Cancer Genomics

癌症基因组学

• 批准号: 8349196
• 负责人: Thomas Ried
• 金额: $ 56.34万
• 依托单位: DIVISION OF BASIC SCIENCES - NCI
• 依托单位国家: 美国
• 资助国家: 美国
• 起止时间: 至
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/8349196
• 关键词: 17p; 18q; 20q; 4q34; 6p21.1; 8q24; 8q24.3; Accounting; Address; Affect; Aneuploidy; Cancer Cluster; Cancer Etiology; Cancer cell line; Carcinoma; Cell Cycle Checkpoint; Centrosome; Cervix carcinoma; Cessation of life; Chromosomal Gain; Chromosomal Instability; Chromosomal Rearrangement; Chromosomal translocation; Chromosome Arm; Chromosome Band; Chromosome Breakage; Chromosome Mapping; Chromosome abnormality; Chromosomes; Chromosomes, Human, Pair 13; Chromosomes, Human, Pair 3; Chromosomes, Human, Pair 7; Chromosomes, Human, Pair 8; Chronic Myeloid Leukemia; Clinical; Colon Carcinoma; Colonic Neoplasms; Colorectal; Colorectal Cancer; Complementary DNA; Complex; Cytogenetic Analysis; Cytogenetics; DNA; DNA Sequence Rearrangement; Data; Development; Diagnosis; Diagnostic; Disease; Distant Metastasis; Down-Regulation; Dysplasia; Epithelial; Epithelial Cells; Europe; Event; Evolution; Experimental Models; Gene Cluster; Gene Expression; Gene Expression Profile; Gene Expression Profiling; Genes; Genetic Polymorphism; Genetic Variation; Genome; Genomics; Goals; Hematologic Neoplasms; Heterochromatin; Histones; Human; Human Genome; Impairment; Inherited; Laboratories; Large Intestine Carcinoma; Lead; Lesion; Maintenance; Malignant Neoplasms; Malignant neoplasm of cervix uteri; Maps; Mediating; Metastatic Neoplasm to the Liver; Microarray Analysis; Modeling; Molecular Abnormality; Molecular Cytogenetics; Molecular Profiling; Mus; Mutation; Neoplasm Metastasis; Oligonucleotide Microarrays; Oligonucleotides; Oncogene Activation; Oncogenes; Outcome; PRL gene; Pathway interactions; Philadelphia Chromosome; Positioning Attribute; Primary Neoplasm; RNA Interference; Rectal Tumors; Recurrence; Reporting; Resolution; Risk; Role; Signal Transduction; Site; Solid Neoplasm; Source; Spectral Karyotyping; Staging; Stratification; Surveys; System; TCF7L2 gene; Tissue Harvesting; United States; Variant; WNT Signaling Pathway; Work; arm; base; cancer cell; cancer gene expression; cancer genome; cancer genomics; cancer type; chromosome 4q loss; comparative genomic hybridization; established cell line; improved; loss of function; lymph nodes; mouse model; notch protein; novel; outcome forecast; overexpression; pressure; therapeutic target; transcription factor; tumor; tumorigenesis

Systematic exploration of genomic alterations in colorectal cancer cell lines and their consequences on global gene expression levels: Specific genomic lesions have been identified in hereditary forms of colorectal cancer, however the mechanism responsible for the development of spontaneous colorectal cancer, which accounts for nearly 85% of all cases, remains unknown. These tumors are invariably aneuploid and contain both numerical as well as structural aberrations. While we have previously analyzed the extent to which gross genomic copy number imbalances affect gene expression in primary colon and rectal tumors, the inability to perform chromosome analyses on harvested tissue precluded our ability to look at the affect of structural alterations. We therefore combined Spectral Karyotyping, chromosome and array-based CGH to obtain high resolution mapping of colorectal cancer cell lines commonly utilized as model experimental systems. These results were combined with both centrosome analysis and gene expression profiling to devise a model for the effects of genomic alterations on gene expression leading to the development of colorectal carcinoma. As such, high-resolution aCGH confirmed the preponderance of chromosome breakpoints at sites of copy number variants in the human genome, a novel mechanism of DNA breakage in cancer that we recently described in primary colon carcinomas. Precision mapping of breakpoints and global gene expression profiling facilitated our ability to specifically address the consequences of chromosomal aberrations, both copy number alterations and structural rearrangements, with respect to their affect on gene expression. Although we did identify several instances where genes within the immediate proximity of breakpoints appeared to be preferentially altered in their expression, an event frequently observed in hematologic malignancies, the rearrangements by and large served to mediate a change in the copy number of genomic regions. The large coefficient of correlation (R= 0.69) between genomic copy number and the average expression of all genes mapping within those segments points to a more subtle and complex outcome. We did, however, identify several putative colorectal oncogenes whose high-level genomic amplification correlated with increased gene expression. These will be further explored as potential diagnostic and therapeutic targets. Chromosomal breakpoints in primary colon cancer cluster at sites of structural variants in the genome: Colorectal cancer is the second leading cause of cancer death in Europe and the United States, with about 300,000 new cases and 200,000 deaths each year. Cytogenetic and molecular cytogenetic studies clearly established that the colorectal cancer genome is defined by a specific distribution of genomic imbalances, most prominently gains of chromosomes and chromosome arms 7, 8q, 13, and 20q, as well as losses of chromosomes 4q, 8p, 17p, and 18q. Within the last decade, microarray technology has been extensively applied to survey the cellular transcriptome of common solid tumors, including colorectal cancer, and, for colon cancers, gene expression signatures were subsequently correlated with clinical outcome. However, high-resolution mapping of chromosomal copy number changes has only recently been achieved using BAC or cDNA clone-based arrays. Chromosome 8q is one of the most frequently gained chromosomal arms in colorectal cancers, and it is conceivable that it contains more oncogenes than just the MYC oncogene, which maps to chromosome band 8q24.21. A potential role of chromosome 8q for the development of lymph node metastases has been previously reported, and overexpression of a gene, PRL-3, that maps to chromosome 8q24.3 has been implied in the development of liver metastases. Moreover, the 8q24 locus contains SNPs that are associated with an increased risk for the development of colon cancer. Recently, a new class of genetic variation among human has become recognized as a major source of genetic diversity. Termed structural variations, these polymorphisms can present themselves as copy number variants (CNVs) and segmental duplications, which can be a CNV, but are not necessarily so. These polymorphisms can induce chromosomal rearrangements. One of our previous analyses of chromosomal aberrations in cell lines established from different carcinomas indicated that genomic copy number changes can be triggered by jumping translocations, many of which originated in the pericentromeric heterochromatin of several chromosomes. These regions frequently contain segmental duplications and other structural variants of the genome. Taken together, these data enticed us to systematically explore the genomic aberration profile of chromosome 8 and the potential involvement of structural variants of the human genome in the genesis of chromosomal aberrations in this common cancer. We therefore established a high-resolution map of genomic copy number changes in 51 primary colon carcinomas using comparative genomic hybridization on both a BAC-based genomic tiling array for chromosome 8 and, for a subset of those, using a 185K oligonucleotide platform for whole genome coverage. This analysis confirmed the dominant role of this chromosome. Unexpectedly, the position of breakpoints suggested co-localization with structural variants in the human genome. In order to map these sites with increased resolution and to extend the analysis to the entire genome, we analyzed a sub-set of these tumors (n=32) by comparative genomic hybridization on an 185K oligonucleotide array platform. Our comprehensive map of the colon cancer genome confirmed recurrent and specific low-level copy number changes of chromosomes 7, 8, 13, 18, and 20, and unveiled additional, novel sites of genomic imbalances including amplification of a histone gene cluster on chromosome 6p21.1-21.33 and deletions on chromosome 4q34-35. The systematic comparison of segments of copy number change with gene expression profiles showed that genomic imbalances directly affect average expression levels. Strikingly, we observed a significant association of chromosomal breakpoints with structural variants in the human genome: 41 per cent of all copy number changes occurred at sites of such copy number variants (p<2.2e-16). Such an association has not been described before and reveals a yet underappreciated plasticity of the colon cancer genome; it also points to potential mechanisms for the induction of chromosomal breakage in cancer cells. The systematic integration of genomic copy number changes with gene expression profiles in colorectal carcinomas revealed 44 highly overexpressed genes mapping to localized amplicons on chromosome 13, which is recurrently gained. RNA interference based silencing identified eight candidates whose loss of function resulted in viability reduction of at least 20% in colorectal cancer cell lines. Global expression profiles, established for each gene following RNAi defined their functional space. One candidate, LNX2, is involved in regulating notch signaling; silencing LNX2 resulted in reduced NOTCH levels, in downregulation of the transcription factor TCF7L2, and in markedly reduced WNT-signaling. Genomic amplification of chromosome 13 and overexpression of LNX2 therefore constitutively activates the WNT-pathway, supporting evidence for a NOTCH-WNT axis in colorectal cancer.

系统性探索结直肠癌细胞系的基因组改变及其对整体基因表达水平的影响：在遗传性结直肠癌中已发现特定的基因组病变，但自发性结直肠癌的发生机制（占近 85%）所有案件中，仍然未知。这些肿瘤总是非整倍体，并且包含数字和结构畸变。虽然我们之前已经分析了总基因组拷贝数不平衡对原发性结肠和直肠肿瘤中基因表达的影响程度，但无法对收获的组织进行染色体分析使我们无法研究结构改变的影响。因此，我们结合了光谱核型分析、染色体和基于阵列的 CGH，以获得通常用作模型实验系统的结直肠癌细胞系的高分辨率图谱。这些结果与中心体分析和基因表达谱相结合，设计了一个模型，用于研究基因组改变对基因表达的影响，从而导致结直肠癌的发展。因此，高分辨率 aCGH 证实了人类基因组中拷贝数变异位点上染色体断裂点的优势，这是我们最近在原发性结肠癌中描述的癌症 DNA 断裂的一种新机制。断点和全局基因表达谱的精确定位有助于我们专门解决染色体畸变的后果，包括拷贝数改变和结构重排，以及它们对基因表达的影响。尽管我们确实发现了几个实例，其中断点附近的基因似乎优先改变其表达，这是在血液恶性肿瘤中经常观察到的事件，但重排总体上有助于介导基因组区域拷贝数的变化。基因组拷贝数与这些片段内所有基因的平均表达之间的巨大相关系数（R = 0.69）表明了更微妙和复杂的结果。然而，我们确实鉴定了几种假定的结直肠癌基因，其高水平基因组扩增与基因表达增加相关。这些将作为潜在的诊断和治疗靶点得到进一步探索。 原发性结肠癌的染色体断点聚集在基因组结构变异位点：结直肠癌是欧洲和美国癌症死亡的第二大原因，每年约有 300,000 例新发病例和 200,000 例死亡。细胞遗传学和分子细胞遗传学研究清楚地表明，结直肠癌基因组是由基因组失衡的特定分布定义的，最显着的是染色体和染色体臂 7、8q、13 和 20q 的增加，以及染色体 4q、8p、17p 的丢失和 18q。在过去的十年中，微阵列技术已广泛应用于调查常见实体瘤（包括结直肠癌）的细胞转录组，并且对于结肠癌，基因表达特征随后与临床结果相关。然而，最近才使用基于 BAC 或 cDNA 克隆的芯片实现了染色体拷贝数变化的高分辨率图谱。 8q 染色体是结直肠癌中最常见的染色体臂之一，可以想象，它包含的癌基因不仅仅是 MYC 癌基因（映射到染色体带 8q24.21）。先前已报道过 8q 染色体在淋巴结转移发展中的潜在作用，并且映射到染色体 8q24.3 的基因 PRL-3 的过度表达已暗示在肝转移的发展中。此外，8q24 位点包含与结肠癌发生风险增加相关的 SNP。最近，人类中一类新的遗传变异已被认为是遗传多样性的主要来源。这些多态性被称为结构变异，它们可以表现为拷贝数变异（CNV）和片段重复（可以是 CNV，但不一定如此）。这些多态性可以诱导染色体重排。我们之前对不同癌症建立的细胞系中染色体畸变的一项分析表明，跳跃易位可以触发基因组拷贝数变化，其中许多起源于几条染色体的着丝粒周围异染色质。这些区域经常包含基因组的片段重复和其他结构变异。总而言之，这些数据促使我们系统地探索 8 号染色体的基因组畸变谱，以及人类基因组的结构变异在这种常见癌症染色体畸变的发生中的潜在参与。因此，我们使用基于 BAC 的 8 号染色体基因组平铺阵列上的比较基因组杂交，以及使用全基因组的 185K 寡核苷酸平台，建立了 51 个原发性结肠癌的基因组拷贝数变化的高分辨率图谱。覆盖范围。该分析证实了该染色体的主导作用。出乎意料的是，断点的位置表明与人类基因组中的结构变异共定位。为了以更高的分辨率绘制这些位点并将分析扩展到整个基因组，我们通过在 185K 寡核苷酸阵列平台上进行比较基因组杂交来分析这些肿瘤的子集 (n=32)。我们的结肠癌基因组综合图谱证实了 7、8、13、18 和 20 号染色体反复出现的特定低水平拷贝数变化，并揭示了其他新的基因组失衡位点，包括 6p21 号染色体上组蛋白基因簇的扩增.1-21.33 和染色体 4q34-35 上的缺失。拷贝数变化片段与基因表达谱的系统比较表明，基因组失衡直接影响平均表达水平。引人注目的是，我们观察到染色体断点与人类基因组结构变异之间存在显着关联：所有拷贝数变化的 41% 发生在此类拷贝数变异位点 (p<2.2e-16)。这种关联以前从未被描述过，并且揭示了结肠癌基因组的可塑性尚未被充分认识。它还指出了诱导癌细胞染色体断裂的潜在机制。结直肠癌中基因组拷贝数变化与基因表达谱的系统整合揭示了 44 个高度过表达的基因，这些基因映射到 13 号染色体上的局部扩增子，这是反复获得的。基于 RNA 干扰的沉默确定了 8 个候选者，其功能丧失导致结直肠癌细胞系活力降低至少 20%。 RNAi 后为每个基因建立的全局表达谱定义了它们的功能空间。 LNX2 是候选者之一，参与调节 Notch 信号传导；沉默LNX2会导致NOTCH水平降低、转录因子TCF7L2下调以及WNT信号传导显着减少。因此，13 号染色体的基因组扩增和 LNX2 的过度表达会组成性激活 WNT 通路，支持结直肠癌中 NOTCH-WNT 轴的证据。