Colorectal Cancer Transcriptome: Effects of Genomic Instability and Aneuploidy

结直肠癌转录组：基因组不稳定性和非整倍性的影响

基本信息

批准号：
9343721
负责人：
Thomas Ried
金额：
$ 98.16万
依托单位：
DIVISION OF BASIC SCIENCES - NCI
依托单位国家：
美国
项目类别：
财政年份：
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/9343721
关键词：
13q 17p 18q 20q Address Affect Aneuploidy Architecture Bypass C57BL/6 Mouse Cancer cell line Carcinoma Cell Line Cell Nucleus Cell model Cells Chromosome Arm Chromosome Positioning Chromosome Territory Chromosome Transfer Chromosome abnormality Chromosomes Chromosomes, Human, Pair 18 Chromosomes, Human, Pair 19 Chromosomes, Human, Pair 7 Code Collaborations Colon Colon Carcinoma Colonic Neoplasms Colorectal Adenocarcinoma Colorectal Cancer Complement Cytogenetics DNA copy number Data Diploidy Disease Down-Regulation Epithelial Epithelial Cells Eukaryota Event Evolution Exhibits Gene Amplification Gene Deletion Gene Expression Gene Expression Profiling Genes Genetic Genetic Transcription Genome Genomic Instability Genomics Goals Homologous Gene Human Human Chromosomes Immune Interphase Laboratories Large Intestine Laser Scanning Confocal Microscopy Maintenance Malignant Neoplasms Maps Mathematics Mediating Mesenchymal Methods Modeling Molecular Cytogenetics Molecular Profiling Mucous Membrane Mus Nature Normal Cell Nuclear Nuclear Structure Nude Mouse Assay Oligonucleotide Microarrays Oncogenes Pathway interactions Pattern Peripheral Phenotype Positioning Attribute Primary Carcinoma Primary Neoplasm Rectal Cancer Rectum Recurrence Role Sampling Series Serum Signal Transduction Solid Neoplasm Staging Structure-Activity Relationship System Thinking Tissues Transcript Trisomy Tumor Biology Tumor Cell Line Tumor Suppressor Genes Tumor-Derived Tumorigenicity Up-Regulation Validation base cancer cell carcinogenesis cell type colon cancer cell line colon tumorigenesis comparative genomic hybridization density design established cell line mouse model novel pre-clinical research study therapeutic target transcriptome tumor tumorigenic

项目摘要

By systematically integrating gene expression profiles and genomic imbalances of carcinomas using comparative genomic hybridization, we could show that DNA copy number gains of recurrently aneuploid chromosomes and chromosome arms 7, 8q, 13q, and 20q, and losses of 17p and 18q correlated significantly with the expression profiles of resident genes. Taken together, our results demonstrate that both, the high-level, significant transcriptional deregulation of specific genes and the average transcript levels of genes residing on aneuploid chromosomes coexist in colorectal adenocarcinomas (and other rumors of epithelial origin). In order to characterize patterns of global transcriptional deregulation in primary colon carcinomas, we performed gene expression profiling of some 300 tumors, including colon and rectum using oligonucleotide microarrays. For most of these tumors, expression profiles were compared to those from matched normal mucosa samples. We established a relationship between specific genomic imbalances, which were mapped for many of the analyzed colon tumors by comparative genomic hybridization, and alterations of global transcriptional activity. Previously, we had conducted a similar analysis of primary rectal carcinomas. The systematic comparison of colon and rectal carcinomas revealed a significant overlap of genomic imbalances and transcriptional deregulation, including activation of the Wnt/b-catenin signaling cascade, suggesting similar pathogenic pathways. 1) Nuclear topography of aneuploid chromosomes and their consequences on transcriptional activity The 3D-position of chromosome territories in interphase nuclei is non-random and is conserved in evolution. Gene rich chromosomes, such as human chromosome 19, are located towards the center of the nucleus, whereas gene poor chromosomes, such as chromosome 18, are predominantly peripheral in many different cell types. We were eager to explore to which extent this remarkable conservation is maintained in cells containing chromosomal aneuploidies, in particular because we have previously established that these chromosomes are transcriptionally active. Therefore, a relationship could exist between nuclear position and transcriptional activity. We investigated, first, whether aneuploid chromosomes assume a nuclear position similar to that of their endogenous homologues. Using 3D-FISH and confocal laser scanning microscopy, we showed that human chromosomes 7, 18, or 19 introduced via microcell mediated chromosome transfer (MMCT) into the parental diploid colon cancer cell line DLD-1 maintain their conserved position. Our data is thus consistent with the model that each chromosome has an associated zip code that determines its nuclear localization. Whether the nuclear localization determines, or is determined by, the transcriptional activity of resident genes has yet to be ascertained. 2) Aneuploidy, oncogene amplification, and epithelial/mesenchymal transition govern transformation of murine epithelial cells: models for human cancer. We extended these analyses and designed a novel mouse model for colon cancer. Normal primary murine epithelial colon cells were selectively isolated from the large intestine of eight different isogenic C57BL/6 mice. A portion of the primary colon cells were grown in culture under reduced serum conditions while another fraction of these normal cells were cryopreserved for further analysis. The cells were sequentially recovered from culture based on distinct morphological changes: first, cells were in the pre-immortal stage and were actively growing; second, the cells bypassed crisis, formed colonies and became immortal; third, the cells formed foci, became less adherent, and exhibited became tumorigenic when injected into immune-compromised mice. The cells were analyzed at each stage using molecular cytogenetic methods and gene expression profiling. SKY identified recurrent structural and numerical aberrations. Array CGH revealed regions of gene amplifications and deletions. Global gene expression profiling identified deregulated genes specific to each stage of transformation. Three of the late transformed mouse colon cell lines produced tumors in nude mouse assays. This is a unique murine model that reproduces a continued progression of alterations which is common in human colon tumorigenesis. The similarity of the cytogenetic and genetic aberration profiles suggest that this model can serve as a preclinical system for the validation of therapeutic targets. As in human tumors, chromosomal aneuploidies resulted in the transcriptional deregulation of resident genes; in other words, genomic copy number is positively and linearly correlated with transcription levels.

通过系统地整合使用比较基因组杂交癌的基因表达谱和癌的基因组失衡，我们可以表明，DNA拷贝数的复制数量相互反复出现的非整倍体染色体和染色体臂7、8q，8q，13q和20q，以及17p和18Q的损失显着相关居民基因的表达谱。综上所述，我们的结果表明，居住在大倍性染色体上的高级，显着的转录放松管制以及在结直肠腺癌中共存的基因的平均转录水平（以及其他关于上皮起源的谣言）。为了表征原代结肠癌中全球转录放松管制的模式，我们使用寡核苷酸微阵列进行了大约300个肿瘤的基因表达分析，包括结肠和直肠。对于大多数这些肿瘤，将表达谱与匹配的正常粘膜样品的表达谱进行比较。我们建立了特定的基因组失衡之间的关系，这些失衡是通过比较基因组杂交和全球转录活性改变的许多分析结肠肿瘤映射的。以前，我们已经对原发性直肠癌进行了类似的分析。结肠和直肠癌的系统比较表明，基因组失衡和转录放松管制的显着重叠，包括激活Wnt/B-catenin信号级联，表明相似的致病途径。 1）非整型染色体的非整倍型染色体的核形态图及其对转录活性的后果。相互核中染色体区域的3D位置是非随机的，并且在进化中是保守的。富含基因的染色体，例如人类19号染色体，位于细胞核的中心，而基因较差的染色体（例如18染色体）在许多不同的细胞类型中主要是外围的。我们渴望探索这种显着的保护在含有染色体非整倍性的细胞中，特别是因为我们先前已经确定这些染色体具有转录活性。因此，核位置与转录活性之间可能存在关系。首先，我们研究了非整倍型染色体是否假定的核位置类似于其内源性同源物的核位置。使用3D-FISH和共聚焦激光扫描显微镜，我们表明通过Microcell介导的染色体转移（MMCT）引入的人类染色体7、18或19中，进入了亲本二倍体二倍体结肠癌细胞系DLD-1保持其保守位置。因此，我们的数据与每个染色体具有决定其核定位的相关邮政编码的模型一致。核定位是确定还是取决于居民基因的转录活性尚未确定。 2）非整倍性，癌基因扩增和上皮/间质转变控制鼠上皮细胞的转化：人类癌症的模型。我们扩展了这些分析，并为结肠癌设计了一种新型的小鼠模型。从八个不同的同源性C57BL/6小鼠的大肠中选择性地分离出正常的原发性鼠上皮结肠细胞。在减少的血清条件下，在培养中生长了一部分原代细胞，而这些正常细胞的另一比例则是冷冻保存的，以进一步分析。基于不同的形态变化从培养中依次恢复细胞：首先，细胞处于育儿前阶段，并正在积极生长。其次，这些细胞绕过危机，形成菌落并变得不朽。第三，形成焦点的细胞变得不那么粘附，并且当注射到免疫功能低下的小鼠中时，表现出了肿瘤性。使用分子细胞遗传学方法和基因表达分析对细胞进行分析。天空确定了复发性结构和数值畸变。阵列CGH揭示了基因扩增和缺失的区域。全球基因表达谱分析鉴定出对每个转化阶段特有的放松管制基因。三个转化的小鼠结肠系在裸小鼠测定中产生肿瘤。这是一个独特的鼠模型，可再现在人类结肠肿瘤发生中常见的持续变化发展。细胞遗传学和遗传像差谱的相似性表明，该模型可以用作验证治疗靶标的临床前系统。与人类肿瘤一样，染色体脑倍整倍性会导致居民基因的转录放松管制。换句话说，基因组拷贝数与转录水平呈正性关系。

项目成果

期刊论文数量（12）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

Chromosomal aneuploidy affects the global proteome equilibrium of colorectal cancer cells.

DOI：
10.3233/acp-140088
发表时间：
2013
期刊：
Analytical cellular pathology (Amsterdam)
影响因子：
0
作者：
Gemoll T;Habermann JK;Becker S;Szymczak S;Upender MB;Bruch HP;Hellman U;Ried T;Auer G;Jörnvall H;Roblick UJ
通讯作者：
Roblick UJ

Genetic instability and mammary tumor formation in mice carrying mammary-specific disruption of Chk1 and p53.

DOI：
10.1038/onc.2010.163
发表时间：
2010-07-15
期刊：
Oncogene
影响因子：
8
作者：
Fishler T;Li YY;Wang RH;Kim HS;Sengupta K;Vassilopoulos A;Lahusen T;Xu X;Lee MH;Liu Q;Elledge SJ;Ried T;Deng CX
通讯作者：
Deng CX

Horizontal transmission and retention of malignancy, as well as functional human genes, after spontaneous fusion of human glioblastoma and hamster host cells in vivo.

DOI：
10.1002/ijc.26327
发表时间：
2012-07-01
期刊：
INTERNATIONAL JOURNAL OF CANCER
影响因子：
6.4
作者：
Goldenberg, David M.;Zagzag, David;Heselmeyer-Haddad, Kerstin M.;Garcia, Lissa Y. Berroa;Ried, Thomas;Loo, Meiyu;Chang, Chien-Hsing;Gold, David V.
通讯作者：
Gold, David V.

Genomic instability influences the transcriptome and proteome in endometrial cancer subtypes.

DOI：
10.1186/1476-4598-10-132
发表时间：
2011-10-31
期刊：
Molecular cancer
影响因子：
37.3
作者：
Habermann JK;Bündgen NK;Gemoll T;Hautaniemi S;Lundgren C;Wangsa D;Doering J;Bruch HP;Nordstroem B;Roblick UJ;Jörnvall H;Auer G;Ried T
通讯作者：
Ried T

Short telomeres result in chromosomal instability in hematopoietic cells and precede malignant evolution in human aplastic anemia.