bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 1208: Analysis of the combinatorial antiproliferative effect of pan RAF inhibitor AZ-628 and MEK1-inhibitor AZD-6244 on a large panel of tumor cell lines
Authors: Chakrabarti Alokta , Feger Daniel , Umber Sarah , Stus Orysya , Birkle Marianne , Siedentopf Oliver , Ehlert Jan E.
Published: July 2017

Cancer is a highly complex, multigenic disease with tumor cells underlying constant transition. Single drug treatments against specific targets frequently result in only partial success because mutations and redundant pathways cause drug resistance. Therefore, drug combinations that effect different synergistically acting targets in the cancer cell in parallel have become a promising strategy to improve the success in many fields of cancer therapy. One example for such an approach is the co-treatment of B-Raf driven tumors with Raf and MEK1 inhibitors. In our study, we determined the combinatorial effect of the pan-Raf inhibitor AZ-628 and the MEK1 inhibitor AZD-6244 on the viability of a large panel of more than 100 tumor cell lines. Whittaker et al. (Mol.CancerTher, 2015) could already show that this drug combination has a significant synergistic effect in several melanoma and colon cancer cell lines. The authors showed evidence that synergistic activity was correlated with enhanced mutation-triggered RAS/RAF/MAPK signaling with a special role for C-Raf in resistance due to a negative feedback mechanism. We here applied the combination of AZD-6244 and AZ-628 in a broad checkerboard pattern to a multitude of cell lines from other entities beyond melanoma and colorectal cancer. Based on these results we correlated the observed synergistic and non-synergistic effects with gene expression profiles of these cell lines and analyzed the requirement of a MAPK activating signaling. Our approach revealed that synergistic activity is not confined to melanoma and colon cancer but is observed in tumors from other entities as well. This observation may expand the usefulness of MEK/Raf inhibitor co-treatment to a larger panel of cancer types.

Citation Format: Alokta Chakrabarti, Daniel Feger, Sarah Umber, Orysya Stus, Marianne Birkle, Oliver Siedentopf, Jan E. Ehlert. Analysis of the combinatorial antiproliferative effect of pan RAF inhibitor AZ-628 and MEK1-inhibitor AZD-6244 on a large panel of tumor cell lines [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1208. doi:10.1158/1538-7445.AM2017-1208
Abstract 121: Identification and characterization of calcium channel blockers as inhibitors of YAP/TAZ and glioblastoma cells
Authors: Li Wei , Liu Zhijun , Xavier Jennifer , Wang Hong-Gang
Published: July 2017

Glioblastomas (GBM) are the most aggressive primary brain tumors. Despite major advances in neuroimaging and neurosurgical techniques over the past decades, the neurosurgical management of GBM patients remains challenging. Median survival of the patients is about 14.6 months. In order to radically alter the clinical course of these tumors, it is important to develop targeted therapies based on identified oncogenic mutations and signaling pathways that drive their development and sustain their maintenance. In a screen for small molecules, which can inhibit the growth of human glioblastoma cells, we identified a set of calcium channel blockers (CCB). We found that these CCB induce cell death through an apoptosis-independent process. To understand the mechanisms of the non-apoptotic cell death induced by these CCB, we dissected cellular signaling which is responsible for the cell death induction. We found that these CCB are able to inhibit YAP and TAZ, two oncogenic effectors of the Hippo tumor suppressor pathway. Importantly, GBM cells expressing the YAP active mutant or overexpressing YAP are less sensitive to these CCB. These results suggested that inhibition of YAP/TAZ is a mechanism by which CCB suppress tumor cell growth. The Hippo pathway is an essential signaling network in regulating tissue homeostasis. In this pathway, the transcription co-activators YAP and TAZ promote a gene expression program favoring cell proliferation, survival and self-renewal. In normal brain, the nuclear accumulation of YAP is largely limited to regions harboring neural progenitor cells. However, increased nuclear accumulation of YAP is found in various brain tumors, especially those more aggressive subsets of gliomas. In addition, high expression of YAP is associated with reduced mean survival in astrocytoma patients. Our results identified a novel approach to target the Hippo pathway for GBM treatment. We will present our work in further characterizing these regulations and therapeutic potentials of these calcium channel blockers in the conference.

Citation Format: Wei Li, Zhijun Liu, Jennifer Xavier, Hong-Gang Wang. Identification and characterization of calcium channel blockers as inhibitors of YAP/TAZ and glioblastoma cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 121. doi:10.1158/1538-7445.AM2017-121
Abstract 1212: Co-targeting epidermal growth factor receptor (EGFR) and anaplastic lymphoma kinase overcomes EGFR inhibitor resistance in head and neck squamous cell carcinoma patient-derived models
Authors: Ouyang Xiaoming , Barling Ashley , Lesch Aletha , Tyner Jeffrey , Jeng Sophia , Zheng Christina , Courtneidge Sara A. , McWeeney Shannon , Kulesz-Martin Molly
Published: July 2017

Background: HNSCC is the sixth most common cancer worldwide. EGFR is overexpressed in up to 90% of HNSCC and associated with poor outcome. An EGFR monoclonal antibody is the only approved molecular targeted therapy for HNSCC, however, resistance eventually occurs in all patients.

Methods: Functional screens including a small-molecule kinase inhibitor panel and an RNAi screen panel were used to identify agents that synergized with EGFR inhibitors in reducing cell viability in HNSCC patient-derived tumor cells. Effective combination therapies were validated in scale-up experiments in 2D and 3D, and their true targets were evaluated using siRNAs to rule out off-target effects of the drugs. Cell viability, cell number and cell colony formation ability were tested upon siRNA treatment. qRT-PCR and immunofluorescent staining was used to test ALK expression in tumor cells before and after anti-EGFR treatment.

Results: Two ALK inhibitors on the drug screen panel showed synergistic effects with EGFR inhibitors in 6/8 HNSCC patients’ tumor cells, despite ineffectiveness of single drug. Scale-up dose-response experiments confirmed patient cell sensitivity to 4 different ALK inhibitors in combination with the EGFR inhibitor Gefitinib. siRNA targeting ALK synergized with Gefitinib in reducing cell viability in the patient cells that responded to EGFR/ALK inhibitor combinations, indicating specificity to ALK. Scale-up RNAi experiments confirmed synergy between siRNAs targeting ALK and EGFR in reducing cell viability, cell number, and colony formation ability. Inhibition of EGFR by siRNA or Gefitinib each increased ALK expression at the mRNA level and protein level, suggesting induction of ALK as a novel mechanism of EGFR inhibitor resistance in HNSCC.

Conclusion: We identified EGFR/ALK inhibitor combinations as a potential strategy for treating EGFR inhibitor resistant HNSCC.

Citation Format: Xiaoming Ouyang, Ashley Barling, Aletha Lesch, Jeffrey Tyner, Sophia Jeng, Christina Zheng, Sara A. Courtneidge, Shannon McWeeney, Molly Kulesz-Martin. Co-targeting epidermal growth factor receptor (EGFR) and anaplastic lymphoma kinase overcomes EGFR inhibitor resistance in head and neck squamous cell carcinoma patient-derived models [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1212. doi:10.1158/1538-7445.AM2017-1212
Abstract 1220: Coordinated chemical-genetics approach identifies PTP4A3-mediated regulation of colon cancer cell migration and extracellular matrix interactions
Authors: McQueeney Kelley E. , Salamoun Joseph M. , Blanco Isabella K. , Pekic Paula , Ahn Jennifer , Sharlow Elizabeth R. , Wipf Peter , Lazo John S.
Published: July 2017

Aberrant regulation of protein phosphorylation is an exceedingly common driver of human cancers. It is notable that we understand much less about the role of protein tyrosine phosphatases in human malignancies compared to tyrosine kinases. The membrane-associated, intracellular, protein tyrosine PTP4A3 is highly overexpressed in multiple tumor types including colorectal cancer and has been associated with tumor metastases. We have, therefore, investigated the role of PTP4A3 in colon cancer migration and invasion. The Ptp4a3 gene was expunged from colon tumor cells derived from Ptp4a3flox/flox mice and the resulting cells exhibited impaired migration, invasion, and colony formation compared to the wildtype isogenic cells. We characterized a potent, selective, and noncompetitive small molecule inhibitor of PTP4A3, JMS-631-053, which also disrupted colon cancer cell migration, invasion, and colony formation. PTP4A3 deletion increased the expression of extracellular matrix and adhesion genes, including the tumor suppressor Emilin 1. Expression of these extracellular matrix genes is mutually exclusive with PTP4A3 expression in tumors derived from patients with colorectal cancer. These chemical and biological reagents reveal a previously unknown communication between the intracellular PTP4A3 phosphatase and the extracellular matrix and support continued efforts to pharmacologically target PTP4A3 for cancer therapy.

Citation Format: Kelley E. McQueeney, Joseph M. Salamoun, Isabella K. Blanco, Paula Pekic, Jennifer Ahn, Elizabeth R. Sharlow, Peter Wipf, John S. Lazo. Coordinated chemical-genetics approach identifies PTP4A3-mediated regulation of colon cancer cell migration and extracellular matrix interactions [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1220. doi:10.1158/1538-7445.AM2017-1220
Abstract 1222: Developing kinase inhibitors with polypharmacological profiles for the treatment of resistant cancers
Authors: Rao Suman , Li Tan , Everley Robert , Du Guangyan , Sorger Peter , Gray Nathanael
Published: July 2017

Small molecule kinase inhibitors targeting a specific oncoprotein driving cancer cells have shown great clinical success in the past (e.g. imatinib against leukemia). However, resistance to targeted therapies quickly arises due to plasticity associated with cancer cell signaling and tumor heterogeneity. One way to overcome this problem is to rationally design drugs with polypharmacology that can target multiple signaling pathways engaging in cancer cell proliferation and survival. To this end, we have developed a strategy based on combining phenotypic screens of small molecule inhibitors and affinity-based mass spectrometry to identify drugs with multi-targeted properties and piloted this approach using the highly resistant KRAS mutant non-small cell lung cancer cell lines. We began this study by screening kinase inhibitors targeting MEK, ERK, PI3K, Akt and mTOR and found that the lung cancer cells were largely resistant to single drugs but showed enhanced sensitivity towards triple inhibition of MEK, ERK and PI3K. These cell lines were then screened with a library of covalent and non-covalent kinase inhibitors in an attempt to identify a small molecule inhibitor that could mimic the activity of the triple drug combination. This led to the discovery of SM1-71 that not only recapitulated the growth inhibitory activity of MEK+ERK+PI3K inhibition, but also blocked phosphorylation of ERK, Akt, mTOR and S6K in cells. Target profiling of the drug was carried out using chemoproteomics, which revealed that SM1-71 inhibited 55 kinases at a 1μM concentration. Dose-dependent evaluation further determined the IC50 of inhibition across the 55 kinases and rank ordered them based on binding affinity. Top hits including MEK1, MEK2, ERK1, ERK2, AURKA, SRC and RPS6KA3 were confirmed using alternate kinase screens and cellular assays. Growth factor receptors such as IGF1R, MET and EGFR were also identified and further validated using cell-based assays. Taken together, these results elucidated the polypharmacology associated with SM1-71 and uncovered key targets responsible for inducing strong cytotoxicity in KRAS mutant lung cancer cells. Through the combination of phenotypic screens and mass spectrometry-based target identification, we have demonstrated the proof of principle for developing kinase inhibitors with polypharmacology targeting resistant cancers.

Citation Format: Suman Rao, Tan Li, Robert Everley, Guangyan Du, Peter Sorger, Nathanael Gray. Developing kinase inhibitors with polypharmacological profiles for the treatment of resistant cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1222. doi:10.1158/1538-7445.AM2017-1222
Abstract 1228: Nintedanib selectively inhibits the activation and tumor-promoting effects of fibroblasts from lung adenocarcinoma patients
Authors: Alcaraz Jordi , Gabasa Marta , Ikemori Rafael , Reguart Noemí
Published: July 2017

Nintedanib (BIBF 1120) is a multikinase inhibitor recently approved to treat lung adenocarcinoma (ADC) patients based on the therapeutic benefits reported in clinical trials on ADC but not on squamous cell carcinoma (SCC), which are the two most common lung cancer subtypes. However, the biological processes underlying the selective anticancer function of nintedanib in ADC remain obscure. To shed light on this gap of knowledge, we examined the role of tumor-associated fibroblasts (TAFs) in the differential effects of nintedanib in ADC and SCC. Because TAFs are largely quiescent and activated in vivo, we focused on the antifibrotic effects of nintedanib on TAFs stimulated with TGF-β1, which is a potent fibroblast activator frequently upregulated in lung cancer. Nintedanib dose-dependently inhibited the TGF-β1-induced expression of activation markers in both ADC-TAFs and control fibroblasts derived from uninvolved parenchyma, whereas such inhibiton was very modest in SCC-TAFs, thereby suggesting that TAF activation is regulated by different mechanisms in ADC and SCC. Remarkably, nintedanib abrogated the stimulation of growth and invasion in a panel of carcinoma cell lines induced by secreted factors from activated TAFs in ADC but not SCC. These results reveal that nintedanib is a potent inhibitor of fibrosis and its associated tumor-promoting effects in ADC, and strongly suggest that the subnormal antifibrotic response of SCC-TAFs to nintedanib may underlie the lack of therapeutic benefits of this drug in SCC. Our findings also support that preclinical models based on carcinoma-TAF interactions may help unraveling the resistance mechanisms of SCC-TAFs to nintedanib and testing new combined therapies to further expand the therapeutic effects of this drug.

Citation Format: Jordi Alcaraz, Marta Gabasa, Rafael Ikemori, Noemí Reguart. Nintedanib selectively inhibits the activation and tumor-promoting effects of fibroblasts from lung adenocarcinoma patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1228. doi:10.1158/1538-7445.AM2017-1228
Abstract 1256: Non-steroidal anti-inflammatory drugs induce ER stress and have an immunomodulatory role in the suppression of colorectal tumorigenesis
Authors: Fletcher Rochelle E. , Zhang Lin , Leibowitz Brian , Yu Jian
Published: July 2017

Colorectal cancer (CRC) is the second-leading cause of cancer-related deaths in the United States. A number of epidemiological studies, clinical trials, and animal studies have demonstrated the chemopreventive effect of non-steroidal anti-inflammatory drugs (NSAIDs) on CRC. However, the exact mechanism by which NSAIDs suppress colorectal tumorigenesis has remained unclear. Our previous study showed that NSAID-induced death receptor signaling, along with loss of the gatekeeper APC tumor suppressor, triggers a synthetic lethal interaction and apoptotic death in an otherwise normal cell. In this study, we determined how NSAIDs induce death receptor signaling, and found a critical role of the endoplasmic reticulum (ER) stress response. Treating CRC cells with the NSAIDs sulindac or indomethacin upregulated C/EBP homologous transcription factor (CHOP), a key mediator of the ER stress response that is required for the induction of death receptor 5 (DR5) by NSAIDs. Blocking ER stress abolished the apoptotic effect of NSAIDs in CRC cells and in normal colonic epithelial cells with knockdown of APC, and also suppressed the chemopreventive activity of NSAIDs in APCMin/+ mice. Furthermore, we identified plasma membrane translocation of calreticulin in cells undergoing NSAID-induced apoptosis, suggesting the involvement of immunomodulation in this tumor suppression. Our results provide novel insight into the chemopreventive mechanism of NSAIDs, which may help design more effective chemopreventive strategies and agents.

Citation Format: Rochelle E. Fletcher, Lin Zhang, Brian Leibowitz, Jian Yu. Non-steroidal anti-inflammatory drugs induce ER stress and have an immunomodulatory role in the suppression of colorectal tumorigenesis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1256. doi:10.1158/1538-7445.AM2017-1256
Abstract 126: A chemogenomic approach reveals the action of splicing modulators at the branch point adenosine binding pocket defined by the PHF5A/SF3b complex
Authors: Teng Teng , Tsai Jennifer , Puyang Xiaoling , Seiler Michael , Peng Shouyong , Aird Daniel , Buonamici Silvia , Caleb Benjamin , Chan Betty , Corson Laura , Feala Jacob , Fekkes Peter , Karr Craig , Korpal Manav , Mizui Yoshiharu , Park Eunice , Palacino James , Smith Peter , Subramanian Vanitha , Wu Jeremy , Yu Lihua , Chicas Agustin , Warmuth Markus , Larsen Nicholas , Zhu Ping
Published: July 2017

Dysregulation of RNA splicing can cause various forms of cancer and neuromuscular disorders. Thus, developing compounds with splicing-modulating activity represents a promising therapeutic approach for these diseases. Natural products such as pladienolide, herboxidiene, and spliceostatin have been identified as potent splicing modulators that bind SF3B1, a member of the SF3b subcomplex that assembles into the U2 snRNP. Using integrated chemogenomic, structural and biochemical approaches, we show that PHF5A, another core component of the SF3b complex, is also targeted by these modulators. Whole exome sequencing of E7107 (pladienolide analogue) and herboxidiene resistant clones identified common mutations in either PHF5A-Y36, SF3B1-K1071, SF3B1-R1074, or SF3B1-V1078, which confers resistance to these modulators as assessed by splicing modulation and cell growth inhibition, suggesting a common site of interaction for these splicing modulators. We determine the crystal structure of human PHF5A and find that Y36 is located on the surface in a region of high sequence conservation. Analysis of the cryo-EM spliceosome Bact complex from yeast shows that these mutations cluster in a well-defined pocket surrounding the branch point adenosine suggesting a possible competitive mode of action for these modulators. Whole-transcriptome RNA-seq analysis reveals that PHF5A Y36C alters the profile of splicing modulators from inducing intron-retention events to exon-skipping events. Furthermore, the differential in GC content between adjacent introns and exons correlates with the relative intron strength, making some splicing events more susceptible to modulation. Collectively, we propose that PHF5A-SF3B1 is a central node for binding to these small-molecule splicing modulators offering novel approaches to modulate specific splicing events.

Citation Format: Teng Teng, Jennifer Tsai, Xiaoling Puyang, Michael Seiler, Shouyong Peng, Daniel Aird, Silvia Buonamici, Benjamin Caleb, Betty Chan, Laura Corson, Jacob Feala, Peter Fekkes, Craig Karr, Manav Korpal, Yoshiharu Mizui, Eunice Park, James Palacino, Peter Smith, Vanitha Subramanian, Jeremy Wu, Lihua Yu, Agustin Chicas, Markus Warmuth, Nicholas Larsen, Ping Zhu. A chemogenomic approach reveals the action of splicing modulators at the branch point adenosine binding pocket defined by the PHF5A/SF3b complex [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 126. doi:10.1158/1538-7445.AM2017-126
Abstract 1271: Genetic variants in the 16q24.3 region of melanocortin-1-receptor (MC1R) and prostate cancer risk: A Mendelian randomization analysis of 39,000 cases and 25,000 controls
Authors: Weinstein Stephanie J. , Layne Tracy M. , Huang Jiaqi , Karlins Eric , Chanock Stephen J. , Albanes Demetrius , Consortium the PRACTICAL
Published: July 2017

We previously reported that men with naturally red hair had a significantly lower risk of prostate cancer (HR=0.46, 95% CI 0.24-0.89) compared with the most prevalent hair color, light brown (Br J Cancer 2013;109(3):747-750). The red hair phenotype is encoded by variants in the melanocortin-1-receptor (MC1R) gene that controls expression of the eumelanin and pheomelanin pigments. In order to re-examine this association through the relatively unbiased Mendelian randomization approach, we examined single nucleotide polymorphisms (SNPs) in and near MC1R in relation to prostate cancer risk using data from the Prostate Cancer Association Group to Investigate Cancer Associated Alterations in the Genome (PRACTICAL) consortium. The analysis includes 38,868 men diagnosed with prostate cancer and 25,210 controls from 35 studies participating in PRACTICAL Consortium (Nat Gen 2014;46(10)1103-1109). Logistic regression modeling was used to estimate the odds ratio (OR) and confidence interval (CI) for the per allele prostate risk associations with 148 genotyped SNPs and 164 imputed SNPs. Variants demonstrating nominal significance (alpha-error p<0.05) as well as those reaching a stringent Bonferroni threshold of p<0.0003 adjustment for multiple comparisons were examined. We identified prostate cancer risk associations with 30 genotyped and 36 imputed polymorphisms that were nominally significant, three of which achieved Bonferroni significance and were in a region of 16q24.3 that includes MC1R, GAS8 (growth arrest specific-8, an alleged tumor suppressor that is deleted in some prostate cancers), and transcription factor-25 (TCF25). These were rs4628973 and rs3743824 that were in high LD (r2=0.931; prostate cancer risk associations p=0.00029 and 0.00023, respectively), as well as rs6500461 that was independently associated with risk (r2=0.20 with rs4628973; p=0.00020). This large-scale Mendelian randomization analysis suggests genetic variants near MC1R, which directs melanocyte melanin synthesis, secretion and human pigmentation, may be associated with risk of prostate cancer.

Citation Format: Stephanie J. Weinstein, Tracy M. Layne, Jiaqi Huang, Eric Karlins, Stephen J. Chanock, Demetrius Albanes, the PRACTICAL Consortium. Genetic variants in the 16q24.3 region of melanocortin-1-receptor (MC1R) and prostate cancer risk: A Mendelian randomization analysis of 39,000 cases and 25,000 controls [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1271. doi:10.1158/1538-7445.AM2017-1271
Abstract 1273: Pathway analysis of insulin-like growth factor candidate genes and risk of pediatric rhabdomyosarcoma
Authors: Morimoto Libby , Shao XIaorong , Chokkalingam Anand , Wiemels Joseph , Ma Xiaomei , Metayer Catherine
Published: July 2017

Pediatric rhabdomyosarcoma (RMS) is the most common soft tissue sarcoma in children under 15 years of age. Due largely to its rarity, the etiology of pediatric RMS is poorly understood. Patterns of fetal growth were previously shown to be independent risk factors for RMS among non-Hispanic white (NHW) children; however, the underlying biologic mechanisms remain unclear. Alterations in the insulin-like growth factor (IGF) system, the primary regulator of growth during the fetal and early life period, may provide clues. Using an innovative linkage between the California birth records and cancer registry information, we conducted a population-based case-control study (1982-2009) of candidate genes involved in IGF signaling and risk of pediatric RMS. Fifteen genes involved in the IGF pathway were selected: IGF1, IGF2, IGF1R, IGF2R, IGFBP1, IGFBP2, IGFBP3, IGFBP4, IGFBP5, IGFBP6, INS, INSR, IRS1, GH1, and GHRH. DNA extracted from the archived newborn blood spots of all available RMS cases (n=644) was genotyped on the Illumina OmniExpress Exome array (n=964,043 SNPs); after stringent quality control (QC), a total of 633 RMS cases (360 embryonal RMS [eRMS] and 197 alveolar RMS [aRMS]) were available for analysis. A total of 815 controls genotyped on the Illumina OmniExpress Exome array and 3,922 controls genotyped on the Affymetrix Axion LAT array (n=801,830 SNPs) from the same base population of California children, with no evidence of RMS, were included in this analysis. After imputation to increase coverage of the genome and post-imputation QC to identify and remove platform effects, a total of 5,556,335 SNPs were available for analysis. Among NHW children, SNPs in IGF1 (rs10860869, p=0.0031) and IGF1R (rs62023616, p=0.00074; rs62023648, p=0.00076) were significantly associated with RMS risk after adjustment for multiple comparisons. Analyses stratified by histologic subtype showed that these associations were limited to eRMS, and of stronger magnitude. Among Hispanic children, 12 SNPs in IGF1R (p-value range: 0.0007-0.0027) and 3 SNPs in IGFBP1 (p-values: 0.0016-0.0023) were significantly associated with eRMS risk. The SNPs found to be associated with RMS were located in intergenic and intronic areas of the genes, areas that may influence gene regulation. Our results support the hypothesis that genetic variation in IGF1 signaling pathway modulate the risk of RMS, especially eRMS, among NHW and Hispanic children.

Citation Format: Libby Morimoto, XIaorong Shao, Anand Chokkalingam, Joseph Wiemels, Xiaomei Ma, Catherine Metayer. Pathway analysis of insulin-like growth factor candidate genes and risk of pediatric rhabdomyosarcoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1273. doi:10.1158/1538-7445.AM2017-1273
Abstract 1276: Gene-environment interaction relevant to estrogen and risk of breast cancer
Authors: Park JooYong , Choi Ji-Yeob , Chung Seokang , Song Nan , Park Sue K , Han Wonshik , Noh Dong-Young , Ahn Sei-Hyun , Kim Mi-Kyung , Yoo Keun-Young , Zheng Wei , Kang Daehee
Published: July 2017

Introduction:

Many established reproductive risk factors for breast cancer are mediated by hormonal mechanisms, and most parts are involved in estrogens. In addition, the estrogen level controlled by genetic factors might be a sort of determinants to breast cancer risk involving estrogen metabolism. This study aims to examine gene and environment interaction (GxE) between candidate genes which are involved in estrogen metabolism and environmental factors which are related to estrogen exposure.

Methods:

GxE analyses were conducted in the Korean 1,970 breast cancer cases and 2,052 controls which were recruited in the Seoul Breast Cancer Study (SEBCS), a multicenter case control study. 137 candidate genes involved in estrogen metabolism were searched from couple of databases and 11,555 SNPs (2,472 typed SNPs and 9,083 imputed SNPs) from the range of candidate genes were included in GxE analyses with 8 established environmental factors. Statistical analyses were performed by using GxEScan (ver. Beta 0.4.0; http://biostats.usc.edu/software) for GxE test.

Results:

There were three significant interaction between 11,555 SNPs and 8 environmental factors. Firstly, interaction rs851998 nearby ESR1 with height was shown in the GE|2df model (p-2df = 1.1x10-4) This SNP had protective effect marginally (ORG = 0.82, 95% CI: 0.75-0.90) and further protective effect for women whose height is smaller than 160cm (OR G | height ≥ 160cm = 0.78, 95% CI: 0.70-0.87, p = 1.09x10-5). Second interaction was shown between rs13035764 of NCOA1 and age at menarche in the GE|2df model (p-2df = 1.2x10-3). This SNP also had protective effect marginally (ORG = 0.85, 95% CI: 0.77-0.97) and more protective effect when age at menarche is 14 years and over (OR G | age at menarche ≥ 14years = 0.82, 95% CI: 0.73-0.97, p=3.6x10-4). Lastly, there was marginally significant interaction between rs4140979 of FSHR and age at first full term pregnancy (FFTP) in the EDGxE model. Although this SNP had no marginal effect, qualitative interaction was shown with FFTP (OR G | FFTP < 27years = 0.88, 95% CI: 0.78-1.00, p=0.0482; OR G | Nulliparity or FFTP ≥ 27 years = 1.30, 95% CI: 1.10-1.53, p=0.002).

Conclusion:

Three significant interactions were identified by focusing two step methods. Replication should be performed in the independent and larger population due to statistical limitation.

Citation Format: JooYong Park, Ji-Yeob Choi, Seokang Chung, Nan Song, Sue K Park, Wonshik Han, Dong-Young Noh, Sei-Hyun Ahn, Mi-Kyung Kim, Keun-Young Yoo, Wei Zheng, Daehee Kang. Gene-environment interaction relevant to estrogen and risk of breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1276. doi:10.1158/1538-7445.AM2017-1276
Abstract 1281: Germline mutations in NBN conferring DNA damage response defects are found in patients with multiple cancer types
Authors: Topka Sabine , Walsh Michael F. , Maria Ann , Lincoln Annie , Mandelker Diana , Zhang Liying , Ladanyi Marc , Berger Michael F. , Robson Mark E. , Vijai Joseph , Offit Kenneth
Published: July 2017

Nibrin, the protein encoded by the NBN gene forms a complex with Mre11 and Rad51 (MRN complex) that is crucial for DNA damage repair. Mutations in NBN are found in >90% of patients with Nimjegen breakage syndrome (NBS), an autosomal recessive disorder characterized by growth retardation, microcephaly, radiosensitivity, immunodeficiency and increased cancer risk. Most of NBS patients harbor the common founder mutation c.657del5 that leads to expression of a hypomorphic 70kDa C-terminal fragment produced by alternative translation initiation. Cell lines derived from these patients show increased sensitivity to DNA-damaging agents, chromosome instability, and abnormal cell cycle checkpoint function. Several studies have addressed cancer incidence in individuals with germline NBN mutations, showing increased cancer risk for individuals harboring the c.657del5 founder mutation and for carriers of the R215W missense mutation across multiple cancer types. For other NBN mutations conflicting reports exist as to their association with cancer risk. Here, we report newly identified NBN germline frameshift and truncating mutations in patients with multiple cancer types, including prostate, lung, breast cancer, acute lymphocytic leukemia, and chronic lymphocytic leukemia. Modeling these mutations in an NBN-deficient cellular background showed expression of a novel C-terminal truncated fragment that can bind to Mre11. Cells expressing these mutant proteins display attenuated DNA damage repair function and decreased overall survival following induction of DNA damage. Impaired Chk2 phosphorylation was also observed, indicating cell cycle checkpoint deficiencies. Thus, the NBN germline mutations identified here could contribute to genomic instability predisposing to tumorigenesis. Further in vitro studies with these and additional germline mutations occurring in cancer patients are ongoing, in order to better understand the role of this pathway of DNA damage repair in susceptibility to malignancies.

Citation Format: Sabine Topka, Michael F. Walsh, Ann Maria, Annie Lincoln, Diana Mandelker, Liying Zhang, Marc Ladanyi, Michael F. Berger, Mark E. Robson, Joseph Vijai, Kenneth Offit. Germline mutations in NBN conferring DNA damage response defects are found in patients with multiple cancer types [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1281. doi:10.1158/1538-7445.AM2017-1281
Abstract 1284: Identification of potential cancer regulatory germline single-nucleotide polymorphisms in the non-coding genome
Authors: Kulkarni Diptee A. , Song Kijoung , Guo Karl
Published: July 2017

Tumorigenesis in sporadic cancers is mainly driven by somatic genetic alterations such as driver mutations in protein coding genes or chromosomal changes comprising deletions, amplifications or translocations resulting in loss of tumor suppressor proteins, gain of oncogenic proteins or expression of aberrant fusion proteins, respectively. Some cancers lack such somatic changes, but are addicted to expression of certain genes for their sustained proliferation and survival. There is evidence of such oncogenic addiction to LIM domain only 1 (LMO1) expression in neuroblastoma (NB). Genome-wide association studies (GWAS) have identified robust associations between germline single-nucleotide polymorphisms (SNPs) within LMO1 and NB susceptibility with the causal SNP being rs2168101. Investigation of the mechanism of NB dependency on LMO1 showed that LMO1 expression in NB cells is regulated by rs2168101, which resides within a highly conserved tissue-specific super enhancer in LMO1 intron 1 and drives LMO1 expression through GATA3 transcription factor binding. This makes LMO1-dependent NB a unique example of sporadic cancer driven by germline genetic variation. Numerous GWAS have identified significant associations between germline SNPs in the non-coding genome and cancer risk or outcomes. To identify additional examples of regulatory SNPs as cancer drivers, we merged published genome-wide significant associations from cancer GWAS with genome regulatory data from ENCODE (Encyclopedia of DNA Elements; Nature. 2012 Sep 6; 489 (7414): 57-74)) and searched for clusters of cancer associated SNPs that resided within gene regulatory elements. Gene regulatory elements were defined as those marked by active epigenetic features and chromatin accessibility in cancer cell lines. Of the ~1,600 unique, genome-wide significant SNPs from cancer GWAS with regulatory evidence, we identified 46 clusters of 3 or more putative regulatory SNPs near 28 genes. These clusters were particularly enriched within ovarian cancer associated loci. Mechanistic studies such as reporter assays and genome editing in relevant cell types are being considered to identify the causal SNPs from these clusters regulating gene expression and driving tumorigenesis, which in turn may lead us to new cancer targets.

Citation Format: Diptee A. Kulkarni, Kijoung Song, Karl Guo. Identification of potential cancer regulatory germline single-nucleotide polymorphisms in the non-coding genome [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1284. doi:10.1158/1538-7445.AM2017-1284
Abstract 1287: Multigene panel testing and risk estimates in 10,233 ovarian cancer cases
Authors: Lilyquist Jenna , LaDuca Holly , Polley Eric , Shimelis Hermela , Hu Chunling , Moore Raymond , Hart Steven N. , Couch Fergus J. , Dolinsky Jill , Goldgar David E.
Published: July 2017

Germline pathogenic variants in BRCA1 and BRCA2 account for 10% of ovarian cancer (OC), including ovarian, fallopian tube, and primary peritoneal carcinomas. Pathogenic variants in BRIP1, RAD51C, RAD51D, and other cancer predisposition genes have been observed in another 2% to 5% of OCs. However, the specific genes associated with OC and estimates of risk associated with pathogenic variants in the individual genes are not well defined. We sought to determine the relevance of multigene panel testing results for OC cases. The study was focused on 140,449 individuals, including 10,233 OC cases, receiving clinical panel testing of cancer predisposition genes. Standardized relative risks (SRR) for pathogenic variants in 18 cancer predisposition genes were estimated using reference controls from the Exome Aggregation Consortium (ExAC). The median (range) age at diagnosis of OC was 57 (21-90) years. OC cases were 76.2% Caucasian, 3.6% African American, 4.6% Asian, 4.7% Hispanic, and 10.9% unknown/other. Among the 10,233 OC cases, 1391 (13.6%) had pathogenic mutations, including 1032 pathogenic mutations among the 7793 Caucasian OC cases (13.2%). Using the non-Finnish European ExAC (excluding TCGA samples) reference controls, the allele frequency for all pathogenic variants in each gene was summed and compared to the frequency of mutations in the Caucasian OC cases. Pathogenic variants in the known OC predisposition genes: BRCA1, BRCA2, BRIP1, MSH2, MSH6, RAD51C, and RAD51D were associated with a high risk of OC (SRR>4.0). Additionally, significant associations were observed for pathogenic variants in suspected OC risk genes ATM and PALB2 (SRR=2.06 and 2.78, respectively). This study identified several genes routinely screened on multigene panel testing that confer high or moderate risks of OC. Associations with known OC predisposition genes were confirmed. In addition, this study provides evidence that PALB2 is a moderate risk OC gene, and that ATM may confer lower to moderate risks of OC. If confirmed in future studies, these risks should be carefully considered in future screening and management of OC patients. In contrast, BARD1 and genes in the MRN complex were not associated with clinically relevant risks of OC.

Citation Format: Jenna Lilyquist, Holly LaDuca, Eric Polley, Hermela Shimelis, Chunling Hu, Raymond Moore, Steven N. Hart, Fergus J. Couch, Jill Dolinsky, David E. Goldgar. Multigene panel testing and risk estimates in 10,233 ovarian cancer cases [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1287. doi:10.1158/1538-7445.AM2017-1287
Abstract 1291: Mutation analysis of endometrial cancer in a population-based study by targeted next-generation sequencing
Authors: Chen Maxine , Crous-Bou Marta , Downing Michael J. , Busch Evan L. , Glass Kimberley , Prescott Jennifer , Mutter George L. , Vivo Immaculata De
Published: July 2017

Endometrial carcinoma (EC), a malignancy that arises from the epithelial lining of the uterus, is heterogeneous at histologic and molecular levels. Risk factors and outcomes also differ by type. Though prior studies characterized the genomic landscape of endometrial carcinoma, few integrated histologic, clinical, and prospectively collected epidemiologic data into the analysis. We collected formalin-fixed paraffin embedded tumor tissue from women enrolled in the Nurses’ Health Study who were diagnosed with EC between 1976 and 2012. We targeted 50 cancer related genes for high-throughput sequencing to identify genetic variants in 37 ECs and correlate findings with immunohistochemical, histologic, and epidemiologic data. Case selection was designed to include maximal power to discover genetic changes associated with p53 immunohistochemical status and clinical stage of disease at diagnosis. Mutations most frequently occurred in TP53 (57%), PTEN (46%), and PIK3CA (38%). TP53 mutations were seen in 83% of ECs that immunostained positive for mutant p53, with the most frequent TP53 mutations occurring in R248. Well-differentiated endometrioid tumors had elevated frequencies of PTEN and PIK3CA mutations compared to less differentiated tumors (p < 0.05). The mutation profiles of these samples are consistent with previous studies, supporting the viability of archival paraffin-embedded tissue in mutation detection. This study’s interdisciplinary approach to tumor characterization may help inform future development of personalized models for EC.

Citation Format: Maxine Chen, Marta Crous-Bou, Michael J. Downing, Evan L. Busch, Kimberley Glass, Jennifer Prescott, George L. Mutter, Immaculata De Vivo. Mutation analysis of endometrial cancer in a population-based study by targeted next-generation sequencing [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1291. doi:10.1158/1538-7445.AM2017-1291
Abstract 1303: A genome-wide association study of prostate cancer in Latinos
Authors: Hopp Hannah , Ingles Sue , Huff Chad , Sheng Xin , Weaver Brandi , Stern Mariana , Strom Sara , Thompson Ian , Conti David , Haiman Christopher A.
Published: July 2017

Recent studies estimate that individuals of African or Latin American ancestry represent less than 4% of samples analyzed to date in genome-wide association studies. The clinical value of genetic information in guiding personalized medicine in populations of non-European ancestry will require additional discovery and risk locus characterization efforts in these populations. Here, we performed a genome-wide association study (GWAS) meta-analysis of prostate cancer in Latino men to search for risk loci that may be important in this population. We combined GWAS data for 1034 cases and 1046 controls genotyped with the Illumina 660 Beadarray with GWAS data for 1235 cases and 1053 controls genotyped with the Illumina Oncoarray as part of the ELLIPSE U19 GAME-ON Consortium. A total of ~11 million genotyped and imputed SNPs of ≥1% frequency were tested for association with prostate cancer risk in logistic regression models controlling for age, study and genetic ancestry. Genome-wide significant associations were observed with 24 variants all located at 8q24 (128.484-128.548), and which capture the first reported prostate cancer susceptibility locus in ‘region 1’ of 8q24. The most significant association genome-wide was with SNP rs7824776 (risk allele frequency, 0.35; OR=1.69, p=3.4x10-11). No novel genome-wide significant associations were noted outside of 8q24. We observed a high degree of generalizability of known prostate cancer risk loci, with 78 (76%) of the 103 known risk variants having effects that were directionally consistent in their association with prostate cancer risk as previously reported, of which 31 (30%) were statistically significant with p < 0.05. In addition to these findings from the largest GWAS of prostate cancer in Latinos conducted to date, we will also present the results investigating effect heterogeneity by local ancestry (i.e. proportion Native American vs. European). In addition, we will present a comparison of polygenic risk models between Latinos, African Africans and men of European ancestry that incorporate the known risk loci to better understand how genetic risk tracks with population differences in prostate cancer incidence.

Citation Format: Hannah Hopp, Sue Ingles, Chad Huff, Xin Sheng, Brandi Weaver, Mariana Stern, Sara Strom, Ian Thompson, David Conti, Christopher A. Haiman. A genome-wide association study of prostate cancer in Latinos [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1303. doi:10.1158/1538-7445.AM2017-1303
Abstract 1306: Two distinct regulatory mechanisms underlie estrogen receptor negative breast cancer susceptibility at the 2p23.2 locus
Authors: Harro Carly M. , Mendoza-Fandino Gustavo , Woods Nicholas T. , Li Xueli , Couch Fergus J. , Monteiro Alvaro N.
Published: July 2017

Genome Wide Association Studies (GWAS) are designed to identify single nucleotide polymorphisms (SNPs) mapping to genomic regions associated with a particular trait or disease. Currently, 19 genomic loci associated with risk for estrogen receptor negative breast cancer have been identified. However, for most of these loci the mechanisms driving susceptibility have remained elusive. The 2p23.2 locus, defined by SNP rs67073037 (p = 4.76 x 10-9), contains 79 SNPs exhibiting genome-wide significant associations as well as four candidate genes: SPDYA, TRMT61B, WDR43, and FAM179A. Post-GWAS functional analysis revealed two candidate causal regulatory elements: an enhancer-like element defined by SNP rs44017214 located in the first intron of the WDR43 gene; and a segment in the 3’-UTR region of WDR43 defined by SNPs rs11680458 and rs11331880 which are predicted to have allele specific binding of non-coding microRNAs miR-548 and miR-376, respectively. We validated allele specific transcription factor binding to rs44017214 using competitive binding of USF1/USF2 to the risk allele in both MCF10A and CAL51 cell lines in Electrophoretic Mobility Shift Assays (EMSA). Additionally, rs44017214 was removed using CRISPR-cas9, and expression of neighboring genes was evaluated by qRT-PCR. No change in expression was found for any gene in a 2 Mb region surrounding the SNP, with the exception of PLB1. This suggests that the enhancer element in the intron of WDR43 has PLB1 as its target. To assess the miRNA binding site impact on WDR43 expression the pMIR-REPORT Luciferase allele-specific vector was co-transfected with miR-141/200, miR548, or miR-376 in MCF10A cells. The rs1131880 allele C in the WDR43 3’-UTR lead to the suppression of luciferase expression by miR-376 compared to the G allele. This study reveals two independent regulatory mechanisms within the 2p23.2 locus; (i) modulation of enhancer activity by allele specific binding of transcription factors USF1/USF2 to rs4401714, and (ii) decreasing the expression of WDR43 through the formation of a miR-376 binding site at the 3’-UTR of the WDR43 gene. Elucidating the functional significance of these common variants in the novel susceptibility loci 2p23.2 furthers our knowledge of the etiology of estrogen receptor negative breast cancer.

Citation Format: Carly M. Harro, Gustavo Mendoza-Fandino, Nicholas T. Woods, Xueli Li, Fergus J. Couch, Alvaro N. Monteiro. Two distinct regulatory mechanisms underlie estrogen receptor negative breast cancer susceptibility at the 2p23.2 locus [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1306. doi:10.1158/1538-7445.AM2017-1306