Carrie Graveel

The identification of E2F1-specific target genes

The E2F family of transcriptional regulators consists of six different members. Analysis of E2F-regulated promoters by using cultured cells suggests that E2Fs may have redundant functions. However, animal studies have shown that loss of individual E2Fs can have distinct biological consequences. Such seemingly conflicting results could be due to a difference in E2F-mediated regulation in cell culture vs. animals. Alternatively, there may be genes that are specifically regulated by an individual E2F which have not yet been identified. To investigate this possibility further, we have analyzed gene expression in E2F1 nullizygous mice. We found that loss of E2F1 did not cause changes in expression of known E2F target genes, suggesting that perhaps E2F1-specific promoters are distinct from known E2F target promoters. Therefore, we used oligonucleotide microarrays to identify mRNAs whose expression is altered on loss of E2F1. We demonstrate by chromatin immunoprecipitation that several of the promoters that drive expression of the deregulated mRNAs selectively recruit E2F1, but not other E2Fs, and this recruitment is via an element distinct from a consensus E2F binding site. To our knowledge, these are as yet undocumented examples of promoters being occupied in asynchronously growing cells by a single E2F family member. Interestingly, the E2F1-specific target genes that we identified encode proteins having functions quite different from the function of known E2F target genes. Thus, whereas E2F1 may share redundant functions in cell growth control with other E2F family members, it may also play an important biological role distinct from the other E2Fs.

Expression profiling and identification of novel genes in hepatocellular carcinomas.

Liver cancer is the fifth most common cancer worldwide and unlike certain other cancers, such as colon cancer, a mutational model has not yet been developed. We have performed gene expression profiling of normal and neoplastic livers in C3H/HeJ mice treated with diethylnitrosamine. Using oligonucleotide microarrays, we compared gene expression in liver tumors to three different states of the normal liver: quiescent adult, regenerating adult, and newborn. Although each comparison revealed hundreds of differentially expressed genes, only 22 genes were found to be deregulated in the tumors in all three comparisons. Three of these genes were examined in human hepatocellular carcinomas and were found to be upregulated. As a second method of analysis, we used Representational Difference Analysis (RDA) to clone mRNA fragments differentially expressed in liver tumors versus regenerating livers. We cloned several novel mRNAs that are differentially regulated in murine liver tumors. Here we report the sequence of a novel cDNA whose expression is upregulated in both murine and human hepatocellular carcinomas. Our results suggest that DEN-treated mice provide an excellent model for human hepatocellular carcinomas.

A mouse model of activating Met mutations.

Tyrosine kinase–activating mutations in Met have been observed in hereditary papillary renal carcinomas (HPRC) and their transforming potential has been examined both in vitro and in tumor xenografts. To study the influence of these mutations in the mouse germline, we generated mice with targeted mutations in the murine met locus. Five mouse lines with mutant Met were created: WT, D1226N, Y1228C, M1248T, and M1248T/L1193V. Unexpectedly, the different mutant Met lines developed unique tumor profiles including carcinomas, sarcomas, and lymphomas. More surprising was that we observed nonrandom duplication of the mutant met allele in a majority of tumors from the mutant mouse lines. This selective chromosomal amplification has been observed in patients with HPRC. This study illustrates the importance of activating Met mutations in tumorigenesis and indicates that mutations within the kinase domain distinctly affect downstream signaling. Our Met mutant mice will provide a valuable model for testing Met inhibitors on tumors containing activating mutations present in human cancers and for understanding the molecular events critical for Met-mediated tumorigenesis.

No effect of loss of E2F1 on liver regeneration or hepatocarcinogenesis in C57BL/6J or C3H/HeJ mice

The E2F family of transcription factors regulates the expression of genes needed for DNA synthesis and cell‐cycle control. However, the individual contributions of the different E2F family members in regulating proliferation in various tissues have not been well characterized. Mouse liver is an excellent system for investigating proliferation because its growth state can be experimentally manipulated. As observed in cell culture systems, E2F1 protein is present at low levels in the quiescent liver, with an increase in expression during proliferation. Therefore, we expected that E2F1 may play an important role in cell‐growth control during periods of robust proliferation. Using E2F1‐nullizygous mice, we performed partial hepatectomies to investigate the role of E2F1 in the synchronous proliferation of adult hepatocytes. We found that E2F1 deficiency resulted in only minor changes in gene expression and that the timing of liver regeneration was not altered in E2F1 nullizygous mice. E2F1 has displayed properties of both a tumor suppressor and an oncogene in different model systems. Therefore, we investigated the role of E2F1 in rapidly growing liver tumor cells in strains of mice that have high (C3H/HeJ) and low (C57BL/6J) rates of hepatocarcinogenesis. We observed no significant differences in the number of liver tumors that developed after diethylnitrosamine treatment of wild type versus E2F1‐nullizygous mice. We suggest that abundant levels of E2F4 in the mouse liver compensate for loss of E2F1. Mol. Carcinog. 25:295–303, 1999.

In vivo Efficacy Studies in Cell Line and Patient-derived Xenograft Mouse Models

[Abstract] In vivo xenograft models derived from human cancer cells have been a gold standard for evaluating the genetic drivers of cancer and are valuable preclinical models for evaluating the efficacy of cancer therapeutics. Recently, patient-derived tumorgrafts from multiple tumor types have been developed and shown to more accurately recapitulate the molecular and histological heterogeneity of cancer. Here we detail the procedures for developing patient-derived xenograft models from breast cancer tissue, cell-based xenograft models, serial tumor transplantation, tumor measurement, and drug treatment.

Analysis of gene expression alterations in mouse and human hepatocellular carcinomas

Liver cancer is the fifth most common cancer worldwide, with 437,000 cases reported in 1990. Yet a mutational model has not yet been developed for liver cancer, as it has for certain other cancers, such as colon cancer. A thorough understanding of the molecular events leading to neoplastic transformation of the liver requires a detailed comparison of the gene expression pattern in normal liver cells with that in cancer cells. We have performed gene expression profiling of normal and neoplastic livers. Using oligonucleotide microarrays, we compared liver tumors (from diethylnitrosamine-treated C3H/HeJ mice) with three different states of the normal liver: quiescent adult, regenerating adult and newborn. Although each comparison revealed hundreds of differentially expressed genes, only 22 genes were found to be deregulated in the tumors in all three comparisons. We also employed representational difference analysis to clone fragments of messenger RNAs differentially expressed in liver tumors versus regenerating livers. Although many of the same mRNAs were identified as in the oligonucleotide microarray experiments, we also cloned several new mRNAs that are differentially regulated in liver tumors. We have cloned the mouse complementary DNA of novel 4 and are currently isolating the human homologue of this unknown gene. We are using representational difference analysis and oligonucleotide microarrays to identify genes whose expression is deregulated in the development of human hepatocellular carcinomas. Using these models and techniques, we hope to identify common genetic alterations in the progression of liver cancer in both humans and mice.