treatment; design; driver mutation; experimental study; genetic variant; genome-wide; genomic locus; histological specimens; insight; mouse model; neoplastic cell; permissiveness; programs; promoter; prospective; screening; segregation; single cell analysis; stem cells; tumor; tumor progression; whole genome

PROJECT SUMMARY/ABSTRACT Cancer has long been thought of as a disease caused by genetic mutations that enable a cell to grow out of control. However, there is growing awareness of the importance of epigenetic aberrations – disruptions in the systems that control the transcriptional potential of genes – in cancer initiation and progression. Sufficient levels of DNA methyltransferase activity, which are responsible for the deposition of DNA methylation (an important epigenetic mark), have been shown to be necessary for formation of intestinal polyps in mouse models of colorectal cancer (CRC). Furthermore, hypermethylation of many genetic loci has been noted in CRC tissue samples. These hypermethylated loci are significantly enriched in genes targeted by the polycomb repressive complex (Polycomb Target Genes or PTGs), which play important roles in development and differentiation. Thus, suppression of PTGs by aberrant DNA methylation could contribute to the development and progression of CRC. However, it is unclear when and where these PTG hypermethylation (PTGH) events arise. They may arise as a result of genetic mutations, but studies of the cancer genome have failed to find any mutation linked to PTGH. Also, PTGH events have been found in histologically normal colorectal tissue. Thus, it is possible that PTGH accumulates over time in normal colorectal tissue, with excessive levels of this mark allowing malignant transformation. If this is the case, at least some PTGH events should be found clonally (in every cell of a tumor), because they existed in the founding cell of the tumor. The experiments outlined here are designed to test this model by constructing a detailed map of DNA methylation in human colorectal tumors and adjacent mucosa. Specifically, they aim to test the hypotheses that 1) PTGH exists in tumor-adjacent colorectal mucosa in a spatial and cellular distribution consistent with accumulation over time, and that 2) PTGH events are clonally present within CRC tumors. To achieve these goals, the proposed studies use bulk and single-cell whole-genome bisulfite sequencing techniques to measure genome-wide DNA methylation at single-base resolution. These studies will greatly strengthen our understanding of the cellular and spatial distribution of PTGH in CRC, giving us a better understanding of when and where this mark arises. Ultimately, these findings could help to develop more sensitive screening tests or earlier treatments for colorectal cancer. These studies will be conducted as part of the applicant’s training in a joint MD-PhD program sponsored by Michigan State University College of Human Medicine and Van Andel Institute (VAI). VAI provides a rich environment for research training, combining ample scientific resources with opportunities to learn from world- class scientists in a focused setting. The applicant will receive mentorship from leading experts in the field of DNA methylation, single-cell analysis, and bioinformatics, as well as many opportunities for collaboration, professional development, and continued clinical activity throughout the training program.

项目概要/摘要 长期以来，癌症一直被认为是一种由使细胞生长的基因突变引起的疾病 然而，人们越来越意识到表观遗传畸变的重要性——破坏。 控制基因转录潜力的系统——在癌症的发生和进展中足够。 DNA 甲基转移酶活性水平，其负责 DNA 甲基化的沉积（ 重要的表观遗传标记），已被证明对于小鼠模型中肠息肉的形成是必要的 此外，CRC 组织中许多基因位点高度甲基化。 这些超甲基化位点在多梳抑制性靶向的基因中显着富集。 复合物（多梳靶基因或 PTG），在发育和分化中发挥重要作用。 通过异常 DNA 甲基化抑制 PTG 可能有助于 CRC 的发生和进展。 然而，尚不清楚这些 PTG 超甲基化 (PTGH) 事件可能发生的时间和地点。 癌症是由基因突变引起的，但对癌症基因组的研究未能发现任何与基因突变相关的突变 此外，在组织学正常的结直肠组织中也发现了 PTGH 事件。 PTGH 随着时间的推移在正常结直肠组织中积累，该标记水平过高会导致恶性病变 如果是这种情况，至少应该克隆地发现一些 PTGH 事件（在肿瘤的每个细胞中）， 因为它们存在于肿瘤的创始细胞中，这里概述的实验旨在测试这一点。 通过构建人类结直肠肿瘤和邻近粘膜中 DNA 甲基化的详细图谱来建立模型。 具体来说，他们的目的是测试以下假设：1) PTGH 在空间上存在于肿瘤邻近的结直肠粘膜中。 和细胞分布与随时间的积累一致，并且 2) PTGH 事件是克隆存在的 为了实现这些目标，拟议的研究使用了批量和单细胞全基因组。 亚硫酸氢盐测序技术以单碱基分辨率测量全基因组 DNA 甲基化。 研究将极大地加强我们对结直肠癌中 PTGH 的细胞和空间分布的理解， 最终，这些发现可以帮助我们更好地了解该标记出现的时间和地点。 更敏感的筛查测试或更早的结直肠癌治疗。 这些研究将作为申请人赞助的医学博士-博士联合项目培训的一部分进行 密歇根州立大学人类医学学院和范安德尔研究所 (VAI) 提供了丰富的研究成果。 研究培训环境，将丰富的科学资源与向世界学习的机会相结合 申请人将获得该领域领先专家的指导。 DNA甲基化、单细胞分析和生物信息学，以及许多合作机会， 专业发展，并在整个培训计划中持续进行临床活动。