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1.  Development of a Colon Cancer GEMM-Derived Orthotopic Transplant Model for Drug Discovery and Validation 
Purpose
Effective therapies for KRAS mutant colorectal cancer (CRC) are a critical unmet clinical need. Previously, we described GEMMs for sporadic Kras mutant and non-mutant CRC suitable for preclinical evaluation of experimental therapeutics. To accelerate drug discovery and validation, we sought to derive low-passage cell lines from GEMM Kras mutant and wild-type tumors for in vitro screening and transplantation into the native colonic environment of immunocompetent mice for in vivo validation.
Experimental Design
Cell lines were derived from Kras mutant and non-mutant GEMM tumors under defined media conditions. Growth kinetics, phosphoproteomes, transcriptomes, drug sensitivity, and metabolism were examined. Cell lines were implanted in mice and monitored for in vivo tumor analysis.
Results
Kras mutant cell lines displayed increased proliferation, MAPK signaling, and PI3K signaling. Microarray analysis identified significant overlap with human CRC-related gene signatures, including KRAS mutant and metastatic CRC. Further analyses revealed enrichment for numerous disease-relevant biological pathways, including glucose metabolism. Functional assessment in vitro and in vivo validated this finding and highlighted the dependence of Kras mutant CRC on oncogenic signaling and on aerobic glycolysis.
Conclusions
We have successfully characterized a novel GEMM-derived orthotopic transplant model of human KRAS mutant CRC. This approach combines in vitro screening capability using low-passage cell lines that recapitulate human CRC and potential for rapid in vivo validation using cell line-derived tumors that develop in the colonic microenvironment of immunocompetent animals. Taken together, this platform is a clear advancement in preclinical CRC models for comprehensive drug discovery and validation efforts.
doi:10.1158/1078-0432.CCR-12-2307
PMCID: PMC3951107  PMID: 23403635
Kras; MAPK; PI3K; colorectal cancer; GEMM; orthotopic model
2.  Concomitant BRAF and PI3K/mTOR Blockade is Required for Effective Treatment of BRAFV600E Colorectal Cancer 
Purpose
BRAFV600E mutations are associated with poor clinical prognosis in colorectal cancer (CRC). Whereas selective BRAF inhibitors are effective for treatment of melanoma, comparable efforts in CRC have been disappointing. Here, we investigated potential mechanisms underlying this resistance to BRAF inhibitors in BRAFV600E CRC.
Experimental Design
We examined phosphatidyl inositol 3-kinase (PI3K)/mammalian target of rapamycin (mTOR) signaling in BRAFV600E CRC cell lines after BRAF inhibition and cell viability and apoptosis after combined BRAF and PI3K/mTOR inhibition. We assessed the efficacy of in vivo combination treatment using a novel genetically engineered mouse model (GEMM) for BRAFV600E CRC.
Results
Western blot revealed sustained PI3K/mTOR signaling upon BRAF inhibition. Our BRAFV600E GEMM presented with sessile serrated adenomas/polyps, as seen in humans. Combination treatment in vivo resulted in induction of apoptosis and tumor regression.
Conclusions
We have established a novel GEMM to interrogate BRAFV600E CRC biology and identify more efficacious treatment strategies. Combination BRAF and PI3K/mTOR inhibitor treatment should be explored in clinical trials.
doi:10.1158/1078-0432.CCR-12-2556
PMCID: PMC3815598  PMID: 23549875
colon cancer; mouse models; targeted therapy
3.  Synthetic Lethal Interaction of Combined BCL-XL and MEK Inhibition Promotes Tumor Regressions in KRAS Mutant Cancer Models 
Cancer cell  2012;23(1):121-128.
SUMMARY
KRAS is the most commonly mutated oncogene, yet no effective targeted therapies exist for KRAS mutant cancers. We developed a pooled shRNA-drug screen strategy to identify genes that, when inhibited, cooperate with MEK inhibitors to effectively treat KRAS mutant cancer cells. The anti-apoptotic BH3 family gene BCL-XL emerged as a top hit through this approach. ABT-263 (navitoclax), a chemical inhibitor that blocks the ability of BCL-XL to bind and inhibit pro-apoptotic proteins, in combination with a MEK inhibitor led to dramatic apoptosis in many KRAS mutant cell lines from different tissue types. This combination caused marked in vivo tumor regressions in KRAS mutant xenografts and in a genetically engineered KRAS-driven lung cancer mouse model, supporting combined BCL-XL/MEK inhibition as a potential therapeutic approach for KRAS mutant cancers.
doi:10.1016/j.ccr.2012.11.007
PMCID: PMC3667614  PMID: 23245996
4.  Adenoma-linked barrier defects and microbial products drive IL-23/IL-17-mediated tumour growth 
Nature  2012;491(7423):254-258.
Approximately 2% of colorectal cancer is linked to pre-existing inflammation known as colitis-associated cancer, but most develops in patients without underlying inflammatory bowel disease. Colorectal cancer often follows a genetic pathway whereby loss of the adenomatous polyposis coli (APC) tumour suppressor and activation of β-catenin are followed by mutations in K-Ras, PIK3CA and TP53, as the tumour emerges and progresses1,2. Curiously, however, ‘inflammatory signature’ genes characteristic of colitis-associated cancer are also upregulated in colorectal cancer3,4. Further, like most solid tumours, colorectal cancer exhibits immune/inflammatory infiltrates5, referred to as ‘tumour elicited inflammation’6. Although infiltrating CD4+ TH1 cells and CD8+ cytotoxic T cells constitute a positive prognostic sign in colorectal cancer7,8, myeloid cells and T-helper interleukin (IL)-17-producing (TH17) cells promote tumorigenesis5,6, and a ‘TH17 expression signature’ in stage I/II colorectal cancer is associated with a drastic decrease in disease-free survival9. Despite its pathogenic importance, the mechanisms responsible for the appearance of tumour-elicited inflammation are poorly understood. Many epithelial cancers develop proximally to microbial communities, which are physically separated from immune cells by an epithelial barrier10. We investigated mechanisms responsible for tumour-elicited inflammation in a mouse model of colorectal tumorigenesis, which, like human colorectal cancer, exhibits upregulation of IL-23 and IL-17. Here we show that IL-23 signalling promotes tumour growth and progression, and development of a tumoural IL-17 response. IL-23 is mainly produced by tumour-associated myeloid cells that are likely to be activated by microbial products, which penetrate the tumours but not adjacent tissue. Both early and late colorectal neoplasms exhibit defective expression of several barrier proteins. We propose that barrier deterioration induced by colorectal-cancer-initiating genetic lesions results in adenoma invasion by microbial products that trigger tumour-elicited inflammation, which in turn drives tumour growth.
doi:10.1038/nature11465
PMCID: PMC3601659  PMID: 23034650
5.  In Vivo Optical Molecular Imaging of Matrix Metalloproteinase Activity Following Celecoxib Therapy for Colorectal Cancer 
Molecular imaging  2012;11(5):417-425.
We present an optical molecular imaging approach to measure the efficacy of the COX-2 inhibitor celecoxib on tumor growth rate through its effect on MMP activity. A xenograft model of colorectal cancer was generated in nude mice, which were then randomized to receive celecoxib vs vehicle. MMP activity was measured by an enzyme-activatable optical molecular probe. A novel genetically engineered mouse (GEM) model of colorectal cancer was also used to assess celecoxib’s effect on MMP activity, which was measured by quantitative fluorescence colonoscopy. Subcutaneously implanted xenograft tumors were 84% (SD 20.2%) smaller in volume in the treatment group versus control. Moreover, treated animals exhibited only a 7.6% (SEM 9%) increase in MMP activity, versus 106% (SEM 8%) for untreated animals. There was an apparent linear relationship (r = 0.91) between measured MMP activity and tumor growth rate. Finally, in the GEM model experiment, treated murine tumors remained relatively unchanged in volume and MMP activity; however, untreated tumors grew significantly and showed an increase in MMP activity. This method may provide for the improved identification of patients for whom COX-2 inhibition therapy is indicated, by allowing one to balance the patient’s cardiovascular risk with the cancer’s responsiveness to celecoxib.
PMCID: PMC3683544  PMID: 22954186
optical molecular imaging; colorectal cancer; COX-2 inhibitor; matrix metalloproteinases; molecular endoscopy
6.  EGFR-mediated re-activation of MAPK signaling contributes to insensitivity of BRAF mutant colorectal cancers to RAF inhibition with vemurafenib 
Cancer discovery  2012;2(3):227-235.
BRAF mutations occur in 10–15% of colorectal cancers (CRCs) and confer adverse outcome. While RAF inhibitors such as vemurafenib (PLX4032) have proven effective in BRAF mutant melanoma, they are surprisingly ineffective in BRAF mutant CRCs, and the reason for this disparity remains unclear. Compared to BRAF mutant melanoma cells, BRAF mutant CRC cells were less sensitive to vemurafenib, and P-ERK suppression was not sustained in response to treatment. Although transient inhibition of phospho-ERK by vemurafenib was observed in CRC, rapid ERK re-activation occurred through EGFR-mediated activation of RAS and CRAF. BRAF mutant CRCs expressed higher levels of phospho-EGFR than BRAF mutant melanomas, suggesting that CRCs are specifically poised for EGFR-mediated resistance. Combined RAF and EGFR inhibition blocked reactivation of MAPK signaling in BRAF mutant CRC cells and markedly improved efficacy in vitro and in vivo. These findings support evaluation of combined RAF and EGFR inhibition in BRAF mutant CRC patients.
doi:10.1158/2159-8290.CD-11-0341
PMCID: PMC3308191  PMID: 22448344
BRAF; vemurafenib; EGFR; colorectal cancer; melanoma
7.  Comprehensive Proteome Analysis of an Apc Mouse Model Uncovers Proteins Associated with Intestinal Tumorigenesis 
Tumor-derived proteins may occur in the circulation as a result of secretion, shedding from the cell surface, or cell turnover. We have applied an in-depth comprehensive proteomic strategy to plasma from intestinal tumor–bearing Apc mutant mice to identify proteins associated with tumor development. We used quantitative tandem mass spectrometry of fractionated mouse plasma to identify differentially expressed proteins in plasma from intestinal tumor–bearing Apc mutant mice relative to matched controls. Up-regulated proteins were assessed for the expression of corresponding genes in tumor tissue. A subset of proteins implicated in colorectal cancer were selected for further analysis at the tissue level using antibody microarrays, Western blotting, tumor immunohistochemistry, and novel fluorescent imaging. We identified 51 proteins that were elevated in plasma with concordant up-regulation at the RNA level in tumor tissue. The list included multiple proteins involved in colon cancer pathogenesis: cathepsin B and cathepsin D, cullin 1, Parkinson disease 7, muscle pyruvate kinase, and Ran. Of these, Parkinson disease 7, muscle pyruvate kinase, and Ran were also found to be up-regulated in human colon adenoma samples. We have identified proteins with direct relevance to colorectal carcinogenesis that are present both in plasma and in tumor tissue in intestinal tumor–bearing mice. Our results show that integrated analysis of the plasma proteome and tumor transcriptome of genetically engineered mouse models is a powerful approach for the identification of tumor-related plasma proteins.
doi:10.1158/1940-6207.CAPR-08-0153
PMCID: PMC2874864  PMID: 19240248
8.  Proteomic Approaches to Cancer Biomarkers 
Gastroenterology  2009;138(1):46-51.e1.
doi:10.1053/j.gastro.2009.11.020
PMCID: PMC2873613  PMID: 19931265
9.  New insights into the molecular pathogenesis of colorectal cancer 
Although there have been tremendous advances in the management of colorectal cancer (CRC), there is still a need for improved therapeutic approaches. On a molecular genetic level, CRC is one of the best-understood solid malignancies, and these insights can serve as a foundation for the design of novel targeted therapies. We present new genetic and epigenetic pathways that highlight the heterogeneous mechanisms in CRC pathogenesis, including the roles of the MYH DNA repair gene and of aberrant DNA hypermethylation and imprinting. We then describe some of the successful targeted therapies that inhibit COX2, EGFR, and VEGF as well as potential new targets that have been revealed by studies of molecular genetics.
doi:10.1016/j.ddmec.2006.10.005
PMCID: PMC2819006  PMID: 20151020
10.  Uncovering transcriptional interactions via an adaptive fuzzy logic approach 
BMC Bioinformatics  2009;10:400.
Background
To date, only a limited number of transcriptional regulatory interactions have been uncovered. In a pilot study integrating sequence data with microarray data, a position weight matrix (PWM) performed poorly in inferring transcriptional interactions (TIs), which represent physical interactions between transcription factors (TF) and upstream sequences of target genes. Inferring a TI means that the promoter sequence of a target is inferred to match the consensus sequence motifs of a potential TF, and their interaction type such as AT or RT is also predicted. Thus, a robust PWM (rPWM) was developed to search for consensus sequence motifs. In addition to rPWM, one feature extracted from ChIP-chip data was incorporated to identify potential TIs under specific conditions. An interaction type classifier was assembled to predict activation/repression of potential TIs using microarray data. This approach, combining an adaptive (learning) fuzzy inference system and an interaction type classifier to predict transcriptional regulatory networks, was named AdaFuzzy.
Results
AdaFuzzy was applied to predict TIs using real genomics data from Saccharomyces cerevisiae. Following one of the latest advances in predicting TIs, constrained probabilistic sparse matrix factorization (cPSMF), and using 19 transcription factors (TFs), we compared AdaFuzzy to four well-known approaches using over-representation analysis and gene set enrichment analysis. AdaFuzzy outperformed these four algorithms. Furthermore, AdaFuzzy was shown to perform comparably to 'ChIP-experimental method' in inferring TIs identified by two sets of large scale ChIP-chip data, respectively. AdaFuzzy was also able to classify all predicted TIs into one or more of the four promoter architectures. The results coincided with known promoter architectures in yeast and provided insights into transcriptional regulatory mechanisms.
Conclusion
AdaFuzzy successfully integrates multiple types of data (sequence, ChIP, and microarray) to predict transcriptional regulatory networks. The validated success in the prediction results implies that AdaFuzzy can be applied to uncover TIs in yeast.
doi:10.1186/1471-2105-10-400
PMCID: PMC2797023  PMID: 19961622
11.  Cytotoxic Effect of Recombinant Mycobacterium tuberculosis CFP-10/ESAT-6 Protein on the Crucial Pathways of WI-38 Cells 
To unravel the cytotoxic effect of the recombinant CFP-10/ESAT-6 protein (rCFES) on WI-38 cells, an integrative analysis approach, combining time-course microarray data and annotated pathway databases, was proposed with the emphasis on identifying the potentially crucial pathways. The potentially crucial pathways were selected based on a composite criterion characterizing the average significance and topological properties of important genes. The analysis results suggested that the regulatory effect of rCFES was at least involved in cell proliferation, cell motility, cell survival, and metabolisms of WI-38 cells. The survivability of WI-38 cells, in particular, was significantly decreased to 62% with 12.5 μM rCFES. Furthermore, the focal adhesion pathway was identified as the potentially most-crucial pathway and 58 of 65 important genes in this pathway were downregulated by rCFES treatment. Using qRT-PCR, we have confirmed the changes in the expression levels of LAMA4, PIK3R3, BIRC3, and NFKBIA, suggesting that these proteins may play an essential role in the cytotoxic process in the rCFES-treated WI-38 cells.
doi:10.1155/2009/917084
PMCID: PMC2702506  PMID: 19584916
12.  Low-volume, high-throughput sandwich immunoassays for profiling plasma proteins in mice: identification of early-stage systemic inflammation in a mouse model of intestinal cancer 
Molecular oncology  2007;1(2):216-225.
Mouse models of human cancers may provide a valuable resource for the discovery of cancer biomarkers. We have developed a practical strategy for profiling specific proteins in mouse plasma using low-volume sandwich-immunoassays. We used this method to profile the levels of 14 different cytokines, acute-phase reactants, and other cancer markers in plasma from a mouse models of intestinal tumors and their wild-type littermates, using as little as 1.5 microliters of diluted plasma per assay. Many of the proteins were significantly and consistently up-regulated in the mutant mice. The mutant mice could be distinguished nearly perfectly from the wild-type mice based on the combined levels of as few as three markers. Many of the proteins were up-regulated even in the mutant mice with few or no tumors, suggesting the presence of a systemic host response at an early stage of cancer development. These results have implications for the study of host responses in mouse models of cancers and demonstrate the value of a new low-volume, high-throughput sandwich-immunoassay method for sensitively profiling protein levels in cancer.
doi:10.1016/j.molonc.2007.06.001
PMCID: PMC2658882  PMID: 19305640
13.  A mouse plasma peptide atlas as a resource for disease proteomics 
Genome Biology  2008;9(6):R93.
A publicly available repository for high-quality peptide and protein data, identified by LC-MS/MS analysis.
We present an in-depth analysis of mouse plasma leading to the development of a publicly available repository composed of 568 liquid chromatography-tandem mass spectrometry runs. A total of 13,779 distinct peptides have been identified with high confidence. The corresponding approximately 3,000 proteins are estimated to span a 7 logarithmic range of abundance in plasma. A major finding from this study is the identification of novel isoforms and transcript variants not previously predicted from genome analysis.
doi:10.1186/gb-2008-9-6-r93
PMCID: PMC2481425  PMID: 18522751
14.  The Central Role of CD4+ T Cells in the Antitumor Immune Response  
The Journal of Experimental Medicine  1998;188(12):2357-2368.
The induction of optimal systemic antitumor immunity involves the priming of both CD4+ and CD8+ T cells specific for tumor-associated antigens. The role of CD4+ T helper cells (Th) in this response has been largely attributed to providing regulatory signals required for the priming of major histocompatibility complex class I restricted CD8+ cytolytic T lymphocytes, which are thought to serve as the dominant effector cell mediating tumor killing. However, analysis of the effector phase of tumor rejection induced by vaccination with irradiated tumor cells transduced to secrete granulocyte/macrophage colony-stimulating factor indicates a far broader role for CD4+ T cells in orchestrating the host response to tumor. This form of immunization leads to the simultaneous induction of Th1 and Th2 responses, both of which are required for maximal systemic antitumor immunity. Cytokines produced by these CD4+ T cells activate eosinophils as well as macrophages that produce both superoxide and nitric oxide. Both of these cell types then collaborate within the site of tumor challenge to cause its destruction.
PMCID: PMC2212434  PMID: 9858522
cancer; vaccine; T helper cell; macrophage; eosinophil

Results 1-14 (14)