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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Nov 01, 2015 |
| Title |
Mouse frozen liver: vehicle-control vs. CCl4+DEN treated |
| Organism |
Mus musculus |
| Experiment type |
Genome variation profiling by genome tiling array
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| Summary |
Hepatocellular carcinoma (HCC) is a prevalent human cancer with rising incidence worldwide. Human HCC is frequently associated with chronic liver inflammation and cirrhosis, pathophysiological processes that are a consequence of chronic viral infection, disturbances in metabolism, or exposure to chemical toxicants. To better characterize the pathogenesis of HCC, we used a human disease-relevant mouse model of fibrosis-associated hepatocarcinogenesis. In this model, marked liver tumor response caused by a pro-mutagenic chemical N-nitrosodiethylamine in presence of liver fibrosis was associated with epigenetic events indicative of genomic instability. Therefore, we hypothesized that DNA copy number alterations (CNAs), a feature of genomic instability and a common characteristic of cancer, are concordant between human HCC and mouse models of fibrosis-associated hepatocarcinogenesis. We evaluated DNA CNAs and changes in gene expression in the mouse liver (normal, tumor and non-tumor cirrhotic tissues). In addition, we compared our findings to those in human HCC (tumor and non-tumor cirrhotic/fibrotic tissues). We observed that while fibrotic liver tissue is largely devoid of DNA CNAs, highly frequently occurring DNA CNAs are found in mouse tumors, which is indicative of a profound increase in chromosomal instability in HCC. When compared to CNAs in human HCC, we found that 33% of genes in these segments are similarly affected in the mouse tumors. Our results suggest that CNAs most commonly arise in neoplastic tissue rather than in fibrotic liver, and demonstrate the utility of this mouse model in replicating the molecular features of human HCC.
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| Overall design |
Genomic DNA was extracted from frozen liver samples from vehicle-control and DEN+CCl4-treated mice using a DNEasy kit (Qiagen, Valencia, CA). Eighteen mouse tumor samples were included in the study, as well as 18 matched non-tumor samples taken from fibrotic, non-tumorous, surrounding liver tissue from the same mice. Liver DNA from 6 vehicle control-mice was pooled and used as the reference genome in the aCGH experiments. Copy number alterations were identified using the normalized data.
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| Contributor(s) |
Chappell GA, Silva GO, Uehara T, Pogribny IP, Rusyn II |
| Citation(s) |
26778414 |
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| Submission date |
Aug 07, 2015 |
| Last update date |
Jan 31, 2016 |
| Contact name |
Grace Chappell |
| E-mail(s) |
gchappell@toxstrategies.com
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| Organization name |
ToxStrategies, Inc.
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| Department |
Health Sciences
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| Street address |
9390 Research Blvd, Bldg 2, Ste. #100
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| City |
Austin |
| State/province |
TX |
| ZIP/Postal code |
78723 |
| Country |
USA |
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| Platforms (1) |
| GPL10449 |
Agilent-027411 SurePrint G3 Mouse CGH Microarray 4x180K (Feature Number version) |
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| Samples (36)
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| Relations |
| BioProject |
PRJNA292323 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE71849_RAW.tar |
814.3 Mb |
(http)(custom) |
TAR (of TXT) |
| Processed data included within Sample table |
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