bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract B49: The role of LKB1 as a tumor suppressor in esophageal squamous cell cancer
Authors: Tzao Ching , Hsueh An-Li , Chen Ban-Hen , Guo Yaw-Wen , Lee Guang-Guan Sun, Shih-Chun
Published: June 2012

Background: LKB1, also known as STK11, encodes serine/threonine kinase 11 that is frequently mutated in the Peutz- Jeghers syndrome. LKB1 functions as a tumor suppressor in a variety of human cancers, including colon and lung. We investigated the functional role of LKB1 in esophageal squamous cell carcinoma (ESCC).

Methods: Resected ESCC tumors from 65 patients were used for immunohistochemistry to determine LKB1 expression. Cytotoxicity (MTT) assay was used to test chemosensitivity to common chemotherapeutic agents for ESCC, including cisplatin, 5-FU and taxol, along with migration assay in selected ESCC cell lines (KYSE 170 and KYSE 510, kindly provided by Dr. Yutaka Shimada at University of Toyama, Japan). LKB1 was overexpressed in KYSE 170 cells and was knocked down in KYSE 510 cells using human LKB1 (pCMV6-XL5- cDNA, OriGene) and its shRNA (OriGene), respectively. Expression of LKB1, E-cadherin and p53 pathway-related proteins (ie p21 and PUMA) in LKB1-overexpessed or knock-down cells and its vector controls by Western blot analysis. Mice tumor xenografts with LKB1- overexpressed KYSE 170 cell line were used to test tumor growth and their chemosensitivity in vivo with comparisions to the vector controls. Pearson's correlation was used to correlate clinicopathologic variables with LKB1 expression along with survival analyses by log-rank test, Kaplan-Meier survivial analysis and multivariate analysis with Cox proportional hazards regression model.

Results: LKB1 expression correlated inversely with tumor staging (P = 0.003). Patients with high expression of LKB1 showed better survival compared to those with low expression (P = 0.0002). When further examined by multivariate analysis, LKB1 expression correlated positively with patients’ survival (P = 0.004) with a hazard ratio (HR) of 3.415. Compared with vector control and LKB1 knockdown KYSE 510 cell line, cell proliferation was significantly suppressed in LKB1 overexpressed KYSE 170 cells with an upregulation of p21 and p53-upregulated modifier of apoptosis (PUMA). LKB1 overexpression increased E-cadherin expression in KYSE 170 cells with an inihibition in their migration. LKB1 overexpressed KYSE 170 cells were more sensitive to chemotherapeutic agents in vitro and in vivo compared to the vector controls.

Conclusions: LKB1 expression in resected ESCC predicted patients’ outcome and it served as an independent survival predictor. LKB1 overexpression increased chemosensitivity with a decrease in cell proliferation and migration while upregulating p53-pathway related suppressors and E-cadherin in ESCC cells. Our results suggested a role of LKB1 as a tumor suppressor gene in ESCC.

Citation Information: Clin Cancer Res 2010;16(14 Suppl):B49.
Abstract B5: Sequence analysis of HSP90-encoding genes in breast tumor tissue identifies a novel 9 bp deletion in HSP90AB1
Authors: Lichter David I. , Danaee Hadi , Tayber Olga , Sintchak Michael , Kuida Keiske , Atienza Josephine M. , Miyake Hiroshi , Blakemore Stephen J.
Published: June 2012

The 90 kDa heat-shock protein (HSP90) functions as a ubiquitous cellular chaperone in cells, and is required for the function and stability of many client proteins such as ERBB2, EGFR, BCR-ABL, MET, androgen and estrogen receptors, BRAF and HIF-1α.1 There are four primary genes that encode for HSP90 in humans: HSP90AA1 and HSP90AB1 (cytosolic), HSP90B1 (endoplasmic reticulum) and TRAP1 (mitochondrial). Increased HSP90 expression has been associated with poor prognosis in cancer, and inhibiting HSP90 can lead to degradation of many oncogenic client proteins via the proteasome pathway.1

HSP90 has been the subject of intense drug discovery activities, with several therapeutics under clinical investigation.2 However, the data on single nucleotide polymorphisms (SNPs) and potential somatic mutations within the HSP90-encoding genes in tumor tissue is limited. Target allelic variation can alter drug binding and therapeutic response, as demonstrated by Iressa™'s reported specific efficacy in EGFR-mutant non-small cell lung cancer patients.3 Therefore, it is critical to understand target allelic variance as part of a drug development program.

To facilitate drug development efforts around HSP90, we investigated allelic variation within the coding regions of HSP90AA1 (second isoform) and HSP90AB1 genes in 49 formalin-fixed paraffin- embedded human breast tumor samples. Sample SNP data were compared to control data from the NCBI Entrez SNP database. We observed four synonymous changes within HSP90AA1, and two synonymous changes within HSP90AB1. Intriguingly, we also observed a heterozygous 9-base deletion in exon 1 of HSP90AB1 within one breast tumor patient sample. This deletion results in an alanine>valine substitution at amino acid 22 and a loss of amino acid 23-25 (glutamine, leucine, methionine). The deleted region includes one turn of a 3-turn alpha helix, located within the N-terminal domain structure of the HSP90AB1 protein. Full details of HSP90 allelic variance within breast tumor tissue, and a discussion of the potential functional significance of the deletion, will be provided.

References:

1. Pearl LH, Prodromou C, Workman P. The HSP90 molecular chaperone: an open and shut case for treatment. Biochem J. 2008;410:439-53.

2. Hahn JS. The HSP90 chaperone machinery: From structure to drug development. BMB Reports. 2009;42(10):623-30.

3. Sequist LV, Bell DW, Lynch TJ, Haber DA. Molecular predictors of response to epidermal growth factor receptor antagonists in non- small-cell lung cancer. J Clin Oncol. 2007;25(5):587-95.

Citation Information: Clin Cancer Res 2010;16(14 Suppl):B5.
Abstract B50: A new class of diazonamide analogs with improved antitumor activity
Authors: Li Lin , Wei Qi , Zhou Ming , Ramesh Vijayashree , Wang Xiaodong , Harran Patrick G. , Wang Lai
Published: June 2012

Diazonamide A is a natural product originally isolated from a marine organism. It potently induces G2/M cell cycle arrest. Its molecular mode of action is not fully understood but its potential as a cancer therapeutic is high. We previously reported that AB5, a close analog of diazonamide A, exhibits potent anti-tumor activity in mouse xenograft models. Tumor regression occurs in the absence of systemic toxicity typical of anti-mitotic chemotherapy. Here we show for the first time that the natural diazonamide compound possesses strong tumor killing activity in vivo xenograft models. To streamline our diazonamide synthesis and to define a minimal pharmacophore, we prepared a series of truncated structures. One of these, JP1838, was found to be as potent as AB5. Its simplified structure and shortened synthesis allowed for extensive structure activity relationship analyses. Several modifications markedly improved activity. One analog, JP2295, is >20 fold more potent than AB5 in a MIA Paca-2 pancreatic cancer xenograft model. More importantly, in HPAC pancreatic cancer and HCT-116 colon cancer xenograft models, JP2295 demonstrates greater efficacy and less toxicity than docetaxel and vinorelbine. Safety studies were therefore carried out in NIH Swiss mice. At doses10-fold higher than required for strong efficacy, JP2295 does not exhibit toxicities common to docetaxel and vinorelbine treatments. These include body weight loss, neutropenia, and myelosuppression. Such a large therapeutic window is unique for a small molecule antimitotic and suggests further development is warranted.

Citation Information: Clin Cancer Res 2010;16(14 Suppl):B50.
Abstract B53: Cytotoxic effect of 21kDa protein and antitumor effect of 31KDa protein derived from mushroom, schizophyllum commune
Authors: Wu Yu-Sheng , Chang Po-Yen , Chen Su-Nan
Published: June 2012

The present study attempts to the purified proteins from mushrooms that way activate and stimulate the proliferation of immune cell, resulting in the onset phagocytosis and nature killer cell (NK cell) activity, and promotes the cytotoxicity of tumor cell. In this study 21 and 30 KDa protein from fermentation liquid of the mushroom Schizophyllum commune were purified that exhibit a distinct cytotoxic capability: The 21 KDa protein was demonstrated to be capable of stimulating the NK cell activity, while the 30 KDa protein prevent the proliferation of Lewis lung carcinoma in vitro. Furthermore it was also forward that 21 KDa protein stimulate the the proliferation of mouse splenocyte at a various concentration levels without agglutinating the red blood cell of ICR mouse. Our result showed that when we used concentration level of 27 µg/ml protein, a significant activity of NK cell was obtained (p< 0.05). In addition 30 KDa protein may activate macrophage RAW264.7 enhance to production of nitric oxide and TNF-α, However, the production of nitric oxide by RAW264.7 was relied on the dose of 30 KDa protein in vitro. Based on the results, the purified proteins protein from Schizophyllum commune were potent immue stimulants and has a potential for development as a novel pharmacological agent.

Citation Information: Clin Cancer Res 2010;16(14 Suppl):B53.
Abstract B54: Molecular basis of oncogene cooperation in liver cancer
Authors: Balakrishnan Asha , Lim Lionel , Cairo Stefano , Chandriani Sanjay , Jones Kirk D. , Buendia Marie-Annick , Goga Andrei
Published: June 2012

Combinations of genetic alterations in cancer genes lead to aberrant signaling properties and drive cellular transformation. Whether each oncogene gives rise to unique signals or combinations of oncogenes lead to new properties of cancer cells remains unclear. Using cell-based and animal model systems it has been shown that certain oncogenes can cooperate with each other to induce a fully malignant tumor phenotype. In addition, the combination of oncogenes and the extent of cooperation between them to give rise to a tumor may vary in different cancers.

Cooperativity between MYC and RAS oncogenes has been observed in different cancer types. MYC is often overexpressed and sometimes amplified in cancer, while, activating RAS mutations occur in about 30% human cancers. Hepatocellular carcinoma (HCC) is among the four leading causes of cancer-related death. Currently, except for early surgical intervention or liver transplantation, no effective cures exist. Overexpression of both MYC and activated HRAS together in primary human liver tumors has been associated with aggressive forms of liver cancer with an especially poor prognosis. However, a systematic approach to understanding MYC and RAS cooperation in liver cancer has not yet been undertaken. We have discovered that transgenic mice overexpressing MYC, RAS or both MYC and RAS in their liver, give rise to distinct liver tumors. MYC and RAS coexpression led to faster tumor development and decreased survival. To gain a comprehensive view of the molecular changes that contribute to MYC and RAS oncogene cooperation in de novo liver tumors, we combined the conditional transgenic models of liver cancer with global gene expression, signaling pathway analyses and functional studies. Comparisons were made to clinically annotated human tumors and key pathways validated in cell lines and animal models.

We show that tumors driven by either oncogene or a combination of both are phenotypically and molecularly distinct from each other with differential regulation of multiple genes and pathways. Our work suggests that MYC and RAS cooperate through specific genes, such as CCNE1 and multiple signaling pathways including proliferation, apoptosis, angiogenesis and multiple metabolic pathways, to contribute to liver cancer development. We also show molecular alterations across signaling pathways are comparable between mouse and human liver cancers. Primary human liver tumors can be segregated into distinct subsets based on differentially regulated gene sets from cooperating MYC and RAS tumors. These results indicate that molecular changes underlying MYC and RAS cooperation may serve as ideal molecular markers and therapeutic targets for liver cancer.

Citation Information: Clin Cancer Res 2010;16(14 Suppl):B54.
Abstract B7: Genome-wide analysis of CpG methylation for the radiosensitivity
Authors: Kim Eun-Hye , Park Ae-Kyung , Jung-Hyuck Ahn , Park Woong-Yang
Published: June 2012

Epigenetic regulation is one of the most important mechanisms for the development and the progression of human cancers. To understand the epigenetic control of differential sensitivity to radiotherapy, we investigated the DNA CpG methylation profiles of normal lung epithelial cells and lung cancer cell lines using DNA microarray. Among 27K CpG probes in Illumina BeadChip, we found CpG sites of 1091 genes were differentially methylated in radiosensitive H460 and radioresistant H1299 cell lines against normal lung cells. Among the hypermethylated genes in H1299 cells, promoter CpG methylation and mRNA expression of SERPINB5 and S100A6 were validated by methylation-specific PCR and quantitative RT-PCR, respectively. When we suppressed the expression of these two genes using siRNA in H460 cells, the survival fraction of H460 cells were increased upon ionizing radiation. Promoter CpG sites of CAT and BNC1 were hypomethylated in radioresistant H1299 cells and the introduction of siRNA against CAT or BNC1 in H1299 cells could reduce the resistance to ionizing radiation. Here we report the differentially methylated genes by genome-wide CpG methylation profiling in two lung cancer cell lines, which might prove the epigenetic regulation of radiosensitivity in lung cancer cells.

Citation Information: Clin Cancer Res 2010;16(14 Suppl):B7.
Abstract B8: Correlation of the expression of hepcidin mRNA and the serum iron, ferritin, and TIBC levels in hepatocellular carcinoma
Authors: Pawar Smita C.
Published: June 2012

Background: The present study correlated the expression of hepcidin mRNA and the levels of serum iron, ferritin, and TIBC in hepatocellular carcinoma (HCC).

Methods: Samples of cancerous and noncancerous liver tissue were taken from patients with HCC who underwent hepatectomy. Expression of hepcidin mRNA was evaluated by realtime PCR, and compared in tumors differing in their degree of differentiation and number of tumors. Correlations between hepcidin expression and the serum concentration of hepcidin were evaluated, together with the expression of the serum concentration of biochemical markers of iron metabolism.

Results: Hepcidin mRNA expression in non-cancerous and cancerous tissues was 1791.6 (34.3- 25187.4) and 58.7 (1.93235.8), respectively (P < 0.0001). There were no significant differences in hepcidin expression among tumors differing in their degree of differentiation and number of tumors. The serum concentration of hepcidin did not correlate with hepcidin-mRNA expression. The serum iron level was found to be normal (125.4 ± 21.4 mg/dL). The serum ferritin level was also found to be normal 193.5(14.0-232.9 ng/mL). TIBC was (284.8 ±28.3 ng/mL). There were significant correlations between the serum levels of hepcidin and iron, hepcidin-25 and ferritin and hepcidin and TIBC.

Conclusion: The serum hepcidin concentration was correlated with the levels of serum iron and ferritin, but not with the level of hepcidin mRNA expression in either cancerous or non- cancerous liver tissue. Hepcidin is produced in patients with HCC, from non-cancerous liver tissue, even though production is inhibited in cancerous tissue. Expression of hepcidin mRNA is constitutively suppressed in cancerous, but not in non-cancerous liver tissue of patients with HCC.

Citation Information: Clin Cancer Res 2010;16(14 Suppl):B8.
Abstract IA1-1: Systematic functional genomics and cancer target identification and validation
Authors: Hahn William C.
Published: June 2012

Recent advances in genomics now make it possible to consider enumerating all of the genetic lesions in specific cancers. While these approaches will yield critical information regarding the identify, number, and types of alterations found in human tumors, a complementary approach to decipher the molecular basis of malignant transformation depends upon the application of genome scale tools to annotate the function of genes involved in cancer initiation and progression. Over the past several years, we have developed genome scale RNAi libraries and open reading frame expression libraries that permit a systematic evaluation of genes involved in cancer initiation and maintenance. Using these libraries, we have now performed screens in a panel of human cancer cell lines to systematically identify cancer vulnerabilities. By combining these functional approaches with information derived from mapping the structural abnormalities present in cancer genomes, we have identified several new oncogenes that contribute to cancer development. In addition, many commonly occurring and well- validated oncogenes and tumor suppressor genes remain refractory to molecularly targeted therapies. For example, the proto-oncogene KRAS is mutated in a wide array of human cancers, most of which are aggressive and respond poorly to standard therapies. An alternative strategy for targeting KRAS is to identify gene products that, when suppressed or inhibited, result in cell death only in the presence of an oncogenic allele. Through the use of systematic RNAi screens, we have identified two kinases, TBK1 and STK33 that act in a synthetic lethal manner to selectively kill cancer cell lines that depend on mutant KRAS. Taken together, these studies suggest that combining forward and reverse genetic approaches with information derived from the cancer genome characterization projects will yield a comprehensive list of cancer vulnerabilities and establish a general approach for the rational identification of oncogenic and codependent pathways in cancer.

Citation Information: Clin Cancer Res 2010;16(14 Suppl):IA1-1.
Abstract IA1-2: Drugging oncogenic transcription factors
Authors: Verdine Gregory L.
Published: June 2012

One of the most vexing problems in life science is that of “undruggability,” the difficulty of targeting certain biological macromolecules in vivo using existing drug or ligand discovery technologies. It has been estimated that as many as 80% to 90% of all potential targets, including many that have been extensively validated in humans and in animal models, are undruggable. Among the most biologically validated and yet chemically intractable of all targets are transcription factors, master regulatory proteins that are inappropriately activated in a large percentage of human tumors. The Verdine laboratory is developing powerful new chemistry-based platform technologies to address undruggable targets, including transcription factors. Specifically, the lab is developing “synthetic biologics,” molecules that, like biologics, possess the ability to target large flat surfaces, but that, like small molecules, are fully synthetic and hence can be modified at will. Progress on the development of one class of synthetic biologics—hydrocarbon-stapled alpha-helical peptides—for use in targeting transcription factors will be reviewed in this talk.

References:

1. Schafmeister CE, Po J, Verdine GL. An all-hydrocarbon cross-linking system for enhancing the helicity and metabolic stability of peptides. J Am Chem Soc. 2000;122:5891.

2. Walensky LD, Kung AL, Escher I, Malia TJ, Barbuto S, Wright R, Wagner G, Verdine GL, Korsmeyer SJ. Activation of apoptosis in vivo by a hydrocarbon-stapled BH3 helix. Science. 2004; 305:1466.

3. Bernal F, Tyler AF, Korsmeyer SJ, Walensky LD, Verdine GL. Reactivation of the p53 tumor suppressor pathway by a stapled p53 peptide. J Am Chem Soc. 2007;129: 2456.

4. Moellering RE, Cornejo M, Davis TN, Bianco CD, Aster J, Blacklow SC, Kung A, Gilliland DG, Verdine GL, Bradner JE. Direct inhibition of the NOTCH transcription factor complex. Nature. 2009;462:182.

Citation Information: Clin Cancer Res 2010;16(14 Suppl):IA1-2.
Abstract IA2-1: Modeling drug sensitivity and resistance in human tumor-derived cell lines
Authors: Settleman Jeffrey
Published: June 2012

Agccumulating evidence points to the importance of genomic heterogeneity across human tumors as a critical determinant of the variable clinical response to molecularly targeted cancer therapies. We have used cancer cell lines as a model system for examining the relationship between underlying genotypes and sensitivity to candidate anticancer agents. These studies have revealed the utility of large panels of cancer cell lines to capture the genomic heterogeneity of human cancer and to identify clinically relevant genotype- phenotype relationships. These studies have begun to shed light on mechanisms underlying sensitivity as well as de novo and acquired resistance to a variety of small molecule inhibitors. Using this same platform, we have also identified a mechanism of reversible drug tolerance that involves a distinct chromatin state displayed transiently by small subpopulations of cancer cells. This drug-tolerant state can be disrupted by chromatin-modifying agents, potentially yielding a therapeutic opportunity to prevent or delay the development of more stable genetically conferred drug resistance mechanisms.

Citation Information: Clin Cancer Res 2010;16(14 Suppl):IA2-1.
Abstract IA3-1: Variables for individualizing systemic therapy in patients with lung cancer
Authors: Bepler Gerold
Published: June 2012

Selecting the best therapy for a specific patient with non-small cell lung cancer (NSCLC) has always been the goal for physicians when advising patients and their families. Unequivocal tried-and-true parameters are disease stage, general health status, and the social environment. Other variables, such as age, gender, and histopathology are taken into consideration, but their role in therapeutic decision-making is not firmly established. More recently, tumoral molecular markers, either alone or in combination (referred to as molecular signatures), have emerged as variables for clinical decision making. When evaluating the utility of such markers, it is important to distinguish between the prognostic and predictive utility of a marker. A marker associated with patients’ survival independent of therapy is of prognostic value, while a marker associated with patients’ benefit from a specific therapy is of predictive value. This distinction is best illustrated by ERCC1 (excision repair cross-complementing group 1). In tumor specimens collected from participants in the International Adjuvant Lung Trial, ERCC1 was shown to be both prognostic and predictive. In patients randomized to the trial's control group; i.e., those that did not receive adjuvant chemotherapy, high levels of ERCC1 were associated with longer survival (the prognostic value). In contrast, when taking adjuvant chemotherapy into account, high levels of ERCC1 were associated with lack of benefit from adjuvant chemotherapy (the predictive value); i.e., only patients with low tumoral levels of ERCC1 derived benefit from adjuvant chemotherapy. In practice, predictive markers are of greatest value since they can guide clinical decision making, while a purely prognostic marker is of little or no value to clinical decision making. Many other molecular parameters have since emerged that can be used for decision making. These include EGF receptor mutations, eml4/alk rearrangements, Kras mutations, RRM1 expression levels, TS expression levels, and oncogenic pathway signatures. All of these variables have emerged from laboratory investigations and correlative clinical investigations. Prospective validation studies are required to solidify current knowledge, and many are in progress.

Citation Information: Clin Cancer Res 2010;16(14 Suppl):IA3-1.
Abstract IA3-2: Utilization of genomic signatures to guide therapeutic decisions
Authors: Nevins Joseph R.
Published: June 2012

The heterogeneity of human cancers presents major challenges in understanding disease mechanisms as well as in developing an effective therapeutic strategy for the individual patient. The ability to tailor cancer therapy to characteristics of the individual patient, both with a focus on better utilization of existing standard-of-care regimens as well as new investigational drugs. Towards these goals, we have developed gene expression signatures that have the capacity to predict sensitivity to cytotoxic chemotherapeutics, and utilized these in prospective trials to determine their capacity to guide choice amongst multiple options. In addition, we have also made use of expression profiling to develop signatures of oncogenic pathway deregulation that can then be used to profile the state of these pathways within populations of tumors. These pathway signatures have been useful in dissecting disease heterogeneity, identifying subgroups of tumors with again distinct outcomes, and providing a link in pathway activation with therapeutics. We have extended this concept to develop more refined signatures that can dissect the complexities of many of the known signaling pathways, providing a more precise capacity to probe the activity or deregulation of the pathway and linking to a broader array of therapeutics. This approach, when combined with the capacity to predict chemotherapy use, has the potential to identify therapeutic strategies that make use of all available drugs, matched to the characteristics of the individual patient and thus an approach towards the development of personalized treatment options for the individual patient.

Citation Information: Clin Cancer Res 2010;16(14 Suppl):IA3-2.
Abstract IA3-3: Genetic testing for breast and ovarian cancer: From risk assessment to therapeutic targeting
Authors: Domchek Susan M.
Published: June 2012

Germline genetic variation can be used in a number of ways to improve the care of patients. First, such information can be used to predict the development of disease. Knowledge of risk can lead to targeted preventative strategies. Finally, understanding the genetic etiology for the development of an individual's cancer has the potential to lead to targeted drug development. Inherited BRCA1 and BRCA2 mutations are a model for this paradigm. Since these genes were identified in 1994 and 1995, much work has been done to establish mutation-associated cancer risks and potential management strategies. Deleterious mutations in both genes are associated with a high risk of breast and ovarian cancer, as well as lower risks of other tumor types. Risk-reducing salpingo-oophorectomy significantly reduces the risk of breast and ovarian cancer in mutation carriers and work is ongoing to establish the optimal timing of this procedure as well as the potential for hormone replacement therapy. Women with BRCA1 or BRCA2 mutations require increased breast screening with the addition of breast MRI at the minimum. Prophylactic mastectomy is a valid option. More recently attention has turned to the impact of the biological basis of disease in BRCA1/2 mutation carriers with breast and ovarian cancer on decisions regarding systemic therapy. Due to the role of BRCA1 and BRCA2 proteins in cellular functions such as homologous DNA repair, an enhanced sensitivity to platinum agents and reduced sensitivity to spindle poisons has been postulated and supported by in vitro studies and early clinical data. An additional pathway to target that has been recently identified is poly(ADP-ribose) polymerase (PARP). PARP is a key enzyme in the base-excision repair pathway. In vitro, PARP inhibitors given to BRCA1 or BRCA2 deficient cell lines have led to cell death through synthetic lethality. Early clinical trials have demonstrated efficacy for PARP inhibitors in BRCA1 and BRCA2 mutation carriers with advanced breast and ovarian cancer, with objective response rates in heavily pretreated patients of greater than 40%. Genetic testing for BRCA1 and BRCA2 mutations can be seen as a model for translating the biology of a disease into risk assessment, prevention and treatment, thus demonstrating the potential for inherited genetics to directly impact the care of patients.

Citation Information: Clin Cancer Res 2010;16(14 Suppl):IA3-3.
Abstract IA4-1: Gene-based trial matching
Authors: Yeatman Timothy J.
Published: June 2012

In 2006, the Moffitt Cancer Center initiated an ambitious initiative in personalized medicine called Total Cancer Care. One goal of the project was to develop a protocol and informed consent, a biorepository and a clinical and molecular database that would support the next generation of clinical trials. To date, the single protocol has accrued more than 57,000 patients and over 17,000 tumor samples, of which more than 12,000 have been molecularly profiled on a global gene expression microarray. Sequencing analyses now suggest there are a finite number (~12) of cancer pathways activated by specific driver genes. Emerging data suggest gene expression profiles may provide more inclusive portraits of pathway activation than simple canonical gene mutation analysis. The resultant clinical and molecular database we are developing holds promise for developing new trial approaches that may be faster, require fewer patients, and may increase response rates by finding the right patients for the right trials through gene based trial matching. New approaches to trial development and design that leverage a database, and the associated technical and regulatory challenges, will be discussed.

Citation Information: Clin Cancer Res 2010;16(14 Suppl):IA4-1.
Abstract IA5-2: Evolutionary games in cancer therapy
Authors: Gatenby Robert
Published: June 2012

A number of successful systemic therapies are available for treatment of disseminated cancers. However, tumor response to these treatments is almost invariably transient and therapy fails due to emergence of resistant populations. The latter reflects the temporal and spatial heterogeneity of the tumor microenvironment as well as the evolutionary capacity of cancer phenotypes to adapt to therapeutic perturbations. Interestingly, although cancers are highly dynamic systems, cancer therapy is typically administered according to a fixed, linear protocol. Treatment is changed only when the tumor progresses but successful tumor adaptation begins immediately upon administration of the first dose. Applying evolutionary models to cancer therapy demonstrate the potential advantage of using more dynamic, strategic approaches that focus not just on the initial cytotoxic effects of treatment but also on the evolved mechanisms of cancer cell resistance and the associated phenotypic costs. The goal of evolutionary therapy is to prevent or exploit emergence of adaptive tumor strategies. Examples of this approach include adaptive therapy and double bind therapy. The former continuously alters therapy to maintain a stable tumor volume using a persistent population of therapy-sensitive cells to suppress proliferation of resistant phenotypes. The latter uses the cytotoxic effects of an initial therapy to promote phenotypic adaptations that are then exploited using follow-on treatment.

Citation Information: Clin Cancer Res 2010;16(14 Suppl):IA5-2.
Abstract IA5-3: HIFs, hypoxia, and tumor progression
Authors: Simon M. Celeste
Published: June 2012

Hypoxia-inducible factor (HIF)-1α and −2α display unique and sometimes opposing activities in regulating cellular energy homeostasis, cell fate decisions, and oncogenesis. To fully characterize hypoxic adaptations, distinct functions of HIF-1α versus HIF-2α must be elucidated. Macrophages accumulate both HIF-αS under hypoxia, but HIF-2α overexpression in tumor-associated macrophages (TAMs) is specifically correlated with high-grade human tumors and poor prognosis. HIF-1α regulates myeloid-mediated inflammatory and antibacterial activities, in part through control of glycolysis and ATP production. However, the precise role of HIF-2α during macrophage-mediated inflammatory responses remained unclear. We demonstrate here that mice lacking myeloid HIF-2α are resistant to lipopolysaccharide-induced endotoxemia and display a marked inability to mount inflammatory responses to cutaneous and peritoneal irritants. Furthermore, HIF-2α directly regulates pro-inflammatory cytokine/chemokine expression in macrophages activated in vitro. Using independent murine hepatocellular and colitis-associated colon carcinoma models, we show that HIF-2α -deficient macrophages exhibit migratory defects associated with reduced tumor cell proliferation and progression. Of note, HIF-2α modulates macrophage migration by regulating the expression of cytokine receptor M-CSFR and chemokine receptor CXCR4, without altering intracellular ATP levels. Collectively, our data identify HIF-2α as an important regulator of innate immunity, suggesting it may be a useful therapeutic target for treating inflammatory disorders and cancer.

Citation Information: Clin Cancer Res 2010;16(14 Suppl):IA5-3.
Abstract IA8-1: Pancreatic cancer stem cells and metastasis
Authors: Matsui William H.
Published: June 2012

Emerging evidence suggest that cells within an in individual tumor are phenotypically and functionally heterogeneous despite their clonal origins. Moreover, in several human cancers, the capacity to form tumors ectopically in immunodeficient mice is restricted to specific cell populations. The sustained proliferative capacity of these tumor initiating cells or cancer stem cells (CSC) has suggested that they play a major role in disease initiation and relapse, but their role in disease progression is less clear. We have studied the expression of aldehyde dehydrogenase (ALDH), an intracellular enzyme highly expressed in normal stem cells, in pancreatic adenocarcinoma. We found that ALDH+ pancreatic cancer cells are highly clonogenic both in vitro and in vivo and their presence in resected pancreatic primary tumors is significantly associated with shortened overall survival. ALDH+ cells were also commonly found in metastatic pancreatic cancer lesions even in patients whose primary tumors lacked ALDH expression. Progression to metastatic disease requires cell migration to ectopic sites in addition to clonogenic growth potential, and we found that ALDH+ cells expressed lower levels of E-CADHEDRIN and higher levels of SLUG consistent with the epithelial to mesenchymal transition (EMT). Moreover, compared to ALDHneg cells, ALDH+ pancreatic cancer cells were more invasive and migratory in vitro and metastatic in vivo. Therefore, in pancreatic carcinoma, CSC express key functional properties that suggest a major role in the formation of metastases and disease progression.

Citation Information: Clin Cancer Res 2010;16(14 Suppl):IA8-1.
Abstract IA9-1: Is taxol resistance related to tubulin isotypes?
Authors: Horwitz Susan Band
Published: June 2012

Microtubules are an important component of the euraryotic cytoskeleton and are essential for normal cell division. They are also a validated target for antitumor drugs, such as taxol, that bind to the – tubulin subunit in the microtubule polymer. Endogenous resistance or the development of drug resistance during treatment with taxol is a serious clinical problem. Understanding the emergence of taxol resistance and being able to predict patient response would enhance the efficacy of the drug. A number of mechanisms, such as overexpression of P-glycoprotein that acts as an ATP-dependent drug-efflux pump, or mutations in the drug-binding site in tubulin, have been described. Of particular interest to our research, is the aberrant expression of β-tubulin isotypes in cancer.

Tubulin is composed of α- and β-tubulin subunits that exist as heterodimers. In humans, there are seven β-tubulins and eight β-tubulins, each the product of a distinct gene located on different chromosomes. Each isotype can undergo extensive posttranslational modifications such as acetylation, phosphorylation, polyglutamylation, polyglycylation and reversible tyrosination, all of which add to the complexity of the tubulin/microtubule system. Most of the divergence between the isotypes is found in the last 15-20 amino acids at the carboxyl end of tubulin and in addition, most posttranslational modifications of tubulin occur in this region.

For the most part, tubulin isotypes have been detected at the mRNA level or at the protein level with isotype-specific antibodies. Our laboratory has developed proteomic methods, including highresolution isoelectrofocusing, CNBr cleavage and mass spectrometry that allow us to determine the isotype content and posttranslational modifications of tubulin in cells and tissues in a single experiment. We have utilized taxol, which enhances tubulin polymerization, to isolate sufficient tubulin from cells and are developing methods to quantify tubulin isotype expression by mass spectrometry.

The overexpression of βIII-tubulin has been associated with resistance to taxanes in a range of tumor types and in taxol-resistant cells generated in our laboratory. βIII-tubulin is normally expressed only in neuronal cells. However, it is aberrantly expressed in numerous malignant tissues and could be a meaningful prognostic factor for treatment outcome. As has been shown by others in different tumors, in our laboratory an immunohistochemical analysis of 47 tumor specimens from head and neck patients determined that overexpression of β-III tubulin was highly prognostic of survival.

Citation Information: Clin Cancer Res 2010;16(14 Suppl):IA9-1.
Abstract PR1: Genomic discovery of CD44-SLC1A2 gene fusions in gastric cancer
Authors: Tao Jiong , Ramnarayanan Kalpana , Huang Baohua , Tan Iain Beehuat , Ooi Chia Huey , Lee Minghui , Zhang Shenli , Leong Siew Hong , Ivanova Tatiana , Ganesan Kumaresan , Gopalakrishnan Veena , Rha Sun Young , Chung Hyun Cheol , Yap Celestial , Palanisamy Nallasivam , Tan Patrick
Published: June 2012

Among the various genomic abnormalities associated with cancers, fusion genes and transcripts are particularly notable due to their cancer-specific nature and translational potential as diagnostic and therapeutic targets. In pediatric acute lymphoblastic leukemia (ALL), assays detecting the AML-ETO and PML-RAR fusion genes are routinely used to diagnose particular clinical subtypes, and treatment of chronic myelogenous leukemia (CML), a disease once associated with extremely poor prognosis, has been revolutionized by imatinib, an inhibitor of the BCR-ABL fusion gene. While fusion genes are well- known in hematological malignancies, our knowledge of recurrent fusion events in solid epithelial tumors is far less mature. To date, only two fusion genes have been identified in solid tumors, including TMPRSS2-ERG in prostate cancer, and EML4-ALK in non-small cell lung cancer. No recurrent fusion genes have been so far identified in common gastrointestinal cancers such as stomach, colon and esophageal adenocarcinoma. In this study, to identify genes affected by genome rearrangements in gastric cancer (GC), which is the second highest cause of global cancer mortality, we analyzed chromosomal imbalances in a cohort of 123 primary GCs and cell lines, and discovered several tumors exhibiting recurrent genomic breakpoints in the SLC1A2/EAAT2 glutamate transporter. 5’ RNA ligase mediated rapid amplification of cDNA ends (RLM-RACE) analysis of a GC cell line with SLC1A2 breakpoints (SNU16) revealed expression of a CD44-SLC1A2 fusion transcript, computationally predicted to result in a truncated but functional SLC1A2 protein. In an independent tumor panel, CD44-SLC1A2 gene fusions were detected in 4% to 5% of GCs (2/43), but not in adjacent matched normal gastric tissues. Using custom-designed fusion-specific siRNAs, we show that silencing of CD44-SLC1A2 in fusion-positive SNU16 cells significantly reduced cellular proliferation, invasion, and colony formation, but not in cell lines lacking CD44-SLC1A2 expression. CD44-SLC1A2 silencing also significantly reduced intracellular glutamate levels and sensitized SNU16 cells to cisplatin. Fusions of SLC1A2 to upstream CD44 regulatory elements likely causes SLC1A2 transcriptional dysregulation, as tumors expressing abnormally high SLC1A2 levels also tended to be CD44-SLC1A2 positive. CD44-SLC1A2 gene fusions may be one mechanism used by cancers to establish a pro-oncogenic metabolic milieu favoring tumor growth and survival. We believe that our study will be of great interest to the gastric cancer community, as it represents the first recurrent fusion transcript identified in this disease (and for that matter any common gastrointestinal cancer).

Citation Information: Clin Cancer Res 2010;16(14 Suppl):PR1.
Abstract PR2: Therapeutic intervention targeting a Hedgehog-dependent barrier to drug delivery in pancreatic cancer
Authors: Olive Kenneth P. , Jacobetz Michael , Gopinathan Aarthi , Goldgraben Mae , Ireland Heather , Reichelt Stefanie , Howat William J. , Whitebread Nigel , McGovern Karen , Adams Julian , Iacobuzio-Donahue Christine , Griffiths John , Tuveson David
Published: June 2012

Ductal pancreatic tumors are unusually resistant to chemotherapy, exhibiting primary resistance to each of the numerous regimens tested to date. These tumors are also unusually desmoplastic and harbor a sparse and inefficient vasculature. The resulting lack of perfusion appears to play a role in the inefficient delivery of numerous chemotherapeutic agents to the parenchyma of pancreatic tumors. Recent evidence has implicated the sonic hedgehog pathway in promoting desmoplasia through a paracrine signaling mechanism active in pancreatic tumors of both humans and the Kras/p53/PdxCre (KPC) mouse model. We sought to evaluate the dependence of stromal desmoplasia on Hedgehog (Hh) pathway signaling and, by extension, assess the effects of Hh pathway inhibition on drug delivery and chemoresistance.

Using IPI-926, a semisynthetic inhibitor of the Smoothened protein, we found that stromal contribution was markedly diminished within 10 days of inhibition of the Hh pathway. Paradoxically, the depletion of stromal cells was coincident with an increase in microvessel density, despite previous data indicating a pro-angiogenic role for the Hh pathway. These non-cell autonomous changes resulted in an increase in the delivery of small molecules to KPC pancreatic tumors and an increase in apoptosis when administered in combination with gemcitabine. Ultimately, mice treated with both IPI-926 and gemcitabine had a significant extension of survival and a decrease in the incidence of liver metastases. We conclude that the Hh pathway plays an important role in the maintenance of pancreatic tumor stroma and that this contributes to the primary chemoresistance of pancreatic tumors. These data also support the clinical evaluation of agents that target the stroma in pancreatic cancer.

Citation Information: Clin Cancer Res 2010;16(14 Suppl):PR2.
Abstract PR3: Preclinical and molecular profiling data suggest LumB breast cancer as a potential indication for co-targeting IGF1R and mTOR with MK-0646 and MK-8669
Authors: Zhang Theresa , Feldman Igor , Sathyanarayanan Sriram , Haines Brian , Paweletz Cloud , Nebozhyn Michael , Shumway Stuart , Roberts Brian , Arthur William , Strack Peter , Huang Pearl , Dai Hongyue , Buser-Doepner Carolyn , Loboda Andrey , Watters James
Published: June 2012

There has been increasing interest in developing cancer therapies targeting PI3K pathway nodes. However, inhibition of a single node in PI3K pathway such as mTOR by rapamycin analogues results in compensatory activation of survival signaling pathway such as AKT and thereby limiting monotherapy activity. Therefore, in most tumor types, multipathway inhibition, guided by an in-depth understanding of feedback and crosstalk between pathways, may be required for tumor regression. It is well known that that mTOR inhibition upregulates pAKT via the S6K-IRS2 negative feedback loop. Inhibiting both mTOR and IGF1R may therefore ablate such feedback upregulation and lead to clinical response. However, it is unclear which tumor types will respond to the combination in the clinic. Here, we present preclinical and molecular profiling data that supports LumB breast cancer as a potential indication for MK-8669/MK-0646 (mTOR/IGF1 R inhibitor combination). When a panel of over 60 breast cancer cell lines was treated with MK-8669, ER+ cell lines and HER2+ cell lines were clearly more responsive than the triple negative ones. Meanwhile, the status of the MAPK pathway, as captured by a RAS gene expression signature, correlated with resistance to MK-8669 across the panel. Moreover, MK-8669 treatment unregulated multiple key nodes of the IGF1R pathway in the breast cell line panel, especially IRS2, whose upregulation correlated with the response to MK-8669. Furthermore, IGF1R, whose mRNA level correlates with the response to MK-0646 (IGF1 Ri) in multiple internal and external studies, is the highest in a subset of LumB tumors, suggesting a potential dependency on the IGF1R pathway in those tumors. Finally, a comparison between the gene expression profiles of breast cancer cell lines and tumors revealed that the ER+ breast cancer cell lines only represented the LumB, not LumA, subtype of human breast tumors. Taken together, these findings allow us to hypothesize that LumB breast cancer may be enriched in responders to the MK-0646/MK-8669 combination. In 2009, Merck initiated a phase I trial of MK-8669/MK-0646 in which clinical response was observed in LumB breast cancer patients. A phase II clinical trial has been initiated to test the hypothesis retrospectively.

This talk is also presented as Poster A52.

Citation Information: Clin Cancer Res 2010;16(14 Suppl):PR3.
Abstract PR5: Prediction of survival in diffuse large B-cell lymphoma based on the expression of two genes integrating tumor and microenvironment
Authors: Gentles Andrew J. , Alizadeh Ash A. , Alencar Alvaro J. , Kohrt Holbrook E. , Houot Roch , Goldstein Matthew J. , Natkunam Yasodha , Advani Ranjana H. , Gascoyne Randy D. , Briones Javier , Plevritis Sylvia K. , Lossos Izidore S. , Levy Ronald
Published: June 2012

Several gene expression signatures are predictive of prognosis in diffuse large B cell lymphoma (DLBCL), but the lack of practical methods for a genome scale analysis has restricted their clinical applicability. Towards construction of a molecular predictor amenable to rapid testing on routinely obtained diagnostic clinical specimens, we studied genes previously reported to be associated with survival in DLBCL, testing and validating risk scoring models with robust survival associations in the current therapeutic era.

We identified LMO2 expression as a robust univariate predictor of survival and cell of origin classification of DLBCL, with independent prognostic value. We examined bivariate models combining expression of LMO2 with other genes, and identified TNFRSF9 as a tumor microenvironment gene with independent prognostic influence. A combined model integrating both LMO2 and TNFRSF9 expression was independent of “cell of origin” classification, “stromal signatures,” International Prognostic Index (IPI), and added to the predictive power of IPI. A composite model was validated in multiple independent patient cohorts using public microarray data. Using routinely obtained formalin fixed, paraffin embedded diagnostic specimens from an independent cohort, we developed a simple assay validating the clinical utility of this 2-gene model, as well as a composite model integrating the IPI. In conclusion, measurement of a single gene expressed by tumor cells and a single gene expressed by the immune microenvironment is sufficient to predict overall survival in patients with DLBCL treated with R-CHOP. A combined model serves as a robust clinical risk assessment tool.

This talk is also presented as Poster A27.

Citation Information: Clin Cancer Res 2010;16(14 Suppl):PR5.