bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 3537: Otx2 and c-Myc association drives tumor progression in medulloblastoma molecular subtypes 3/4
Authors: Lu Yining , Guda Maheedhara R. , Asuthkar Swapna , Purvis Ian , Labak Collin M. , Jain Neha , Daniels David J. , Martin Sarah E. , Tsung Andrew J. , Velpula Kiran K.
Published: July 2017

Medulloblastoma (MB) is a pediatric brain tumor comprising of four molecular subgroups, with Group 3 and 4 tumors characterized by particularly poor prognosis. While research has advanced our understanding of MB, there is still a pressing need for new knowledge of the functional processes underlying its progression due to a scarcity of therapeutics. Recent studies have identified Orthodenticle homeobox 2 (Otx2), a cerebellar transcription factor, to be highly expressed in MB Group 3/4 subtypes. Datamining studies from Northcott and Robinson datasets revealed co-expression of Otx2 and c-Myc in Group 3/4 tumors. DAB staining conducted in human MB specimens showed increased expression of Otx2 and c-Myc. Colocalization studies confirmed datamining results. Next, we used a clinical Otx2 inhibitor, all-trans retinoic acid (ATRA), in a PDX cell line, P9, and in UW228 cells. Western blot analysis demonstrated reduced levels of c-Myc along with Otx2. In another experiment, we used the c-Myc/Max inhibitor 10058-F4 and observed comparable results to Otx2 inhibition. Real time PCR and immunocytochemistry experiments confirmed the aforementioned results. Further, treatment with ATRA and 10058-F4 showed reduced proliferation and migratory abilities in p9 and UW228 when compared to their respective controls. Mass spectrometry conducted on immune-precipitated Otx2 in P9 cells revealed a plethora of novel interaction partners that drive tumor growth and progression. In addition, western blot analysis in ATRA treated cells showed reduced expression of Max, suggestive of the existence of a feedback loop that link with Otx2 and c-Myc. Collectively our studies highlight Otx2 as a potential contributor to the malignant phenotype and describe its role in mediating the aggressiveness of Group 3/4 medulloblastoma.

Citation Format: Yining Lu, Maheedhara R. Guda, Swapna Asuthkar, Ian Purvis, Collin M. Labak, Neha Jain, David J. Daniels, Sarah E. Martin, Andrew J. Tsung, Kiran K. Velpula. Otx2 and c-Myc association drives tumor progression in medulloblastoma molecular subtypes 3/4 [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 3537. doi:10.1158/1538-7445.AM2017-3537
Abstract 354: Inhibition of Smad3 signaling with a TAT fusion peptide prevented TGF-β-induced fibronectin expression and cell migration in malignant gliomas
Authors: Kang Jeonghan
Published: July 2017

Malignant primary brain tumors represent one of the most common causes of cancer death in the world. Grade IV gliomas (glioblastoma multiform, GBM) are routinely resistant to current chemoradiationchemo radiation therapy with a median progression-free and overall survival for glioblastoma following current chemoradiation of ~7 and 15 months, respectively. While TGF-β functions as a growth inhibitor for most normal cell types, many tumors (including GBMs) have lost this inhibitory response and TGF-β now functions to promote tumor progression and/or dissemination. As aberrant TGF-β signaling is often considered a hallmark of high-grade gliomas, we examined whether inhibition of specific components would impact the malignant phenotype of glioblastoma. The primary mediators of TGF-β action are the Smad proteins (R-Smads), Smad2 and Smad3. Following receptor activation and R-Smad phosphorylation, they translocate to the nucleus to modulate gene expression. Since we previously determined that a cell penetrating peptide conjugate of the HIV TAT protein fused to a 30 amino acid sequence from sorting nexin 9 (SNX9) prevented Smad3, but not Smad2, nuclear import and target gene expression in models of organ fibrosis, we further investigated whether it might similarly impact aspects of GBM proliferation. To that end, twenty-one patient-derived xenografts (PDXs) were examined for their responsiveness to TGF-β. Of those, TGF-β stimulated migration and fibronectin expression in seven (33%), which was prevented by inhibiting Smad3 signaling with the TAT-SNX9 peptide but not a control peptide unable to block Smad3 action. These findings indicate that the TGB-b/Smad3 axis is a potentially important mediator of glioma cell invasion in a significant minority of GBM models. specifically targeting Smad3 might be effective in a subset of gliomas.

This work was supported by Public Health Service grants GM-055816 and GM-054200 from the National Institutes of General Medical Sciences and P50 CA-108961 Developmental Pilot Award from the National Cancer Institute.

Citation Format: Jeonghan Kang. Inhibition of Smad3 signaling with a TAT fusion peptide prevented TGF-β-induced fibronectin expression and cell migration in malignant gliomas [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 354. doi:10.1158/1538-7445.AM2017-354
Abstract 3540: Targeting obesity-related cancer progression with novel leptin receptor antagonists
Authors: Lipsey Crystal C. , Harbuzariu Adriana , Gonzalez-Perez Ruben R.
Published: July 2017

Obesity is a global health issue that has been identified as a risk factor for several types of cancer. High levels of body fat and circulating leptin are typical identifiers of obesity in humans and animals. Leptin is a 16kD protein hormone which is secreted by adipocytes, and maybe secreted from cancer cells, that functions to control satiation via leptin receptor binding. However, obese individuals often develop “leptin resistance”, which is a mechanism that leads to the accumulation of excess leptin. Increased binding of leptin to its receptor (OB-R) due to leptin resistance has been associated with disease progression and poor prognosis in human cancers. Our group has previously shown that leptin-mediated cancer cell proliferation is inhibited by the LPrA2 (leptin peptide receptor antagonist 2). We have prepared novel leptin antagonists and tested their ability to block leptin-induced survival and chemoresistance to Paclitaxel (TAX) and Gemcitabine (GEM) in cancer cells and derived tumorspheres (pancreatic: PANC-1, MiaPaca2 and triple negative breast cancer: MDA-MB231 and MDA-MB468). Western blot protein analyses showed the ability of the antagonists to specifically inhibit leptin-induced phosphorylation of STAT3, and expression of cyclin D, and Notch1 in cancer cells. Additionally, potential toxicity of antagonists was tested using MTT assay with concentrations up to 100X higher than the effective dose in non-malignant breast cells (MCF-10A). Data generated show no toxicity of the novel antagonists in vitro. Leptin-induced proliferation of breast cancer and pancreatic cancer cells (120-160%) was significantly inhibited by the novel antagonists. In addition, leptin-mediated progression of S-phase was also reduced by the antagonists. Leptin increased TAX and GEM chemoresistance in cells and tumorspheres that were efficiently inhibited by the antagonists. These data suggest that the new antagonists could be equally or more effective than LPrA2 for adjuvant treatment of cancer.

Acknowledgements: This work has been supported by Pilot Project Award from MSM/Tuskegee University/UAB Cancer Center partnership grant 5U54CA118638; PC SPORE Grant from UAB to RRGP, and facilities and support services at Morehouse School of Medicine (1G12RR026250-03; NIH RR 03034 and 1C06 RR18386).

Citation Format: Crystal C. Lipsey, Adriana Harbuzariu, Ruben R. Gonzalez-Perez. Targeting obesity-related cancer progression with novel leptin receptor antagonists [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 3540. doi:10.1158/1538-7445.AM2017-3540
Abstract 3541: Metabolic signature characterization in prostate cancer mediated by heme-oxygenase 1
Authors: Arciuch Valeria G. Antico , Anselmino Nicolas , Schuster Federico , Paez Alejandra , Cascardo Florencia , Cotignola Javier , Gueron Geraldine , Vazquez Elba
Published: July 2017

Prostate cancer (PCa) is the second leading cause of cancer-associated death in men, being bone metastases the main cause of mortality. Energetic metabolism alterations have become a new hallmark of cancer, since variations in a single gene can orchestrate changes in metabolic pathways and confer an adaptive advantage. Heme-oxygenase 1 (HO-1) exerts an antitumoral role in PCa inhibiting cell proliferation, migration, tumor growth and angiogenesis. The aim of this work was to assess the role of HO-1 in the metabolic signature of PCa. Through RNA-Seq we found a set of metabolic genes deregulated under pharmacological induction (hemin treatment) or genetic induction of HO-1 in PC3 cells. STAR and ATP5L2 were found upregulated, while HMGCS2, PRODH and ACOT12 were downregulated. These genes encode for steroid hormone metabolism, ATP synthesis, ketogenesis, proline and lipid metabolism. The analysis of the deregulated genes (2-fold) under HO-1 modulation by Gene Ontology revealed alterations in several metabolic pathways such as steroid, tyrosine and lipid metabolism, and ion transport. Bone is the only site of PCa progression, and bone cells are able to produce factors that increase the growth and survival of tumor cells favoring progression. However, the molecular nature of this interaction remains to be elucidated. Our preliminary results performed on co-cultures of PC3 cells (treated or not with hemin) with Raw264.7 (pre-osteoclastic) or MC3T3 (pre-osteoblastic) cells demonstrate that HO-1 is able to direct the metabolic fate of bone precursor cells due to the deregulation of glycolytic genes. HO-1 induction in PC3 cells downregulated the expression of PKM2 and LDHA in co-cultured Raw264.7 and MC3T3 cells (p< 0.05). Based on our results, we propose HO-1 as a key regulator of the metabolic status of PCa cells and a powerful mediator capable of redefining the metabolic signature of bone precursor cells, thus, favoring the establishment of a less aggressive phenotype.

Note: This abstract was not presented at the meeting.

Citation Format: Valeria G. Antico Arciuch, Nicolas Anselmino, Federico Schuster, Alejandra Paez, Florencia Cascardo, Javier Cotignola, Geraldine Gueron, Elba Vazquez. Metabolic signature characterization in prostate cancer mediated by heme-oxygenase 1 [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 3541. doi:10.1158/1538-7445.AM2017-3541
Abstract 3551: Targeting glutamine addiction of PIK3CA mutant colorectal cancers
Authors: Zhao Yiqing
Published: July 2017

Glutamine addiction is a major metabolic reprogramming event that occurs in cancer cells. Many tumors exhibit oncogene-dependent addiction to glutamine. PIK3CA, which encodes the p110α catalytic subunit of phosphatidylinositol 3-kinase α, is the most frequently mutated oncogene in human cancers. However, whether PIK3CA mutations reprogram cancer metabolism is an important unaddressed question. Here we show that oncogenic PIK3CA mutations render colorectal cancers (CRCs) more dependent on glutamine to growth. As a metabolite, glutamine is first converted to glutamate by glutaminase (GLS) and then to α-ketoglutarate (α-KG) by either a transaminase or a glutamate dehydrogenase. Calithera Biosciences recently developed a potent GLS inhibitor called CB-839, which is currently in phase I clinical trials in cancer patients. Using isogenic colorectal cancer cell lines with either WT or mutant PIK3CA allele knockout, we demonstrated that CRCs with PIK3CA mutations are more sensitive to growth inhibition by CB-839. Remarkably, combination of CB-839 with 5-FU induces regression xenograft tumors in PIK3CA mutant CRC models, suggesting that this combinational therapy may be effective approach to treat CRC patients whose tumors harbor PIK3CA mutations. Mechanistically, mutant p110α up-regulates gene expression of glutamate pyruvate transaminase 2 (GPT2) through an AKT-independent PDK1-RSK2-ATF4 signaling axis, thereby facilitating conversion of glutamate to α-KG. Together, our data establish oncogenic PIK3CA mutations as a cause of glutamine addiction in CRCs and that targeting glutamine metabolism may be effective approach to treat CRCs with PIK3CA mutations.

Citation Format: Yiqing Zhao. Targeting glutamine addiction of PIK3CA mutant colorectal 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 3551. doi:10.1158/1538-7445.AM2017-3551
Abstract 3557: miR-155 positively regulates glucose metabolism via PI3K p85-FOXO3a-cMYC axis in breast cancer
Authors: Kim Sinae , Lee Eunji , Chang Suhwan
Published: July 2017

Breast cancer is the most common cancer for women worldwide. Although the oncogenic roles of miR-155 in cancer have been reported, the metabolic function of miR-155 in breast cancer has not been fully elucidated. In this study, we have investigated how the energy metabolic shift occurs after a genetic inactivation or knockdown of miR-155. To this end, we performed metabolic profiling of the miR-155ko/ko or miR-155+/ko primary cancer cells, obtained from mouse breast cancer model. We found, in the absence of miR-155, less glucose uptake and glycolysis in tumor cells. Mechanistically, we revealed PIK3R1(Phosphoinositide-3-Kinase, Regulatory Subunit1, p85) and FOXO3a (Forkhead transcription factor of the O class 3a) are major targets that trigger the metabolic shift. Furthermore, we showed cMYC level was consequently decreased in the absence of miR-155 that results in the down-regulation of proteins playing in glucose uptake and Glycolysis. This finding is further confirmed in mouse allograft model. Finally, we show the miR-155 expression is positively correlates with either energy metabolite levels or standardized uptake values (SUV) of fluoro-deoxy glucose (FDG)-PET Images in triple negative breast tumors. Taken together, our study demonstrates a novel mechanism by which the miR-155 controls energy metabolism in breast cancer, through PI3K p85-FOXO3a-cMYC axis.

Citation Format: Sinae Kim, Eunji Lee, Suhwan Chang. miR-155 positively regulates glucose metabolism via PI3K p85-FOXO3a-cMYC axis in 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 3557. doi:10.1158/1538-7445.AM2017-3557
Abstract 3561: UCP2’s tumor-promoting role via regulating lipid signaling and PLCγ -1 activity
Authors: Sreedhar Annapoorna , Zhao Yunfeng
Published: July 2017

Mitochondrial abnormalities are long suspected to play important roles in tumor cell differentiation, proliferation and metabolism. Dysfunction of mitochondrial-dependent processes appear to be key features of cancerous cells. Among many such abnormal features of cancerous cells, a mitochondrial uncoupling protein 2 (UCP2) is shown to be up-regulated in various aggressive human cancers. Uncoupling proteins are a family of mitochondrial proteins present in the inner mitochondrial membrane whose physiological role is to decrease membrane potential and reactive oxygen species (ROS) production.

UCP2 over-expression recently been proposed as a novel survival mechanism for cancer cells. However, till date, the exact role of UCP2 in cancer remains inconclusive.

We recently reported that UCP2 appears to be a key regulator of cell proliferation, cell cycle and cell death during skin tumorigenesis. Using JB6P+ cells that overexpress UCP2, we showed that UCP2 expression correlated closely with cell proliferation and cell transformation. Moreover, inhibition of UCP2, decreased colony formation and 3D culture growth. Since UCP2 is the crucial player in the regulation of reactive oxygen species, and mitochondrial bioenergetics, we wanted to dissect out the role of UCP2 in redox regulation and tumor promotion.

Our data demonstrated that UCP2 differentially regulated ROS. UCP2 upregulation, decreased superoxide production, whereas increased hydrogen peroxide production with a concomitant increase in manganese superoxide dismutase (MnSOD) expression and activity. Furthermore, hydrogen peroxide was responsible for induction of lipid peroxidation and PLCγ-1 activation in UCP2 overexpressed cells. Moreover, PLCγ-1 activation enhanced tumorigenecity. Strikingly, pharmacological and siRNA mediated inhibition of PLCγ-1 markedly reduced colony formation and 3D growth in vitro. Lastly, restricting hydrogen peroxide production with hydrogen peroxide scavenger catalase, suppressed lipid peroxidation and dampened PLCγ-1 activity.

Taken together, our data suggest that hydrogen peroxide might be the mediator of UCP2’s tumor promoting role, and pharmacological disruption of PLCγ-1, and/or hydrogen peroxide may have clinical utility for UCP2-overexpressed cancers.

This research was funded by NCI and Feist-Wellier Cancer Center of LSUHSC-S

Citation Format: Annapoorna Sreedhar, Yunfeng Zhao. UCP2’s tumor-promoting role via regulating lipid signaling and PLCγ -1 activity [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 3561. doi:10.1158/1538-7445.AM2017-3561
Abstract 3571: Precise somatic mutation prediction in the absence of matching normal DNA
Authors: Kalatskaya Irina , Trinh Quang , Spears Melanie , Bartlett John , Stein Lincoln
Published: July 2017

Accurate identification of somatic mutations is an essential first step for many cancer studies. It is usually done by comparing the genome of the tumour to the reference genome sequence derived from a normal tissue taken from the same donor. However, there are a number of possible scenarios in which matched normal tissues might be not available for comparisons. It is most commonly encountered when performing analysis on retrospective studies with human tissues from clinical trials or pathology archives when normal samples were not collected in the first place or patient consent precludes examination of normal tissue or germline variants. Another common scenario is the use of a cancer cell line as an experimental model, many of which have no information on the donor’s normal genome. In this work, we describe an algorithm to identify somatic single nucleotide variants (SNVs) in Next Generation Sequencing (NGS) data in the absence of normal samples using a machine learning approach. Our algorithm was evaluated using a family of supervised learning classifications across six different cancer types and ~1,600 samples, including cell lines, fresh frozen tissues, and formalin-fixed paraffin-embedded (FFPE) tissues. In addition, our algorithm was tested with both deep targeted sequencing and whole exome sequencing strategies. The algorithm correctly classified between 95% and 98% of somatic mutations with F1-measure ranges from 75.9% to 98.6% depending on the tumour type. We have released the algorithm as a software package called ISOWN (Identification of SOmatic mutations Without matching Normal tissues), which is available as Open Source under Apache License 2.0 from https://github.com/ikalatskaya/ISOWN.

Citation Format: Irina Kalatskaya, Quang Trinh, Melanie Spears, John Bartlett, Lincoln Stein. Precise somatic mutation prediction in the absence of matching normal DNA [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 3571. doi:10.1158/1538-7445.AM2017-3571
Abstract 3578: Methyl2Acetyl: predicting epigenetic and transcriptomic activity from DNA methylation
Authors: Chen Xiang
Published: July 2017

DNA methylation and histone modifications are interconnected and interdependent epigenetic mechanisms that regulate chromatin accessibility in cells. They establish cell’s developmental identity and modulate individual response to endogenous developmental stimuli and environmental changes. Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is a popular assay to study genomewide histone modification profiles. However, ChIP-seq assays require relatively large amounts of starting materials (ranging from ~105 cells using a low cell number protocol to 107 cells in a standard protocol), which remains as a major obstacle for precious biological samples including primary tumor specimens. On the other hand, tagmentation-based whole genome bisulfite sequencing (TWGBS) protocol enables unbiased assessment of the genomewide methylation pattern using ~3,000 cells. Therefore, a quantitative relationship between DNA methylation and epigenetic/transcriptomic activity is in great demand.

In the current study, we developed Methyl2Acetyl, a machine learning framework to infer promoter epigenetic activities (e.g. H3K27Ac enrichment) using TWGBS data as input. The proposed model utilizes random forest learners, which allow automatic extraction of complex interactions among DNA methylation features surrounding transcription start sites. We applied Methyl2Acetyl to a set of pediatric solid tumor samples with high quality H3K27Ac ChIPseq data to evaluate its performance. The model accurately predicted promoter H3K27Ac enrichment in independent test samples (Pearson correlation against measured enrichment: 0.81 ± 0.02). To further test the robustness of our model, we trained a Methyl2Acetyl model on solid tumors and applied it to a set of 10 pediatric leukemia samples. Despite dramatic global methylome differences between solid tumors and leukemia, Methyl2Acetyl predicted promoter H3K27Ac enrichment showed strong concordance with target gene expression level in the same sample (Pearson correlation: 0.75 ± 0.02, classification AUC: 0.89 ± 0.01). Collectively, our data suggested that DNA methylation is predictive of promoter active histone modification enrichment and gene expression activity. Epigenetically active promoters can be imputed from TWGBS data in samples with limiting starting materials.

Citation Format: Xiang Chen. Methyl2Acetyl: predicting epigenetic and transcriptomic activity from DNA methylation [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 3578. doi:10.1158/1538-7445.AM2017-3578
Abstract 359: C1GALT1 activates multiple RTKs and promotes malignant behaviors in pancreatic adenocarcinoma cells
Authors: Kuo Ting-Chun , Juan Hsueh-Fen , Tien Yu-Wen , Huang Min-Chuan
Published: July 2017

Pancreatic adenocarcinoma (PDAC), stands up to the 4th in all cancer mortalities and remains the most in progress in America. Curative resection remains the most and only potential strategy but only 15~20% of patients are candidates. Even though, many of them have dismal prognosis. Aberrant glycosylation illustrates an attribution of cancer, especially fot promoting malignant behaviors in adenocarcinomas. Altered expression of glycans, such as GalNAcα1-O-S/T (Tn antigen) and Galβ1,3-GalNAc-S/T (T antigen), is hallmark of cancers. Core 1 β1,3-galactosyltransferase (C1GALT1) catalyzes the transfer of Gal to Tn antigen to form T antigen. C1GALT1 is reported to contribute to clinicopathological features and malignant phenotypes in various cancers. However, the expression and function of C1GALT1 in PDAC remain unrevealed. Our data showed that C1GALT1 was overexpressed in PDAC tissues and correlated with poor prognosis. C1GALT1 knockdown inhibited viability, migration, and invasion analyzed by MTT, transwell migration, and Matrigel invasion assays, respectively, in PDAC cells, associated with increased Tn antigen but decreased T antigen expression. Conversely, C1GALT1 overexpression promoted these malignant behaviors. C1GALT1 knockdown inhibited AKT and ERK activities in PDAC cells. Consistently, phospho-receptor tyrosine kinase (p-RTK) array showed decreased phosphorylation of several RTKs including EGFR, IGF1R, and FLT3. Additionally, flow cytometry of C1GALT1 knockdown cells showed enhanced apoptosis, which was associated with decreased catalase, Bcl-x, and death receptor DR5 revealed by apoptosis array. We also found that C1GALT1 knockdown arrested G1 progression in PDAC cells. Furthermore, gene set enrichment analysis of cDNA microarray indicated that C1GALT1 regulated cell cycle, cytoskeleton, and chromatin structure in PDAC cells. These findings indicate that higher C1GALT1 expression predicts worse survival of PDAC and enhances malignant characters in PDAC cells, highlighting a fundamental role of C1GALT1 in PDAC development.

Note: This abstract was not presented at the meeting.

Citation Format: Ting-Chun Kuo, Hsueh-Fen Juan, Yu-Wen Tien, Min-Chuan Huang. C1GALT1 activates multiple RTKs and promotes malignant behaviors in pancreatic adenocarcinoma 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 359. doi:10.1158/1538-7445.AM2017-359
Abstract 3590: Somatic variation discovery with GATK4
Authors: Auwera Geraldine A. Van der
Published: July 2017

The Genome Analysis Toolkit or GATK, developed at the Broad Institute, is currently one of the most widely used software toolkits for germline short variant discovery and genotyping in whole genome and exome data. GATK4 is the next generation of GATK; it runs faster and covers more ground, adding somatic SNVs, Indels and CNVs to its variant discovery portfolio.

Given the breathtaking increase in the amount of genomic data produced in recent years, GATK development has come to tackle multiple challenges: a) reflect the cutting-edge of science in terms of depth as well as breadth of analyses offered, b) scale to petabytes of data and c) provide a way to navigate the tradeoff between turn-around-time and cost of analyses. GATK4 addresses all of these challenges through a complete redesign and reimplementation of the original GATK software.

This new version greatly expands the toolkit's scope of action within the variant discovery space by improving somatic mutation calling and adding copy number, structural variant and tumor-heterogeneity analysis tools. For the established tools and algorithms composing the GATK Best Practices pipelines for short variant discovery (including MuTect2, the next generation of the DREAM challenge-winning somatic SNV caller MuTect, developed originally in the Cancer Genome Analysis group at the Broad Institute), GATK4 is a substantial upgrade that streamlines the tools' operation, providing functionally equivalent results in a much faster timeframe through greatly increased efficiency and leaner engineering.

Designed with cloud infrastructure in mind (although it still runs on local infrastructure), GATK4 is implemented with support for Apache Spark, makes key operations hundreds of times faster than previous generations of GATK and comes with end-to-end pipeline implementations that run out of the box on select cloud platforms.

Citation Format: Geraldine A. Van der Auwera. Somatic variation discovery with GATK4 [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 3590. doi:10.1158/1538-7445.AM2017-3590
Abstract 3591: A new method to infer clonal sequences and phylogenies from personal tumor genome profiles
Authors: Miura Sayaka , Gomez Karen , Murillo Oscar , Kumar Sudhir
Published: July 2017

Tumor progression involves the evolution of clonal cell populations that mutate and spread in the body. Genetic profiling has revealed the presence of extensive variation in tumor samples from individual patients. However, a tumor sample for genetic profiling is mixture of different clonal cell populations and needs to be decomposed into clonal sequences to infer the evolutionary history of the tumor. Therefore, we have developed a new method, CloneFinder, and show that the clone sequences present in each tumor sample can be accurately inferred from the analysis of multiple tumor sample profiles with our new CloneFinder method. CloneFinder is unique in its use of molecular evolutionary principles to deduce clone sequences at a single-nucleotide resolution along with their frequencies in each sample. It performs better than existing methods, which we found to produce incorrect numbers of clones, clone sequence errors, errors in clonal phylogenies, and biased estimates of cancerous cells in tumors. Application of CloneFinder to a large number of empirical datasets revealed that both early and recently evolved tumors contain ancestral clones at high frequencies. Therefore, our new method provides new insights into the clonal structure of tumors and their evolution within a personal life time.

Citation Format: Sayaka Miura, Karen Gomez, Oscar Murillo, Sudhir Kumar. A new method to infer clonal sequences and phylogenies from personal tumor genome profiles [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 3591. doi:10.1158/1538-7445.AM2017-3591
Abstract 3606: RBP2 promotes tamoxifen resistance by altering ER function and activating IGF1R and EGFR/HER2 signaling in histone methylation-dependent and -independent manners in breast cancer
Authors: Choi Hee-Joo , Son Taekwon , Kim Hyung-Yong , Min Kyueng-Whan , Oh Young-Ha , Lee Jeong-Yeon , Kong Gu
Published: July 2017

Retinoblastoma binding protein 2 (RBP2, also known as JARID1A), a member of the JARID1 family of histone H3 lysine K4 demethylases, has been considered to have an oncogenic potential in several types of human cancers including breast cancer. Although physical interaction between RBP2 and estrogen receptor (ER), a crucial factor for hormone-dependent breast cancer, has been implied, the role of RBP2 in ER-positive (ER+) breast cancer remains largely unknown. Here, we demonstrate that RBP2 is a novel therapeutic target for tamoxifen resistance in ER+ breast cancer as an ER co-regulator and an activator of receptor tyrosine kinase (RTK) signaling. In large cohorts of breast cancer patients including METABRIC, high expression of RBP2 was associated with poor response to tamoxifen therapy in ER+ breast cancer. Consistently, RBP2 induced tamoxifen resistance in ER+ breast cancer both in vitro and in vivo. Using RNA-sequencing analysis, we identified that many RBP2 target genes are overlapped with ER-dependent- and tamoxifen resistance-associated genes. Mechanistically, RBP2 induced not only hyperactivation of ER-dependent transcription but also estrogen agonist activity of tamoxifen-bound ER via the interaction with ER, thus increasing the expression of NRIP1, a co-repressor of ER. RBP2 also formed a transcriptional repressive complex with ER, NRIP1, and HDAC1 to induce H3K4 demethylation-mediated epigenetic gene silencing of IGFBP4 and IGFBP5, leading to the activation of IGF1R and its downstream, PI3K/AKT pathway. Furthermore, enhanced AKT phosphorylation by RBP2 was mediated by not only IGF1R but also EGFR/HER2 signaling via increasing the stability of EGFR and HER2 proteins in a demethylase activity-independent manner. We further confirmed that combinational treatment with tamoxifen and PI3K inhibitor BKM120 restored tamoxifen sensitivity in RBP2-overexpressing breast cancer. Taken together, these findings suggest that RBP2 mediates tamoxifen resistance in ER+ breast cancer by altering ER activity and activating IGF1R and EGFR/HER2 signal pathways in both a histone methylation-dependent and -independent manner. Therefore, RBP2 may be a promising prognostic marker and therapeutic target for endocrine therapy-resistant breast cancer.

Citation Format: Hee-Joo Choi, Taekwon Son, Hyung-Yong Kim, Kyueng-Whan Min, Young-Ha Oh, Jeong-Yeon Lee, Gu Kong. RBP2 promotes tamoxifen resistance by altering ER function and activating IGF1R and EGFR/HER2 signaling in histone methylation-dependent and -independent manners in 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 3606. doi:10.1158/1538-7445.AM2017-3606
Abstract 3617: A paradigm shift for insulin-like growth factor 1 receptor function in triple negative breast cancers
Authors: Obr Alison , Kumar Sushil , Birge Raymond , Wood Teresa
Published: July 2017

Signaling through the insulin-like growth factor type 1 receptor (IGF-1R) is complex in breast cancers. Early studies reported that expression of the IGF-1R correlated with estrogen receptor (ER) expression and predicted a favorable phenotype. Moreover, loss of IGF-1R has been associated with breast tumor progression into a more undifferentiated phenotype. We have generated and characterized a mouse line containing both MMTV-Wnt1 and MMTV-dnIGF-1R (kinase dead-IGF-1R) transgenes (referred to subsequently as bigenic mice) that leads to increased mammary tumor initiation and metastasis. These data support the hypothesis that the IGF-1R functions in suppressing metastasis in certain contexts and subtypes of triple negative breast cancers (TNBCs). Recent analyses of TCGA human datasets support the relevance of our model in human TNBCs that have reduced IGF-1R expression and increased expression of Wnt1 and the Frizzled co-receptor Lrp6. We have identified alterations in a number of target genes that potentially regulate metastasis in the bigenic primary tumors including increases in interleukin-6 (IL-6), Slug, Vimentin, Zeb 1/2 and decreases in E-cadherin expression as assessed by Qiagen specific qPCR and single gene qPCR. Furthermore, a subset of anti-inflammatory chemokines and cytokines were assessed by a targeted qPCR array revealing increases in interleukin-4, interleukin-10, and C-C motif chemokine ligand-2 and decreases in tumor necrosis factor-alpha in the bigenic tumors indicating a tumor associated macrophage phenotype. By flow cytometry analysis, the ratio of CD4+ T cells to CD8+ T cells is increased in the bigenic tumors suggesting a tumor promoting immune microenvironment. However, increased expression of IL-6 in the bigenic tumors is specific to the luminal tumor cells, and inhibition of IGF-1R in the MCF7 human breast cancer cell line results in increases in IL-6, Slug, and Zeb 1/2 expression suggesting the tumor cells activate EMT and a pro-tumorigenic microenvironment in response to decreased IGF-1R. Moreover, inhibition of IGF-1R in human breast cancer cells and MMTV-Wnt1 mouse tumor cells results in increased cell motility and invasion as assessed by the xCELLigence motility assay. Taken together, our data support the hypothesis that IGF-1R acts as a negative regulator of mediators that promote migration, invasion, and metastasis in TNBCs.

Citation Format: Alison Obr, Sushil Kumar, Raymond Birge, Teresa Wood. A paradigm shift for insulin-like growth factor 1 receptor function in triple negative breast 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 3617. doi:10.1158/1538-7445.AM2017-3617
Abstract 3618: PELP1 cytoplasmic mislocalization favors estrogen-induced signaling via AIB1 in ER+ breast cancer models
Authors: Truong Thu H. , Ostrander Julie H. , Lange Carol A.
Published: July 2017

Luminal breast cancers account for ~75% of cases and express (ER) and frequently contain a range of progesterone receptor (PR) positive cells. ER and PR are steroid hormone receptors (SR) that rapidly and dynamically shuttle between the cytoplasm and the nucleus, a process that allows for essential crosstalk with cytoplasmic signaling pathways that serve as direct inputs to SR transcriptional functions. During disease progression, aberrant hormone signaling often leads to expression of altered SR gene programs and endocrine resistance. An emerging biomarker of increased risk and aggressive cancer behavior is cytoplasmic PELP1. Our lab was the first to show that PELP1 forms a functional signaling and transcriptional complex with ER and PR to regulate novel estrogen-driven SR target genes associated with endocrine resistance. PELP1 is primarily nuclear in normal breast tissue, but cytoplasmic localization of PELP1 (cyto-PELP1) is observed in 40-58% of invasive tumors. To elucidate the impact of PELP1 mislocalization on SR signaling pathways and transcription programs, we have generated SR+ breast cancer cell models expressing vector, wild-type (nuclear) PELP1, and cyto-PELP1. Our studies show that cells expressing cyto-PELP1 exhibit increased mammosphere formation relative to WT-PELP1 or vector control cells in response to estrogen. Moreover, we have identified AIB1 (ER co-activator) as a robust binding partner for cytoplasmic, but not nuclear PELP1, through mass spectrometry. This interaction occurs in a hormone-dependent manner as shown by co-immunoprecipitation assays. AIB1 activation (i.e. phosphorylation levels) is increased in cyto-PELP1 cells relative to WT-PELP1 or control cells. Knockdown of AIB1 reduces cyto-PELP1 protein levels and leads to decreased gene expression of key pro-inflammatory and immune regulatory cyto-PELP1 target genes. Our results reveal novel cytoplasmic actions of AIB1 and highlight the significance of delineating the impact of dynamic PELP1 shuttling/mislocalization with respect to altered hormone/SR-driven target gene expression in luminal breast cancer progression. We conclude direct signaling inputs to SR complexes are profoundly altered in the context of PELP1 mislocalization and interaction with AIB1. Our findings are relevant to mechanisms of endocrine resistance that may be targeted by inhibitors of the PELP1/SR interaction.

Citation Format: Thu H. Truong, Julie H. Ostrander, Carol A. Lange. PELP1 cytoplasmic mislocalization favors estrogen-induced signaling via AIB1 in ER+ breast cancer 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 3618. doi:10.1158/1538-7445.AM2017-3618
Abstract 362: Repression of Smad3 by Stat3 and c-Ski/SnoN induces gefitinib resistance in lung adenocarcinoma
Authors: Makino Yojiro , Yoon Jeong-Hwan , Bae Eunjin , Kato Mitsuyasu , Miyazawa Keiji , Ohira Tatsuo , Ikeda Norihiko , Kuroda Masahiko , Mamura Mizuko
Published: July 2017

Cancer-associated inflammation develops resistance to the epidermal growth-factor receptor (EGFR) tyrosine kinase inhibitors (TKIs) in non-small cell lung cancers (NSCLCs) harboring oncogenic EGFR mutations. Stat3-mediated Interleukin (IL)-6 signaling and Smad-mediated transforming growth factor-β (TGF-β) signaling play crucial regulatory roles in cancer-associated inflammation. Here we show that Stat3 represses Smad3 in cooperation with c-Ski and SnoN, whereby renders gefitinib-sensitive HCC827 cells resistant. IL-6 signaling via phosphorylated Stat3 induced gefitinib resistance. By contrast, TGF-β upregulated gefitinib sensitivity. We found that IL-6 signaling via phosphorylated Stat3 repressed, whereas TGF-β upregulated the expression of Smad3 in HCC827 cells. Promoter analyses showed that Stat3 synergized with c-Ski/SnoN to repress Smad-induced transcription of the Smad3 gene. Smad3 induced apoptosis by upregulating pro-apoptotic genes such as Caspase 3 and downregulating anti-apoptotic genes such as Bcl2. Our results suggest that preventing IL-6/Stat3-induced loss of Smad3 can be a therapeutic strategy to prevent gefitinib resistance in NSCLCs with gefitinib-sensitive EGFR mutation.

Citation Format: Yojiro Makino, Jeong-Hwan Yoon, Eunjin Bae, Mitsuyasu Kato, Keiji Miyazawa, Tatsuo Ohira, Norihiko Ikeda, Masahiko Kuroda, Mizuko Mamura. Repression of Smad3 by Stat3 and c-Ski/SnoN induces gefitinib resistance in lung adenocarcinoma [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 362. doi:10.1158/1538-7445.AM2017-362
Abstract 3621: Characterization of the effects of estrogen receptor alpha Y537S and D538G mutations on receptor pharmacology
Authors: Hartman Steven J. , Kleinheinz Tracy , White Jonathan , Daly Stephen , Goodwin Ria , Zhou Wei , Liang Jun , Wang Xiaojing , Ortwine Daniel F. , Friedman Lori , O’Rourke Martin , Metcalfe Ciara , Blake Robert A.
Published: July 2017

The frontline therapy for estrogen receptor alpha (ERα) positive Breast Cancer (ER+BC) involves various forms of endocrine therapy, consisting of either Selective Estrogen Receptor Modulators (SERMs) or aromatase inhibitors. An emerging mechanism of ER+BC resistance to endocrine therapy, and consequently disease relapse, has been associated with a set of “hotspot” mutations in and near to helix-12 of the ERα ligand binding domain. Selective Estrogen Receptor Degraders/Down-regulators (SERDs) represent an important pharmacological strategy being applied to develop treatments for resistant ER+BC. Here, we compare 2 of the most frequent ERα hotspot mutations (Y537S and D538G), with ERα wildtype (WT) and the ability of a set of SERM/SERDs and other ERα ligands to bind, antagonize, degrade/stabilize ERα and affect cell proliferation. Common themes that emerged included the observation that the concentration of each drug required to bind, antagonize or degrade ERα Y537S or ERα D538G was typically higher than that required for ERα WT, although the extent of the shift varied between drugs and the type of measurement. An unexpected observation was that 4-hydroxy-tamoxifen (a major active metabolite of tamoxifen) stabilized nuclear ERα Y537S protein. This represents a potential mechanism that may limit the efficacy of Tamoxifen in treating ERα Y537S ER+BC.

Citation Format: Steven J. Hartman, Tracy Kleinheinz, Jonathan White, Stephen Daly, Ria Goodwin, Wei Zhou, Jun Liang, Xiaojing Wang, Daniel F. Ortwine, Lori Friedman, Martin O’Rourke, Ciara Metcalfe, Robert A. Blake. Characterization of the effects of estrogen receptor alpha Y537S and D538G mutations on receptor pharmacology [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 3621. doi:10.1158/1538-7445.AM2017-3621
Abstract 3623: Preclinical efficacy of the selective GR antagonist, CORT125134
Authors: Hunt Hazel , Belanoff Joseph , Block Thad , Shepherd Stacie P.
Published: July 2017

The role of activation of the glucocorticoid receptor (GR) in the response of several solid tumor types to chemotherapy has been reported by several groups. Skor et al1 have demonstrated that the non-selective GR antagonist mifepristone can potentiate the effect of paclitaxel in a mouse xenograft derived from a human triple negative breast cancer (TNBC) cell line. GR activation is thought to play a role in the regulation of pro- and anti-apoptotic genes. Isikbay et al2 have demonstrated the benefits of combining androgen deprivation therapy with GR antagonism in prostate cancer xenograft model. Signaling via GR appears to be able to compensate for lack of androgen receptor signaling, and to contribute to castrate resistance.

CORT125134 is a novel, selective GR antagonist being developed for the treatment of a variety of solid tumors, in combination with an appropriate standard of care agent. CORT125134 is currently being studied in a Phase1/2 study in solid tumors, in combination with nab-paclitaxel.

The efficacy of CORT125134 in combination with standard of care agents has been investigated in mouse xenograft models of several tumor types. Previous reports of the benefit of adding a GR antagonist to chemotherapy in a TNBC model and an ovarian cancer model have been confirmed. An enhancement of the anti-tumor effect of castration by the addition of a GR antagonist has been confirmed in a model of prostate cancer. In addition, CORT125134 has been shown to provide a significant improvement in the efficacy of paclitaxel in a pancreatic cancer model. In a MIAPaca-2 xenograft model, paclitaxel was given i.v. every 4 days either alone or in combination with CORT125134. The combination provided significantly better tumor group inhibition than paclitaxel alone (p<0.0001). These encouraging results in a pancreatic cancer model extend the potential utility of GR antagonism in a variety of solid tumor types. In the TNBC model, alternative dosing regimens have been investigated, and suggest that stress during dosing is a confounding factor in these studies.

1. Skor MN, Wonder E, Kocherginsky M, et al. Glucocorticoid receptor antagonism as a novel therapy for triple negative breast cancer. Clinical Cancer Res. 2013;19(22):6163-6172.

2. Isikbay M, Otto K, Kregel S, et al. Glucocorticoid receptor activity contributes to resistance to androgen-targeted therapy in prostate cancer. Horm Cancer. 2014;5(2):72-89.

Citation Format: Hazel Hunt, Joseph Belanoff, Thad Block, Stacie P. Shepherd. Preclinical efficacy of the selective GR antagonist, CORT125134 [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 3623. doi:10.1158/1538-7445.AM2017-3623