bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract IA8: Discovering drivers in rare ovarian cancer subtypes
Authors: Huntsman David G.
Published: August 2014

Over the past several years it has become accepted that subtypes of ovarian carcinomas (high grade serous, endometriod, clear cell, low grade serous and mucinous carcinoma) are discrete diseases. Therefore, if we are to improve ovarian cancer morbidity and mortality, cancer prevention, early detection and/or screening strategies must be developed to deal with the challenges posed by each of these diseases. Whereas high grade serous carcinoma is relatively common, the other ovarian carcinoma subtypes represent 30% of cases in total and therefore are all rare. Rare cancers are usually marked by a combination of an unusual cells of origin and unusual mutations or other genomics drivers. We have undertaken a series of genomics studies to identify key drivers in rarer ovarian cancers. Some cancers such as granulosa cell tumors of the ovary and sertoli cell mutations have been found which are either pathognomonic or highly specific for that cancer type. Those mutations have great promise as diagnostics. Since the target cancers are rare such work is not possible without broad ranging international collaborations. For more common entities such as clear cell carcinoma concentrations of mutations can be found such as mutations in ARID1a. As such mutations are nonspecific they are less likely to be used diagnostically however this increases their potential therapeutic value. However, it is likely that the mutations or mutated genes have a specific role in the cell of origin of the cancers involved and therefore cell context specific cell lines of model systems will be required for functional validation.

Although rare cancers are by definition unusual and therefore represent smaller medical problems they are of course highly significant to the patients involved and provide a model through which the stratification of management for common cancers can be undertaken.

Citation Format: David G. Huntsman. Discovering drivers in rare ovarian cancer subtypes. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Ovarian Cancer Research: From Concept to Clinic; Sep 18-21, 2013; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2013;19(19 Suppl):Abstract nr IA8.
Abstract A07: Targeting SETD2 knockout cells: A synthetic lethal approach to treating ccRCC
Authors: Fahey Catherine C. , Hacker Kathryn E. , Jin Jian , Davis Ian J. , Rathmell W. Kimryn
Published: August 2014

Background: Kidney cancer is estimated to affect 65,150 newly diagnosed individuals in 2013. Approximately 70% of these diagnoses will be clear cell renal cell carcinoma (ccRCC). Many targeted therapies for ccRCC are currently being pursued, as ccRCC is resistant to radiation and often does not respond to chemotherapy. The most commonly mutated tumor suppressor gene in ccRCC is VHL, located on chromosome 3. The loss of chromosome 3p is a high frequency event in ccRCC, which often also encompasses the genes PBRM1, BAP1, and SETD2. Mutations in one or more of these genes represent the next most common common genetic alterations in ccRCC. In our preliminary data, we have observed that mutations in SETD2, in particular, area associated with global deficits in chromatin packaging and organization.

Methods: We are pursuing the opportunity to exploit SETD2 loss as a source of cellular fragility by performing a small molecule screen on SETD2 wild type and SETD2 knockout cell lines. We will use a screening set of epigenetically targeted compounds to perform a high throughput screen with cell viability as the endpoint, as well as use a selected few compounds to compare effect on wild type and knockout cells in a more in depth manner.

Results: Preliminarily, we have tested SETD2 knock-down lines to confirm that we can effectively preform all aspects of this screen, and we have observed that one compound may specifically target SETD2 knock-down lines for reduced viability. In our current studies, we are repeating testing with the selected few compounds and beginning the high throughput screen with a SETD2 knockout cell line.

Conclusion: Mutations in chromatin modifying genes in ccRCC present an opportunity for synthetic therapeutic approaches to induce reduced cell viability, as well as to identify unique meaningful interactions between chromatin modifier genes.

Citation Format: Catherine C. Fahey, Kathryn E. Hacker, Jian Jin, Ian J. Davis, W. Kimryn Rathmell. Targeting SETD2 knockout cells: A synthetic lethal approach to treating ccRCC. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Synthetic Lethal Approaches to Cancer Vulnerabilities; May 17-20, 2013; Bellevue, WA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(5 Suppl):Abstract nr A07.
Abstract A09: Induced aggravation of oxidative DNA damage as a targeted synthetic lethal approach in mismatch repair-deficient tumors
Authors: Fontebasso Yari , Lord Christopher J. , Ashworth Alan
Published: August 2014

The post-replicative DNA mismatch repair (MMR) pathway plays a key role in the maintenance of genomic stability. MMR corrects mismatches within the DNA helix that arise due to errors in nucleotide incorporation during either semi-conservative replication or synthesis associated with DNA repair. The importance of this system is testified by the fact that mutations affecting components of this repair pathway cause a “mutator” phenotype and predisposition to a wide variety of malignancies including colorectal, gastric, endometrial, and urothelial cancers. For example, the hereditable disorder Lynch syndrome (hereditary nonpolyposis colon cancer) is associated with germline loss of function mutations in the MMR tumor suppressor genes MLH1, MSH2, PMS2 and MSH6. In addition to this familial syndrome, MMR deficiency is present in 15% to 17% of all colorectal cancer cases and a common cause of nonfamilial MMR deficiency is biallelic hypermethylation of the MLH1 promoter that results in a reduction of MLH1 expression.

Synthetic lethal relationships have been identified that involve specific MMR genes, suggesting that the synthetic lethal paradigm could be applied to MMR deficiency. Previously, efforts to functionally identify genetic DNA mismatch repair synthetic lethalities and potential therapeutic targets have focused on the analysis of either candidate genes or relatively small gene subsets such as protein kinases. In order to define additional SL targets in MMR-deficient genetic backgrounds, we describe here the application of an shRNA screen in matched isogenic dMMR/pMMR (MMR-deficient/MMR-proficient) model cell lines. Using this screening approach, we identify new synthetic lethal interactions between MMR deficiency and components of the base excision repair and of the nucleotide sanitization systems. We propose that selective aggravation of oxidative damage constitutes a promising therapeutic approach in mismatch repair - deficient cancer cells.

Citation Format: Yari Fontebasso, Christopher J. Lord, Alan Ashworth. Induced aggravation of oxidative DNA damage as a targeted synthetic lethal approach in mismatch repair-deficient tumors. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Synthetic Lethal Approaches to Cancer Vulnerabilities; May 17-20, 2013; Bellevue, WA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(5 Suppl):Abstract nr A09.
Abstract A13: Identification of evolutionarily conserved genetic interactions in DNA mismatch repair
Authors: Tosti Elena , Katakowski Joseph A. , Schaetzlein Sonja , Kim Hyun-Soo , Ryan Colm J. , Shales Michael , Roguev Assen , Krogan Nevan J. , Palliser Deborah , Keogh Michael-Christopher , Edelmann Winfried
Published: August 2014

The DNA mismatch repair (MMR) system is responsible for correcting base substitution and insertion-deletion mutations (IDLs) generated during erroneous replication in bacteria, yeast and mammals. MMR complexes also recognize damaged-base mispairs resulting from environmental exposure to DNA damaging agents. The loss of MMR causes a “mutator” phenotype, resulting in the genome-wide accumulation of mutations, and is the underlying cause for Hereditary Non-polyposis Colorectal Cancer / Lynch Syndrome (HNPCC/LS) and a significant proportion of sporadic colorectal cancer (CRC). MMR-deficient tumors also display resistance to DNA damaging agents and, as a consequence, are resistant to a variety of commonly chemotherapeutic agents. Thus, the development of novel therapeutic strategies that more efficiently target MMR-deficient cancer cells would be highly desirable. A promising new direction to identify potential targets for anticancer treatment is the harnessing of synthetic lethality. Here, we have identified conserved synthetic lethal / sick genetic interactions (GIs) for MMR factors between two distant yeast species, S. pombe and S. cerevisiae. We have confirmed several of these negative GIs in mammalian cells, indicating that they are evolutionarily conserved. Specifically, we have identified a negative genetic relationship between Msh2, a major MMR component mutated in colorectal cancer, and Senp6 protease, which regulates the SUMOylation of a range of genome maintenance proteins. Our findings suggest that Senp6 is a promising new target for the treatment of MMR-deficient CRCs.

Citation Format: Elena Tosti, Joseph A. Katakowski, Sonja Schaetzlein, Hyun-Soo Kim, Colm J. Ryan, Michael Shales, Assen Roguev, Nevan J. Krogan, Deborah Palliser, Michael-Christopher Keogh, Winfried Edelmann. Identification of evolutionarily conserved genetic interactions in DNA mismatch repair. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Synthetic Lethal Approaches to Cancer Vulnerabilities; May 17-20, 2013; Bellevue, WA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(5 Suppl):Abstract nr A13.
Abstract A26: Cross-species analysis of genome-wide regulatory models elucidates master regulators of prostate cancer progression and treatment response
Authors: Mitrofanova Antonina , Aytes Alvaro , Lefebvre Celine , Shen Michael , Abate-Shen Cory , Califano Andrea
Published: August 2014

The study of cancer therapeutics in mouse models is impaired by our limited understanding of whether the regulatory mechanisms that mediate their activity are conserved in human patients. To address this limitation, we have constructed a mouse prostate cancer regulatory model (interactome) based on in vivo drug-based perturbations of 15 transgenic models of prostate cancer as well as a human interactome from a large-scale set of molecular profiles of patient derived tissue. For the mouse interactome, we performed molecular perturbations by treatment with small molecules, including inhibitors of the androgen receptor, tyrosine kinase receptors, MAPK, Akt/mTOR, JAK/STAT, and NF-KB signaling pathways as well as several chemotherapeutic agents. We then used a cross-species analysis to independently identify and match master regulators of cancer progression with the therapeutic compounds that optimally abrogate their activity both in the human and in the mouse regulatory models. Cross-species interactome interrogation represents a new paradigm for ‘human to mouse to human’ (H2M2H) analyses, aimed at maximizing translational potential. By interrogating our regulatory models using molecular profiles of cancer progression, we identified two genes, FOXM1 and CENP-F, that are synergistically required for the maintenance of aggressive, metastatic prostate tumors and are predictive of clinical outcome. Indeed, lentivirus mediated shRNA co-silencing of these master regulators dramatically decreases tumorigenesis in vivo. Interrogation of these interactomes using small molecule signatures further identified candidate combinations that successfully abrogate the activity of the FOXM1/CENPF axis in metastatic prostate cancer GEM models, and significantly reduce tumor and metastatic burden in vivo, thus improving survival significantly over standard of care chemotherapy. Our findings suggest that simultaneous targeting of FOXM1 and CENPF may be especially beneficial in patients who have failed conventional chemotherapy.

Citation Format: Antonina Mitrofanova, Alvaro Aytes, Celine Lefebvre, Michael Shen, Cory Abate-Shen, Andrea Califano. Cross-species analysis of genome-wide regulatory models elucidates master regulators of prostate cancer progression and treatment response. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Synthetic Lethal Approaches to Cancer Vulnerabilities; May 17-20, 2013; Bellevue, WA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(5 Suppl):Abstract nr A26.
Abstract A39: Quantitative FRET technology for SUMOylation cascade and high-throughput screening assay for SUMOylation inhibitor in cancer drug discovery
Authors: Liao Jiayu , Wiryawan Hilda , Song Yang , Liu Yan , Jiang Ling , Malik Harbani Kaur , Saaredra Amanda N.
Published: August 2014

The ubiquitin—proteasome system and ubiquitin-like protein pathways, such as SUMOylation, are critical in protein homeostasis and activities in vivo and are emerging as a new strategy to treat many acute and chronic human diseases, such as cancers. Although various kinase inhibitors have been developed as target-based therapy, solid tumors are still challenges in clinical therapy because various resistant are developed after kinase inhibitor treatments, and therapeutic agents with novel mechanisms are urgently needed. SUMO has been shown to modify various critical proteins, such as p53, MDM2, Estrogen receptor and androgen receptors. More recently, a genome-wide siRNA screening shown that inhibition of SUMO E1 ligases can lead to synergistically lethality of c-Myc overexpressed breast cancer cells. However, so far, specific inhibitor of SUMOylation is still not available for the scientific or pharmaceutical communities.

We developed a novel quantitative Förster resonance energy transfer (FRET) technology platform for both basic kinetics parameter determinations and high-through screening (HTS) assays for SUMOylation cascade. The novel theoretical and experimental procedures for protein interactions affinity (Kd) determinations in the SUMOylation cascade, including the interaction between SUMO1 and its E2 ligase, Ubc9, E1 heterodimers(Aos1 and Uba2), E1 and E2 interactions(Uba2 and Ubc9), and E2 and substrate interactions(Ubc9 and RanGap1c) and protease kinetics, Kcat/KM of SENP1 endopeptidase activity have been developed in a systems biology manner. The data are in good agreement with traditional methods. Multiple FRET-based HTS assays have also been developed and HTS campaigns have led to very promising hit that can preferentially kill Non-small cell lung cancer cells. The novel SUMOylation inhibitor can be used for cancer treatments by synergistically lethality strategy.

Note: This abstract was not presented at the conference.

Citation Format: Jiayu Liao, Hilda Wiryawan, Yang Song, Yan Liu, Ling Jiang, Harbani Kaur Malik, Amanda N. Saaredra. Quantitative FRET technology for SUMOylation cascade and high-throughput screening assay for SUMOylation inhibitor in cancer drug discovery. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Synthetic Lethal Approaches to Cancer Vulnerabilities; May 17-20, 2013; Bellevue, WA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(5 Suppl):Abstract nr A39.
Abstract B10: ER stress protein GRP78 as a therapeutic target combined with antiangiogenic therapy in renal cell carcinoma
Authors: Han Kyung Seok , Li Na , Li Estelle , Ladan Fazli , Martin Gleave , So Alan
Published: August 2014

Background: Antiangiogenic therapy deprives oxygen and nutrition from the tumor. These stress conditions cause unfolded or misfolded proteins in tumor cells. Glucose regulated protein 78 (GRP78) binds to unfolded proteins and dissociates from the membrane-bound ER stress sensors. Dissociation of GRP78 from these stress sensors allows their subsequent activation which suppresses global mRNA translation to protect cells from excessive unfolded proteins. We investigated a potential role of GRP78 as a combined therapeutic target in renal cell carcinoma treated with antiangiogenic therapy.

Methods: Renal cell carcinoma cells (Caki-1, Caki-2, UMRC-3 and UMRC-6) were used to investigate the effect of GRP78 knockdown, which was performed by small interfering RNA. Caki-1 xenografts were developed and treated with sunitinib 40mg/kg/day to evaluate in vivo expression of GRP78 during antiangiogenic therapy. Caki-1 cells stably overexpressing GRP78 were developed to investigate the role of GRP78 in cancer cell. Hypoxic stress was induced by 1% hypoxia chamber and hypoglycaemic stress was induced by glucose-free media. Downstream signalling pathways of GRP78 were evaluated by Western blots.

Results: In vitro hypoxia and/or glucose deprivation induced GRP78 upregulation in Caki-1 cells. GRP78 was also induced in Caki-1 xenografts treated by sunitinib. Overexpression of GRP78 increased tumor proliferation in hypoxic and/or hypoglycemic stresses by activating PERK/eIF2α pathway and protected tumor cells from stress-induced apoptosis. Knockdown of GRP78 using small interference RNA inhibited cancer cell survival and induced apoptosis in renal cell carcinoma cells in vitro. GRP78 knockdown also sensitized renal cell carcinoma cells to ER stress-induced apoptosis and hypoxic and hypoplycemic stress-induces apoptosis.

Conclusions: Antiangiogenic therapy induces ER stress by depriving oxygen and glucose from renal cell carcinoma. ER protein GRP78 has a critical role in protecting renal cell carcinoma cells from hypoxic and hypoglycemic stress induced by antiangiogenic therapy. Knockdown of GRP78 sensitizes RCC cells to apoptotic cell death from anti-angiogenic stresses. Our results suggest that GRP78 is a novel therapeutic target in renal cell carcinoma management.

Citation Format: Kyung Seok Han, Na Li, Estelle Li, Fazli Ladan, Gleave Martin, Alan So. ER stress protein GRP78 as a therapeutic target combined with antiangiogenic therapy in renal cell carcinoma. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Synthetic Lethal Approaches to Cancer Vulnerabilities; May 17-20, 2013; Bellevue, WA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(5 Suppl):Abstract nr B10.
Abstract B28: Screening for kinase dependencies in HPV-associated cancer
Authors: Fenton Tim , Brough Rachel , Williams Luke , Bajrami Ilirjana , Ashworth Alan , Lord Chris , Boshoff Chris
Published: August 2014

Human papillomavirus (HPV) is the primary causative agent in cervical cancer, a number of other anogenital cancers and a growing subset of head and neck squamous cell carcinomas (HNSCC). HPV-driven tumour cells exhibit a dependence upon the continued expression of two viral oncogenes, E6 and E7, which act primarily by promoting degradation of the p53 and pRb tumour suppressors. While pharmacological targeting of E6 and E7 has proven difficult, we hypothesized that tumour cells expressing these oncogenes may in turn become dependent upon the activity of specific cellular proteins. Since protein kinases have proven readily targetable using small molecule drugs, we screened a kinome-wide siRNA library against a panel of HPV-negative and HPV-positive HNSCC and cervical cancer cell lines to identify kinases specifically required in HPV-positive cancer cells.

Citation Format: Tim Fenton, Rachel Brough, Luke Williams, Ilirjana Bajrami, Alan Ashworth, Chris Lord, Chris Boshoff. Screening for kinase dependencies in HPV-associated cancer. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Synthetic Lethal Approaches to Cancer Vulnerabilities; May 17-20, 2013; Bellevue, WA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(5 Suppl):Abstract nr B28.
Abstract B38: Targeting FOXM1 in multiple myeloma
Authors: Tompkins Van S. , Gu Zhimin , Xu Hongwei , Tricot Guido , Zhan Fenghuang , Janz Siegfried
Published: August 2014

Unprecedented progress in our understanding of the biologic and molecular genetic underpinnings of multiple myeloma (MM) has recently led to the development of novel targeted therapeutic agents, including proteasome inhibitors, immunomodulatory drugs, CS1-binging antibody, and histone deacetylase inhibitors, which have produced tangible, evidence-based benefits for patients with MM. Nonetheless, the overall outcome remains grim, due in large part to limitations in treating high-risk MM. We recently determined that the level of FOXM1 mRNA expression is of prognostic significance for myeloma patients, as both event-free survival and overall survival were reduced in cases exhibiting high FOXM1 expression. Forty-six of 351 myeloma patients (13.1%) had elevated FOXM1 message, with the majority (29/46, 63%) residing in the MAF/MAFB and proliferation high-risk molecular subgroups. Upregulation of FOXM1 was also observed in patients deemed high-risk using the 70-gene signature as a metric. These results suggest that upregulation of FOXM1 is a feature of high-risk MM, leading to the hypothesis that up-regulation of FOXM1 contributes to increased MM aggressiveness. To evaluate whether targeting FOXM1 results in reduced growth and survival of myeloma cells, MM cell lines exhibiting high levels of FOXM1 were found to have low micromolar sensitivity to treatment with thiostrepton or siomycin A — two thiazole antibiotics known to inhibit FOXM1 activity. Because of known off-target effects of these inhibitors, we are confirming the results using short-hairpin RNA. Our data suggest that developing effective therapeutic strategies against high-risk MM should include consideration of FOXM1 as a new target.

Citation Format: Van S. Tompkins, Zhimin Gu, Hongwei Xu, Guido Tricot, Fenghuang Zhan, Siegfried Janz. Targeting FOXM1 in multiple myeloma. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Synthetic Lethal Approaches to Cancer Vulnerabilities; May 17-20, 2013; Bellevue, WA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(5 Suppl):Abstract nr B38.
Abstract IA21: Oncogenomic-dependent vulnerabilities in lung adenocarcinoma
Authors: White Michael A.
Published: August 2014

Diversity in the genetic lesions that drive cancer initiation and progression is extreme. This diversity exists not only among tumors from different patients, but also among cancer cells within the same patient. This nefarious complexity is, in large measure, responsible for the capacity of this disease to evade current best efforts for effective therapy. “Personalized medicine” has been proposed in response to this conundrum as a mechanism to tailor cancer treatment to a specific tumor's genetic and epigenetic characteristics. However, selection of appropriate treatment is dramatically limited by the paucity of appropriate drugs and by the difficulty of linking treatment options to the appropriate patients. The challenge is to identify authentic intervention targets for development of an appropriately diverse cohort of therapies to contend with disease heterogeneity. We are addressing this challenge by a focused investigation of common vulnerabilities that arise as a consequence of oncogene expression and tumor evolution. Here we will describe a cancer intervention discovery pipeline using parallel genetic and chemical perturbations within an extensive panel of cell lines representative of the molecular lesions detected in lung cancer by national and international cancer genome sequencing efforts. We have found that current first line targeted therapies are discoverable within this panel together with the enrollment biomarkers required to stratify patient treatment regimens. Further, we have found that new genetic and chemical vulnerabilities can be revealed that are linked to recurrent mutations in lung cancer patients that are not currently “actionable.” We are leveraging this approach to stratify lung cancer subtypes and elaborate intervention targets that are linked to those subtypes by robust molecular discriminators.

Citation Format: Michael A. White. Oncogenomic-dependent vulnerabilities in lung adenocarcinoma. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Synthetic Lethal Approaches to Cancer Vulnerabilities; May 17-20, 2013; Bellevue, WA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(5 Suppl):Abstract nr IA21.
Abstract IA4: Synthetic lethal screens in Drosophila
Authors: Perrimon Norbert
Published: August 2014

During development and homeostasis, cells integrate numerous signals that are either systemic or produced by neighboring cells, informing them of the state of the organism, tissues, and neighboring cells. How cells integrate and interpret these various signals is one of the major focuses of our laboratory. We are particularly interested in identifying nodes of signaling networks that allow the crosstalk between canonical pathways and to study the dynamics of signal integration. I will discuss our current studies on the crosstalk between Insulin and Hippo networks and present our approach using mutant cell lines generated with TALENs to perform synthetic lethal screens. Further, I will present both cell lines and in vivo studies in Drosophila gut stem cells aimed to study the dynamics of signaling pathways activation.

Citation Format: Norbert Perrimon. Synthetic lethal screens in Drosophila. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Synthetic Lethal Approaches to Cancer Vulnerabilities; May 17-20, 2013; Bellevue, WA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(5 Suppl):Abstract nr IA4.
Abstract IA5: Functional genomics and synthetic lethality
Authors: Hahn William C.
Published: August 2014

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. The integration of such functional approaches with on-going efforts to identify and enumerate genetic alterations in human tumors will provide a path to discover and validate cancer vulnerabilities. Many commonly occurring and well-validated oncogenes and tumor suppressor genes remain refractory to molecularly targeted therapies. We have used systematic loss and gain of function approaches to identify cancer vulnerabilities in the context of oncogenes and tumor suppressor genes. Specifically, we have launched Project Achilles to systematically identify essential genes in more than 500 cancer cell lines that have been characterized genomically. These studies have provided new insights into genes dependent in cancers that express specific oncogenes, loss of genetic elements and in cancers in which particular signaling pathways are activated. Taken together, these studies suggest that combining forward and reverse genetic approaches with information derived from the cancer genome characterization projects provides a path toward a comprehensive understanding of genes involved in cancer.

Citation Format: William C. Hahn. Functional genomics and synthetic lethality. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Synthetic Lethal Approaches to Cancer Vulnerabilities; May 17-20, 2013; Bellevue, WA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(5 Suppl):Abstract nr IA5.
Abstract PR03: Genome-wide screens for Wnt signaling in human haploid cells
Authors: Lebensohn Andres , Hughes Casey , Marceau Caleb , Rohatgi Rajat , Carette Jan
Published: August 2014

Wnt signaling is at the core of human development and stem cell biology. Defective Wnt signaling leads to several forms of cancer, most notably colorectal cancer. Using HAP1 cells, a human haploid cell line, we conducted a set of genome-wide forward genetic screens to identify new Wnt pathway components. We constructed a HAP1 line harboring a GFP reporter driven by the Wnt-responsive TCF promoter, we mutagenized the cells by insertion of a gene-trap retrovirus throughout the haploid genome, and we sorted the mutagenized population for cells exhibiting phenotypes of interest using FACS. In order to find 1. negative regulators, 2. positive regulators and 3. feedback modulators of the pathway, we sorted for 1. cells expressing GFP in the absence of Wnt, 2. cells with reduced GFP expression after strong Wnt stimulation and 3. cells with enhanced GFP expression after mild Wnt stimulation, respectively. Deep sequencing of amplified genomic DNA flanking the retroviral insertion sites in the sorted cell populations revealed genes whose disruption may have led to the phenotype of interest. Among the most frequently disrupted genes (some with over 150 unique retroviral insertions) we found many of the known components of the canonical Wnt pathway, including LRP6, casein kinase I, APC, β-catenin, DOT1-L, TCF4 and the recently discovered negative feedback regulator ZNRF3. Unexpectedly, the screen for positive regulators revealed retroviral insertions in AXIN2 (a scaffold protein found in the β-catenin destruction complex) predicted to yield a C-terminally truncated form that appears to act as a dominant negative. We are currently assessing hits not previously known to be involved in Wnt signaling.

This abstract is also presented as Poster A40.

Citation Format: Andres Lebensohn, Casey Hughes, Caleb Marceau, Rajat Rohatgi, Jan Carette. Genome-wide screens for Wnt signaling in human haploid cells. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Synthetic Lethal Approaches to Cancer Vulnerabilities; May 17-20, 2013; Bellevue, WA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(5 Suppl):Abstract nr PR03.
Abstract PR09: Synthetic lethal interaction of combined BCL-XL and MEK inhibition promotes tumor regressions in KRAS-mutant cancer models
Authors: Corcoran Ryan B. , Cheng Katherine A. , Hata Aaron N. , Faber Anthony C. , Ebi Hiromichi , Coffee Erin M. , Greninger Patricia , Brown Ronald D. , Godfrey Jason T. , Cohoon Travis J. , Song Youngchul , Lifshits Eugene , Shioda Toshi , Dias-Santagata Dora , Singh Anurag , Settleman Jeffrey , Benes Cyril H. , Mino-Kenudson Mari , Wong Kwok-Kin , Engelman Jeffrey A.
Published: August 2014

Although KRAS is the most commonly mutated oncogene in human cancer, KRAS has proven difficult to target pharmacologically, and no effective therapies exist for KRAS-mutant cancers. Recently, there has been evidence that targeted therapy combinations inhibiting multiple downstream effectors of KRAS may be a promising approach for KRAS-mutant cancers. We developed a pooled shRNA-drug screen strategy to identify genes that, when inhibited, cooperate with MEK inhibitors to kill 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 the vast majority of KRAS-mutant cell lines tested from different tissue types. Mechanistic studies revealed that MEK inhibition led to marked induction of the pro-apoptotic protein BIM in KRAS-mutant cancer cells, but that BIM remained bound and inhibited by BCL-XL. Pharmacologic inhibition of BCL-XL with ABT-263 disrupted this inhibitory complex, allowing BIM to trigger apoptosis. Epithelial differentiation and E-cadherin expression correlated with increased sensitivity to this inhibitor combination across a panel of 30 KRAS-mutant cell lines, while epithelial-to-mesenchymal transition (EMT) correlated with resistance. This combination also caused marked in vivo tumor regressions in three independent KRAS-mutant xenografts and in established lung tumors in two genetically-engineered KRAS-driven lung cancer mouse models. These data support combined BCL-XL/MEK inhibition as a promising therapeutic approach for evaluation in future clinical trials for patients with KRAS-mutant cancers.

This abstract is also presented as Poster B19.

Citation Format: Ryan B. Corcoran, Katherine A. Cheng, Aaron N. Hata, Anthony C. Faber, Hiromichi Ebi, Erin M. Coffee, Patricia Greninger, Ronald D. Brown, Jason T. Godfrey, Travis J. Cohoon, Youngchul Song, Eugene Lifshits, Toshi Shioda, Dora Dias-Santagata, Anurag Singh, Jeffrey Settleman, Cyril H. Benes, Mari Mino-Kenudson, Kwok-Kin Wong, Jeffrey A. Engelman. Synthetic lethal interaction of combined BCL-XL and MEK inhibition promotes tumor regressions in KRAS-mutant cancer models. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Synthetic Lethal Approaches to Cancer Vulnerabilities; May 17-20, 2013; Bellevue, WA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(5 Suppl):Abstract nr PR09.
Abstract PR14: Targeting the GATA2 transcriptional network in K-Ras driven lung adenocarcinoma
Authors: Kumar Madhu S. , Downward Julian
Published: August 2014

Non-small cell lung cancer (NSCLC) is the most prevalent histological cancer subtype in terms of both incidence and mortality, with nearly 1.4 million deaths per year worldwide. Nearly one-third of all NSCLCs have activating mutations in the KRAS oncogene. In spite of thirty years' knowledge of KRAS mutations in lung cancer, it has proven therapeutically intractable, leaving KRAS mutant NSCLC to serve as a marker of poor prognosis. Thus, there is a substantial unmet clinical need to find treatment options for this subset of lung cancers.

By RNA interference screening, we previously discovered a transcription factor, GATA2, is necessary for the survival of KRAS mutant lung cancer cells, but not wild type lung cancer cells. Through an integrative genomic analysis of gene expression and chromatin occupancy, we discovered a GATA2-regulated transcriptional network consisting of the proteasome, IL-1 and Rho pathways. Functional analyses revealed that each of these pathways, though not individually necessary, is partially sufficient to restore viability in response to GATA2 depletion. Using two different genetically engineered mouse models (GEMMs), we found Gata2 is necessary for oncogenic Kras driven lung tumourigenesis. In addition, systemic Gata2 loss, while well tolerated, significantly extended survival in a Kras mutant NSCLC GEMM. Intriguingly, we found that combined treatment of Kras driven mouse models with clinically available inhibitors of the proteasome (bortezomib) and Rho kinase (fasudil) induced tumour regression.

We have now begun exploring and extending these initial therapeutic strategies to the Kras; Trp53 (KP) mouse model. Upon delivery of Cre recombinase to the lungs, KP mice undergo progression from low-grade adenomas to high-grade, invasive metastatic lung adenocarcinoma, more faithfully recapitulating the human disease. We have assessed our GATA2 network therapies through in vivo imaging of incipient lesions by micro-computed tomography, treatment cycles and subsequent re-imaging to determine efficacy. Using this approach, we observed substantial response when combining treatment with bortezomib and fasudil in the KP model. Moreover, introduction of a next-generation inhibitor of Rho kinase (AT13148), an agent in early-stage clinical development, combines with bortezomib to cause significant regression of lung adenocarcinomas in vivo. Taken together, we have elucidated a gene expression network necessary for Ras-driven lung cancer and have devised novel approaches to suppress this network with therapeutically tractable agents.

This abstract is also presented as Poster A14.

Citation Format: Madhu S. Kumar, Julian Downward. Targeting the GATA2 transcriptional network in K-Ras driven lung adenocarcinoma. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Synthetic Lethal Approaches to Cancer Vulnerabilities; May 17-20, 2013; Bellevue, WA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(5 Suppl):Abstract nr PR14.
Abstract PR16: Targeting cancer-specific kinase dependency for precision therapy
Authors: Kothari Vishal , Iris Wei , Shankar Sunita , Kalyana-Sundaram Shanker , Wang Lidong , Ma Linda W. , Vats Pankaj , Grasso Catherine S. , Robinson Dan R. , Wu Yi-Mi , Cao Xuhong , Simeone Diane M. , Chinnaiyan Arul M. , Kumar-Sinha Chandan
Published: August 2014

Precision/ personalized cancer therapy based on clinical sequencing is premised on the identification of genomic aberrations in actionable therapeutic targets. Protein kinases represent the most accessible therapeutic targets across cancers, albeit only very small subsets of cancers harbor canonical targetable aberrations in kinases. Considering that kinases represent the predominant drivers of oncogenesis, functioning directly or downstream of other oncogenic aberrations, we hypothesize that most cancers harbor distinct “kinase dependencies” and thus provide a potent therapeutic avenue in individual cancers. Here, we test the hypothesis that the kinase(s) that display an “off the chart” Outlier Expression in individual cancer samples, impart a dependency on growth and survival that can be exploited therapeutically. Analyzing RNA-Seq data from a compendium of 482 cancer and benign samples belonging to 25 different tissue types we defined sample-specific ‘kinome’ expression profiles. Comparing the expression of kinases within a sample and across sample sets, we identified distinct ‘outlier kinases’ in individual samples, defined as genes showing the highest statistically significant levels of absolute and differential expression. Frequently observed outlier kinases in breast cancer included known therapeutic targets like ERBB2 and FGFR4, distinct from MET, AKT2, and PLK2 in pancreatic cancer. Outlier kinases imparted sample-specific dependencies in various cell lines as assessed by siRNA knockdown or pharmacologic inhibition in vitro and in vivo. Outlier expression of polo-like kinases (PLKs) observed in a subset of KRAS-dependent pancreatic cancer cell lines conferred increased sensitivity to the PLK inhibitor BI 6727. Together, our results suggest that outlier kinases represent effective personalized therapeutic targets that are readily identifiable through RNA-sequencing of tumors. Next, to help translate these observations into treatment options, we are optimizing ex vivo culture of tumor tissues from surgical resections that will be used to test combinations of therapeutics including outlier kinase inhibitors.

This abstract is also presented as Poster B21.

Citation Format: Vishal Kothari, Wei Iris, Sunita Shankar, Shanker Kalyana-Sundaram, Lidong Wang, Linda W. Ma, Pankaj Vats, Catherine S. Grasso, Dan R. Robinson, Yi-Mi Wu, Xuhong Cao, Diane M. Simeone, Arul M. Chinnaiyan, Chandan Kumar-Sinha. Targeting cancer-specific kinase dependency for precision therapy. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Synthetic Lethal Approaches to Cancer Vulnerabilities; May 17-20, 2013; Bellevue, WA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(5 Suppl):Abstract nr PR16.
Abstract A104: A screening method for the identification of potentially effective drug-drug combinations reveals a synergistic interaction between Aurora-A inhibitor MK-5108 and Bcl-xL inhibitor navitoclax.
Authors: Gong Xueqian , Jin Shaoling , Merzoug Farhana , Ye Xiang S. , Lallena MaryJo , Du Jian , Webster Yue , Ma Xiwen , Reinhard Christoph , Iversen Phillip , Buchanan Sean G.
Published: August 2014

Recent developments in understanding the molecular mechanisms of cancer, coupled with large genomic datasets that detail the heterogeneity of the disease, have together led to a wealth of new cancer targets and therapeutic options. However, the restricted efficacy of these new agents and the emergence of resistance suggest that broader and more durable responses may be achieved through combination of these new drugs. To identify drug-drug combinations that may be effective in particular tumor types, we have developed an unbiased "synthetic lethal" screening approach to survey combination space across a diverse panel of tumor cell lines. We used this approach to test a panel of targeted drugs in all-versus-all fashion across 63 cell lines. Synergistic interactions were observed with the combination of an Aurora-A inhibitor, MK-5108, with navitoclax, an inhibitor of Bcl-2 family survival proteins. This combination, which was synergistic in a subset of the tumor cells, was further examined to identify the molecular determinants of synergy. Several features emerged from this analysis including the observation that Bcl-xL expression levels predict resistance to the single agent Aurora-A inhibitor and to synergy of combined MK-5108 and navitoclax.

Citation Information: Mol Cancer Ther 2013;12(11 Suppl):A104.

Citation Format: Xueqian Gong, Shaoling Jin, Farhana Merzoug, Xiang S. Ye, MaryJo Lallena, Jian Du, Yue Webster, Xiwen Ma, Christoph Reinhard, Phillip Iversen, Sean G. Buchanan. A screening method for the identification of potentially effective drug-drug combinations reveals a synergistic interaction between Aurora-A inhibitor MK-5108 and Bcl-xL inhibitor navitoclax. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2013 Oct 19-23; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(11 Suppl):Abstract nr A104.
Abstract A106: Utilization of low passage adenoid cystic carcinoma (ACC) models to identify novel therapies.
Authors: Meade Justin , Wick Michael J. , Vaught Teresa L. , Carlile Jennifer , Tolcher Anthony W. , Rasco Drew , Patnaik Amita , Kaufman Jeffrey , Moskaluk Chris , Papadopoulos Kyriakos P.
Published: August 2014

Background: Adenoid Cystic Carcinoma (ACC) is an uncommon cancer of the head and neck which typically originates in the salivary glands. Treatment options for ACC resection and local radiation therapy although chemotherapy is sometimes used to control metastatic or locally recurrent disease. Patients with ACC may survive for years due to latent tumor growth and lack of lymph node metastasis; however, the high rate of recurrence and metastasis to the lungs lead to a poor prognosis beyond ten years. While no standard of care currently exists, improved understanding of ACC tumor biology and oncogenesis has provided some molecular targets for its treatment. Mutations and alterations of MYB, NFIB and molecules in the FGF, IGF, PI3K and NOTCH signaling pathways amongst others, may serve as targets for current and future therapies. Due to a lack of ACC derived cell lines, a panel of low passage ACC xenograft models designated ACCx5M1, ACCx6, ACCx9, ACCx14 and ACCx16 have been established and through the Adenoid Cystic Carcinoma Research Foundation (ACCRF) are routinely utilized to test agents which target pathways important in ACC.

Methods: Low passage ACC models were established in immune-deficient mice from primary or metastatic patient tissue and once established were confirmed by histologic comparative analysis. Drug sensitivity studies are performed evaluating models towards chemotherapy and targeted agents. Study endpoints included tumor volume and time from treatment initiation with tumor growth inhibition and regression reported at study completion.

Results: To date over seventy FDA-approved and investigational therapies have been evaluated and data has been generated that have contributed to the initiation of two Phase 2 clinical trials in ACC. In addition to chemotherapies, therapies targeting FGF, IGF, VEGF and NOTCH pathways have been tested and we are currently evaluating agents targeting MYB dysregulation.

Conclusion: Low passage ACC models have been used to identify agents potentially useful in the treatment of ACC and models are available through the ACCRF to evaluate potential therapies for the treatment of adenoid cystic carcinoma.

Citation Information: Mol Cancer Ther 2013;12(11 Suppl):A106.

Citation Format: Justin Meade, Michael J. Wick, Teresa L. Vaught, Jennifer Carlile, Anthony W. Tolcher, Drew Rasco, Amita Patnaik, Jeffrey Kaufman, Chris Moskaluk, Kyriakos P. Papadopoulos. Utilization of low passage adenoid cystic carcinoma (ACC) models to identify novel therapies. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2013 Oct 19-23; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(11 Suppl):Abstract nr A106.
Abstract A112: Combined targeting of HER2 and HER3 inhibits tumor growth in both trastuzumab-sensitive and trastuzumab-resistant breast cancer models.
Authors: Steiner Philipp , Wetzel Leslie , Schifferli Kevin , Rothstein Raymond , Tammali Ravinder , Rebelatto Marlon , Xiao Zhan , Pierce Andrew , Hollingsworth Robert
Published: August 2014

HER3 (ERBB3) is a tumor driver in divergent cancer types with high HRG levels or heightened EGFR or HER2 kinase activity via growth signal coupling to the PI3K-AKT pathway. HER3 lacks intrinsic tyrosine kinase activity but is capable of signaling after heterodimerizing with tyrosine kinase ERBB family members EGFR or HER2. Heterodimer formation is driven either by the binding of heregulin (NRG1/HRG) to HER3 (ligand dependent - LD), or alternatively, by overexpression of EGFR or HER2 (ligand-independent - LI). Preclinical evaluation of MEDI3379, a human IgG1 modified monoclonal anti-HER3 antibody that antagonizes both LD and LI signaling, demonstrated tumor growth inhibition in the HER2-expressing MDA-MB-361 breast cancer xenograft model. Anti-tumor activity of MEDI3379 in this model was increased in combination with the HER2-targeting drug trastuzumab to a greater extent than MEDI3379 when combined with either lapatinib or pertuzumab. Combined inhibition of HER2 and HER3 led to strong reduction in pHER3. Unexpectedly, co-administration of MEDI3379 together with trastuzumab in MDA-MB-361 tumor-bearing mice but not in naïve mice resulted in reduced serum levels of trastuzumab. A control antibody combined with trastuzumab in MDA-MB-361 tumor bearing mice did not have this effect. Furthermore, in the trastuzumab-resistant JIMT-1 breast cancer xenograft model which has high HRG and pHER3 levels MEDI3379 but not pertuzumab resensitized JIMT-1 tumors to trastuzumab resulting in synergistic anti-tumor activity and a reduction of pHER3. In vivo resistance to this regimen appeared with prolonged treatment of JIMT-1 tumors and was accompanied by a decrease in homogenous expression of HER2. In conclusion, the use of MEDI3379 in combination with trastuzumab in HER2-amplifed breast cancer cell lines has demonstrated additional tumor growth inhibition over single agent trastuzumab and overcoming trastuzumab-resistance mechanisms. This combination warrants further evaluation in preclinical and clinical studies.

Citation Information: Mol Cancer Ther 2013;12(11 Suppl):A112.

Citation Format: Philipp Steiner, Leslie Wetzel, Kevin Schifferli, Raymond Rothstein, Ravinder Tammali, Marlon Rebelatto, Zhan Xiao, Andrew Pierce, Robert Hollingsworth. Combined targeting of HER2 and HER3 inhibits tumor growth in both trastuzumab-sensitive and trastuzumab-resistant breast cancer models. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2013 Oct 19-23; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(11 Suppl):Abstract nr A112.