bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 242: Large pathway and gene set analysis of GWAS data identifies novel associations for pancreatic cancer
Authors: Walsh Naomi , Zhang Han , Hyland Paula L. , Yang Qi , Mocci Evelina , Zhang Mingfeng , Childs Erica J. , Wang Zhaoming , Chanock Stephen , Hartge Patricia , Hoover Robert , Kraft Peter , Li Donghui , Jacobs Eric J. , Petersen Gloria M. , Wolpin Brian M. , Risch Harvey A. , Amundadottir Laufey T. , Yu Kai , Klein Alison P. , Stolzenberg-Solomon Rachael Z.
Published: August 2018

Objective Genome-wide association studies (GWAS) identify associations of individual SNPs with cancer risk but usually only explain a fraction of the inherited variability. Pathway analysis of genetic variants has been shown for many disorders to be a powerful tool in discovering novel networks of susceptibility genes. Design We have conducted a large agnostic pathway-based meta-analysis of GWAS data using the summary-based adaptive rank truncated product (sARTP) method to identify novel gene sets and pathways associated with pancreatic ductal adenocarcinoma (PDA) in 9,040 cases and 12,495 controls. We performed expression quantitative trait loci (eQTL) analysis and functional annotation of the top SNPs in genes identified in PDA-associated gene sets and pathways. Results We identified 14 gene sets and pathways associated with PDA at FDR < 0.05. Five of the strongest signals (P-value ≤ 1.3x10-5 Bonferroni corrected) were in genes from KEGG maturity onset diabetes of the young, Reactome regulation of beta cell development, Biocarta role of epidermal growth factor (EGF) receptor transactivation by G-protein-coupled receptors in cardiac hypertrophy pathway, Nikolsky breast cancer chr17q11-q21 amplicon gene set, and Pujana ATM Pearson correlation coefficient (PCC) network gene set. We identified and validated rs876493 and three correlated SNPs (PGAP3) and rs3124737 (CASP7) as eQTLs in two normal derived pancreas tissue datasets. Conclusion Our agnostic gene set and pathway analysis integrated with functional annotation and eQTL analysis provides novel insight into genes and pathways that may be biologically relevant for risk of PDA.

Citation Format: Naomi Walsh, Han Zhang, Paula L. Hyland, Qi Yang, Evelina Mocci, Mingfeng Zhang, Erica J. Childs, Zhaoming Wang, Stephen Chanock, Patricia Hartge, Robert Hoover, Peter Kraft, Donghui Li, Eric J. Jacobs, Gloria M. Petersen, Brian M. Wolpin, Harvey A. Risch, Laufey T. Amundadottir, Kai Yu, Alison P. Klein, Rachael Z. Stolzenberg-Solomon. Large pathway and gene set analysis of GWAS data identifies novel associations for pancreatic cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 242.
Abstract 2423: Hypoxia regulates tumor cell invasiveness through altered glycosylation
Authors: Greville Gordon , Llop Esther , Miró Rosa Peracaula , McCann Amanda , Rudd Pauline M. , Saldova Radka
Published: August 2018

Glycosylation, one of the most fundamental post-translational modifications, is altered in many cancers. These alterations have been proven to impact on the progression of the tumor cell and promote survival. In literature published over the last half century, it is obvious there is a clear link between (a) chemo-resistance and hypoxia (b) hypoxia and epigenetics and more recently (c) glycosylation and epigenetics. We aim to bring these paradigms together with the remit of offering a more complete story and opening up new avenues of approach for the detection, diagnosis and treatment of breast and ovarian cancer.

Ovarian and breast cancer cells were exposed to differential hypoxic conditions (0.5%, 1.0%, 2.0%) and normoxia. Firstly, we compared the methylation status of hypoxia exposed cells to the normoxic controls. A combination of hydrophilic interaction liquid chromatography (HILIC) and statistical analyses allowed comparisons of the secreted N-glycans from cells exposed to differential hypoxic conditions. Western blots assessed apoptosis, senescence, autophagy and epithelial to mesenchymal transition. The OrisTM migration assay assessed the migration of the cells pre- and post-differential hypoxic exposure. RT-qPCR was used to measure gene expression of appropriate glycosyltransferases and possible transcription factors (TFs) in these samples to determine any associations with changes seen in N-glycosylation.

There were non-significant trends observed between the percentage oxygen that the cells were exposed to and resultant changes seen in branching and sialylation on secreted N-glycans from the breast and ovarian cancer cell lines. While only some of these changes could be explained by RT-qPCR data, GATA2/3 transcripts, identified in-silico as possible TFs, have been shown to significantly correlate with ST3GAL4 and MGAT5 glycosyltransferases, respectively. Hypoxia exposed cells also displayed increased migration with a greater effect seen in the 0.5% hypoxia exposed samples.

The GATA2 and GATA3 transcription factors are gaining popularity in recent years, with links to cancer stage, increased invasiveness and as possible therapeutic targets. Our recent data shows a strong correlation between GATA2 and GATA3 and the levels of glycosyltransferases involved in branching and sialyation. These glycan changes are known to be strongly involved in cancer cell survival and metastases. Here for the first time we may have a possible mechanism of action linking GATA2 and 3 and invasiveness of breast and ovarian cancer cells.

Citation Format: Gordon Greville, Esther Llop, Rosa Peracaula Miró, Amanda McCann, Pauline M. Rudd, Radka Saldova. Hypoxia regulates tumor cell invasiveness through altered glycosylation [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2423.
Abstract 2429: HIF-1α repressed glycerol-3-phosphate shuttle to reduce oxidative stress in liver cancer
Authors: ZHANG Shuo , LAI Robin Kit-Ho , CHIU David Kung-Chun , XU Iris Mingjing , TSE Aki Pui Wah , WONG Chun-Ming , NG Irene Oi Lin , WONG Carmen Chak Lui
Published: August 2018

Liver cancer is the fifth most prevalent and third most common cancer globally. Hepatocellular carcinoma (HCC), arises from hepatocytes, accounts for more than 80% of liver cancer. HCC cells undergo extensive metabolic rewiring to support their uncontrolled growth. HCC cells encounter extremely high level of oxidative stress which is mostly generated in the electron transport chain. Reactive oxygen species (ROS) rapidly accumulate in the electron transport chain (ETC) during hypoxia due to inadequate electron transfer to O2 in the ETC. The glycerol phosphate (GP) shuttle plays an important role to transfer electron source (NADH) from cytoplasm to mitochondria to initiate the ETC. The GP shuttle is mediated by glycerol 3 phosphate dehydrogenase (GPD) which converts dihydroxyacetone phosphate to glycerol 3 phosphate (G3P) through the oxidation of NADH to NAD+. This contributes to ATP production in the mitochondria. Here, we reported that hypoxia-inducible factor 1 (HIF-1) acts as a transcriptional repressor instead of an activator to suppress transcription of an important ETC component of the glycerol phosphate shuttle (GPD) to reduce activity of the GP shuttle, thereby reducing oxidative stress. GPD expression was significantly reduced under hypoxic condition. Surprisingly, knockout, knockdown, or inhibition of HIF-1 restored GPD expression in hypoxia. GPD expression was significantly under-expressed in tumorous as compared to non-tumorous liver tissues in 91 HCC patients of our center by 2.67 fold. TCGA database containing 49 HCC patients echoed with our in-house data. Downregulation of GPD was associated with poor cellular differentiation and overall survival in HCC patients. Stable overexpression of GPD1 in multiple HCC cell lines increased the levels of G3P as well as NAD+, which is crucial to lactate dehydrogenase (LDHA) activity. GPD overexpression altered mitochondrial activity, ROS levels, and suppressed HCC cell proliferation. Taken together, this study showed that the HIF-1 negatively controls key component of the GP shuttle to maximize HCC growth.

Citation Format: Shuo ZHANG, Robin Kit-Ho LAI, David Kung-Chun CHIU, Iris Mingjing XU, Aki Pui Wah TSE, Chun-Ming WONG, Irene Oi Lin NG, Carmen Chak Lui WONG. HIF-1α repressed glycerol-3-phosphate shuttle to reduce oxidative stress in liver cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2429.
Abstract 2432: The genomic consequences of tumor hypoxia in human cancers
Authors: Bhandari Vinayak , Espiritu Shadrielle M. , Liu Lydia Y. , Lalonde Emilie , Yamaguchi Takafumi N. , Heisler Lawrence E. , Livingstone Julie , Huang Vincent , Shiah Yu-Jia , Sabelnykova Veronica Y. , Yousif Fouad , Chua Melvin L. , Fraser Michael , Kwast Theodorus van der , Boutros Paul C. , Bristow Robert G.
Published: August 2018

Introduction: Localized prostate cancers are classified into risk-groups using clinical measurements like grade and stage to inform treatment decisions. However, these groupings are imprecise: ~30% of intermediate-risk patients suffer relapse of their disease despite precision image-guided radiotherapy or radical prostatectomy. One reason for this variability in response to treatment is the underlying cellular and molecular heterogeneity of tumors. Prostate tumor cells exist within a microenvironment characterized by gradients of oxygen levels and prostate tumors with low levels of oxygen (hypoxia) have poor clinical outcomes.

Methods and Results: To understand the correlates of hypoxia in cancer we conducted a pan-cancer analysis of copy number alterations (CNAs) and single nucleotide variants (SNVs) across 19 cancer types. We measured hypoxia using multiple mRNA-based signatures and discovered numerous CNAs and SNVs enriched or depleted in hypoxic tumors, highlighting the role of hypoxia in shaping the genomic landscape of multiple tumor types. Next, we examined 548 patients with localized prostate cancer and statistically assessed the association of hypoxia with CNAs, SNVs, genomic rearrangements, focal genomic events (i.e. kataegis, chromothripsis), telomere length, clinical indices (i.e. grade, stage) and subclonal architecture. Tumor hypoxia is associated with specific CNAs and SNVs in prostate cancer driver genes. To translate these findings into a biomarker for prostate cancer precision medicine, we integrated tumor microenvironmental data with genomic and pathological information to stratify patients into distinct prognostic groups.

Impact: These data suggest that the aggressiveness of cancers is driven by the interplay of the tumor microenvironment and its genomic mutational profile.

Citation Format: Vinayak Bhandari, Shadrielle M. Espiritu, Lydia Y. Liu, Emilie Lalonde, Takafumi N. Yamaguchi, Lawrence E. Heisler, Julie Livingstone, Vincent Huang, Yu-Jia Shiah, Veronica Y. Sabelnykova, Fouad Yousif, Melvin L. Chua, Michael Fraser, Theodorus van der Kwast, Paul C. Boutros, Robert G. Bristow. The genomic consequences of tumor hypoxia in human cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2432.
Abstract 2434: Regulation of HIF1a stability by an antisense RNA
Authors: Huang Xin , Huang Huang
Published: August 2018

Hypoxia is a hallmark of solid tumors. Hypoxia-inducible factors (HIFs) are the main transcriptional factor that regulate the cellular response to hypoxic stress. HIFs are heterodimers consisting of an oxygen-sensitive alpha subunit (HIFα) and a constitutively active beta subunit (HIF1β, also called aryl hydrocarbon receptor nuclear translocator, ARNT). Among the three homologous HIFα genes, HIF1α, HIF2α, and HIF3α, the functions of HIF1α and HIF2α are best characterized. HIF1α is ubiquitously expressed in essentially all tissue types, while HIF2α expression is more tissue specific. Under normoxia, HIFα is hydoxylated by prolyl-4-hydroxylases (PHDs), targeting it for proteasome destruction mediated by the von Hippel Lindau (VHL) protein, an E3 ubiquitin ligase. Under hypoxic conditions, the activity of PHDs decreases and HIFα is stabilized and forms a dimer with HIF1β. The HIFα/HIF1β dimer is then translocated into the nucleus and binds specifically to the promoters of a large number of target genes involved in adaptation and protection against low oxygen conditions. It is well known that HIFα is stabilized by acute hypoxia and its level decreases under prolonged hypoxic conditions. However, the mechanism remains unknown. Now, we have identified an antisense RNA that regulates the interaction between HIFα and VHL. The induction of the anitsense RNA is responsible for the regulation of HIFα stability under prolonged hypoxia. Our study revealed a novel mechanism regulating HIFα pathway.

Citation Format: Xin Huang, Huang Huang. Regulation of HIF1a stability by an antisense RNA [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2434.
Abstract 2436: Anti-cancer effect by combination treatment of CDK and HSP90 inhibitors through HIF1α inhibition
Authors: Zhao Shuai , Zhou Lanlan , Dicker David T. , El-Deiry Wafik S.
Published: August 2018

Hypoxia-inducible factor 1α (HIF1α) is the main mediator of the adaptive response to intra-tumoral hypoxia. HIF1α overexpression contributes to tumor angiogenesis, cancer cell survival and metastasis. Thus, targeting HIF1α provides new opportunities for cancer therapy. We have previously shown that cyclin-dependent kinase 1 (CDK1) stabilizes HIF1α through direct phosphorylation of its Ser668 residue in a Von Hippel-Lindau (VHL)-independent or p53-independent manner both under hypoxia and at G2/M under normoxia (Warfel et al., Cell Cycle, 2013). Because heat shock protein 90 (HSP90) is a VHL-independent HIF1α stabilizer, we hypothesized CDK and CDK inhibitor effects in the stabilization/destabilization mechanism. We found that CDK1 inhibition disrupts the interaction between HSP90 and HIF1α. Moreover, administration of the CDK1 inhibitor, Ro-3306, partially reversed a heat shock (40°C) response dependent increase in the level of HIF1α, which suggests that CDK1 activity may contribute to HSP90-mediated HIF1α stabilization. Combination treatment with both HSP90 inhibitor and CDK1 inhibition/knockdown decreased HIF1α level more robustly than either single treatment. Dual inhibition of CDK1 and HSP90 not only synergistically decreased cell viability but also remarkably reduced colony formation of HCT116 colon cancer cells. Previously we have also shown that similar to CDK1, CDK4 plays a role in HIF1α stabilization as well. This led us to investigate the effect of CDK4/HSP90 dual inhibition on colorectal cancer cells. The combination treatment of CDK4 knockdown/inhibition and HSP90 inhibition reduced the level of HIF1α in various cancer cell lines (e.g., colorectal, glioblastoma, prostate cancers). The FDA-approved CDK4 inhibitor palbociclib along with ganetespib synergistically inhibited cell viability in SW480 colon cancer cells under hypoxia or normoxia. No reduction in cell viability was noted in WI38 normal cells under normoxia at similar concentrations. In addition, we tested the therapeutic potential of the dual CDKi/HSP90i therapy in vivo. The combination treatment of palbociclib and ganetespib inhibited tumor growth in the HT29 colon cancer cell xenograft mouse model at relatively low doses. Immunohistochemistry staining of the tumor samples revealed higher levels of apoptosis, lower levels of VEGF expression and reduced microvessel formation in the combination treatment group. Our findings provide a compelling rationale for a therapeutic strategy to target HIF1α through the combination of CDK and HSP90 inhibitors in cancer therapy.

Citation Format: Shuai Zhao, Lanlan Zhou, David T. Dicker, Wafik S. El-Deiry. Anti-cancer effect by combination treatment of CDK and HSP90 inhibitors through HIF1α inhibition [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2436.
Abstract 2446: 1-Palmitoyl-2-linoleoyl-3-acetyl-rac-glycerol (PLAG) attenuates gemcitabine-induced neutrophil extravasation
Authors: Jeong Jinseon , Kim Yong Jae , Shin Su-Hyun , Lee Do Young , Moon Byoung-Gon , Sohn Ki-Young , Yoon Sun Young , Kim Jae Wha
Published: August 2018

Neutrophils are the most abundant leukocyte in circulation and are the first responder to foreign particles and/or injury. Some chemotherapeutics are known to induce depletion of blood neutrophils as its high cytotoxicity. However, it is also possible that circulating neutrophils undergo extravasation in response to chemotactic gradients induced by anticancer agents. Here, we found that 1-palmitoyl-2-linoleoyl-3-acetyl-rac-glycerol (PLAG) attenuates gemcitabine-induced neutrophil extravasation via the inhibition of neutrophil-attracting chemokine expression in macrophages using in vivo and in vitro approaches. First, we observed that there were increased neutrophils infiltrated into the peritoneal cavity following gemcitabine treatment in 4T1 tumor-bearing mice. In addition, gemcitabine increased MIP-2 mRNA expression in the peritoneal cells as well as in other tissues of the mice. Likewise, gemcitabine induced the migration of circulating neutrophils into the peritoneal cavity in normal mice, and PLAG effectively decreased neutrophil migration by inhibiting the expression of adhesion molecules. Inhibition of CXCR2 by its antagonist, reparixin, abrogated gemcitabine-induced neutrophil migration, indicating that chemokines produced by gemcitabine mainly support neutrophil activation. In vitro experiments demonstrated that PLAG inhibited NADPH oxidase (NOX)-mediated reactive oxygen species production induced by gemcitabine, which is upstream of MIP-2 and/or CXCL8. Importantly, PLAG downregulated gemcitabine-induced membrane translocation of the cytosolic NOX subunit, Rac1, and phosphorylation of p47phox. We also demonstrated that 1-palmitoyl-2-linoleic-3-hydroxyl-rac-glycerol (PLH), the natural form of diacylglycerol, has no effects on gemcitabine-induced CXCL8 production and dHL-60 migration, suggesting that an acetyl group at the third position of the glycerol backbone may have a key role in the regulation of neutrophil activation. Altogether, this study suggests the potential of PLAG as a therapeutic strategy to modulate chemotherapy-induced neutrophil activation for cancer patients undergoing chemotherapeutic treatment.

Citation Format: Jinseon Jeong, Yong Jae Kim, Su-Hyun Shin, Do Young Lee, Byoung-Gon Moon, Ki-Young Sohn, Sun Young Yoon, Jae Wha Kim. 1-Palmitoyl-2-linoleoyl-3-acetyl-rac-glycerol (PLAG) attenuates gemcitabine-induced neutrophil extravasation [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2446.
Abstract 2448: Chemotherapy drug-induced AXL activation and cell survival signaling via reactive oxygen species that can be inhibited to enhance drug efficacy in mesothelioma
Authors: Oien Derek B. , Garay Tamás , Eckstein Sarah , Chien Jeremy
Published: August 2018

Cellular oxidative stress is characterized by elevated reactive oxygen species (ROS), and is a frequent phenotype of cancer cells. The consequences of ROS are complex, where ROS can promote or inhibit tumorigenesis. In mesothelioma, asbestos exposure to serous membranes induces ROS through iron content and chronic inflammation, and ROS promote cell survival signaling in mesothelioma. On the other hand, a current chemotherapy regime for mesothelioma consisting of a platinum and antifolate agent combination also induce ROS. Mesothelioma is notoriously chemotherapy-resistant, and we propose that ROS induced by cisplatin and pemetrexed may promote cell survival signaling pathways, which ultimately may contribute to chemotherapy resistance. In The Cancer Genome Atlas datasets, we found AXL kinase expression is relatively high in mesothelioma compared to other cancer samples. We showed that ROS induce the phosphorylation of AXL, which was blocked by the selective inhibitor BGB324 in VMC40 and P31 mesothelioma cells. We also showed that cisplatin and pemetrexed induce the phosphorylation of AXL and Akt, which was also blocked by BGB324 as well as by N-acetylcysteine antioxidant. AXL knockdown in these cells enhances sensitivity to cisplatin and pemetrexed. Similarly, AXL inhibitor BGB324 also enhances sensitivity to cisplatin and pemetrexed. Finally, higher synergy was observed when cells were pretreated with BGB324 before adding chemotherapy. These results demonstrate cisplatin and pemetrexed induce ROS that activate AXL, and blocking AXL activation enhances the efficacy of cisplatin and pemetrexed. These results suggest AXL inhibition may represent an effective strategy to enhance the efficacy of chemotherapy in mesothelioma. We further hypothesize AXL signaling may be part of an adaptive response to chemotherapeutic agents, providing transient resistance to cisplatin and pemetrexed that may ultimately contribute to acquired chemotherapy resistance.

Citation Format: Derek B. Oien, Tamás Garay, Sarah Eckstein, Jeremy Chien. Chemotherapy drug-induced AXL activation and cell survival signaling via reactive oxygen species that can be inhibited to enhance drug efficacy in mesothelioma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2448.
Abstract 2453: Eradication of neuroblastoma by suppressing the expression of a single noncoding RNA
Authors: Tee Andrew E. , Liu Pei Y. , Milazzo Giorgio , Hannan Kate M. , Maag Jesper , Bartonicek Nenad , Song Renhua , Jiang Chen C. , Zhang Xu D. , Norris Murray D. , Haber Michelle , Marshall Glenn M. , Li Jinyan , Vandesompele Jo , Mattick John S. , Mestdagh Pieter , Perini Giovanni , Hannan Ross D. , Dinger Marcel E. , Liu Tao
Published: August 2018

N-Myc gene amplification occurs in one quarter of human neuroblastoma tissues, and is a marker for poor patient prognosis. We performed RNA sequencing experiments, and identified 5 transcripts, including RP1NB1, which were most considerably differentially expressed between N-Myc gene amplified and nonamplified human neuroblastoma cell lines. Affymetrix microarray studies revealed that DEPD was one of the few genes considerably downregulated in neuroblastoma cells after RP1NB1 depletion. Chromatin immunoprecipitation assays showed that knocking down RP1NB1 expression reduced histone H3 lysine 4 trimethylation, a marker for active gene transcription, at the DEPD gene promoter. Luciferase assays demonstrated that knocking down RP1NB1 decreased DEPD gene promoter activity. Depletion of RP1NB1 or DEPD with two independent siRNAs or shRNAs significantly reduced ERK protein phosphorylation, N-Myc protein phosphorylation at Serine 62, N-Myc protein stabilization, neuroblastoma cell proliferation and survival. Clonogenic assays showed that knocking down RP1NB1 with doxycycline completely abolished colony formation capacity of neuroblastoma cells stably transfected with doxycycline-inducible RP1NB1 shRNAs. Importantly, treatment with doxycycline in mice xenografted with neuroblastoma cells stably transfected with doxycycline-inducible RP1NB1 shRNA led to tumor eradication. In human neuroblastoma tissues from 600 neuroblastoma patients, high levels of RP1NB1 gene expression correlated with DEPD gene expression and poor patient prognosis. In conclusion, this study identifies the novel long noncoding RNA RP1NB1 as an important regulator of N-Myc protein stability and neuroblastoma tumorigenesis.

Citation Format: Andrew E. Tee, Pei Y. Liu, Giorgio Milazzo, Kate M. Hannan, Jesper Maag, Nenad Bartonicek, Renhua Song, Chen C. Jiang, Xu D. Zhang, Murray D. Norris, Michelle Haber, Glenn M. Marshall, Jinyan Li, Jo Vandesompele, John S. Mattick, Pieter Mestdagh, Giovanni Perini, Ross D. Hannan, Marcel E. Dinger, Tao Liu. Eradication of neuroblastoma by suppressing the expression of a single noncoding RNA [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2453.
Abstract 2458: The androgen receptor-regulated lncRNA landscape reveals a role for ARlnc1 in prostate cancer progression
Authors: Zhang Yajia , Pitchiaya Sethuramasundaram , Cieślik Marcin , Niknafs Yashar S. , Tien Jean C. , Hosono Yasuyuki , Wang Lisha , Qiao Yuanyuan , Cao Xuhong , Ljungman Mats , Jiang Hui , Mehra Rohit , Guo Shuling , Malik Rohit , Chinnaiyan Arul M.
Published: August 2018

The androgen receptor (AR) signaling plays a key role in the development of the normal prostate as well as prostate cancer. While substantial efforts have been undertaken to study AR-regulated protein-coding genes in primary prostate cancer and castration-resistant prostate cancer, few studies have investigated the role of long noncoding RNAs. In this study, we employed transcriptome sequencing to delineate long noncoding RNAs (lncRNAs) associated with AR signaling in prostate cancer progression. ARlnc1 (AR-regulated lncRNA 1) was identified as being the top AR-induced, cancer-associated lncRNA in an integrative analysis of prostate cancer cell lines and tissues. Not only was ARlnc1 induced by AR, but ARlnc1 also was shown to sustain AR signaling by stabilizing the AR transcript via interaction with the AR 3' UTR. Knockdown of ARlnc1 suppressed AR expression, global AR signaling, and prostate cancer growth in vitro and in vivo. Taken together, these data support a role for ARlnc1 in maintaining a positive feedback loop that potentiates AR signaling during prostate cancer progression, and identifies ARlnc1 as a novel therapeutic target.

Citation Format: Yajia Zhang, Sethuramasundaram Pitchiaya, Marcin Cieślik, Yashar S. Niknafs, Jean C. Tien, Yasuyuki Hosono, Lisha Wang, Yuanyuan Qiao, Xuhong Cao, Mats Ljungman, Hui Jiang, Rohit Mehra, Shuling Guo, Rohit Malik, Arul M. Chinnaiyan. The androgen receptor-regulated lncRNA landscape reveals a role for ARlnc1 in prostate cancer progression [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2458.
Abstract 2461: Prognostic impact of telomeric repeat containing RNA expression on long-term oncologic outcomes in colorectal cancer
Authors: Bae SungUk , Jeong Woon Kyung , Bae Seong Kyu , Lee Jae-Ho
Published: August 2018

Purpose: Telomere shortening is associated with colorectal carcinogenesis and transcription from subtelomeres produces telomeric repeat containing RNA (TERRA), a natural inhibitor of telomerase activity (TA). Previous studies on TERRA expression demonstrated downregulation in advanced stages of human tumors.

Materials and Methods: We evaluated the 2p TERRA expression and telomere length using quantitative real-time PCR in 60 patients who underwent surgical resection for colorectal cancer between June 2008 and November 2010.

Results: Patients were grouped according to 2p TERRA expression, with 27 (45%) and 33 (55%) in the low and high TERRA expression groups, respectively. The median follow-up period was 80 months (range 2-103). 2p TERRA expression was marginally significantly associated with preoperative CEA (P = 0.082) and significantly associated with telomere length (P < 0.05). Five-year overall survival rates in the high 2p TERRA expression group and the low expression group were 73.6% and 78.2%, respectively (p = 0.322), and five-year disease-free survival rates in the high 2p TERRA expression group and the low expression group were 66.1% and 75.1%, respectively (p = 0.317).

Conclusions: 2p TERRA expression was marginally significantly associated with preoperative CEA and significantly associated with telomere length; however, it was not prognostic on long-term oncologic outcomes in colorectal cancer.

Citation Format: SungUk Bae, Woon Kyung Jeong, Seong Kyu Bae, Jae-Ho Lee. Prognostic impact of telomeric repeat containing RNA expression on long-term oncologic outcomes in colorectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2461.
Abstract 2462: Epstein-Barr virus-encoded microRNAs regulate the expression of BRCA1 in nasopharyngeal carcinoma
Authors: Lam Ka-Hei , Lung Raymond Wai-Ming , Hau Pok-Man , Yip Kevin Yuk-Lap , Tsao George Sai-Wah , Yu Ken Hung-On , Tong Joanna Hung-Man , Lo Kwok-Wai , To Ka-Fai
Published: August 2018

Nasopharyngeal carcinoma (NPC) is an aggressive epithelial malignancy and is endemic in southern China and Southeast Asia. It is well-known to be associated with Epstein-Barr virus (EBV) infection. The miRNAs derived from EBV BamH1-A rightward transcripts (miR-BARTs) are abundantly expressed in NPC and have been suggested that can contribute to cancer development by regulating several gene expression. In this study, we established comprehensive expression profile of miRNAs in an EBV positive NPC cell line and 5 xenografts by small RNA sequencing. By using the prediction algorithm of miRanda and RNAhybrid, in silico analysis identified that several abundantly expressed miRNAs from viral and cellular genomes could negatively regulate BRCA1 expression via the 3' untranslated region (3'UTR). Notably, the regulatory role of miR-BART17-5p, miR-BART19-3p, miR182-5p on endogenous BRCA1 expression was demonstrated by transient transfection assays in HeLa cells and the direct recognitions were verified by luciferase reporter assays, while the downregulation of BRCA1 in primary NPCs was substantiated in the immunohistochemical (IHC) staining in a cohort of 61 histologically normal nasopharyngeal (NP) and 37 primary NPC cases (p<0.001). Taken togethher, we showed that the highly expressed miRNAs could work co-operatively to modulate BRCA1 activity. It has been reported that BRCA1 deficient tumor cells are defective in repairing the DNA double-strand breaks (DSBs) via error-free homologous recombination (HR). The impaired DSB repair by EBV latent infection may induce genome instability during NPC tumorigenesis and also contribute to sensitizing the tumor cells to ionizing radiation and DNA-damaging agent treatments.

Acknowledgement:

Theme-based Research Scheme (T12-401/13-R) and GRF (14104415, 14138016), Research Grant Council, Hong Kong

Citation Format: Ka-Hei Lam, Raymond Wai-Ming Lung, Pok-Man Hau, Kevin Yuk-Lap Yip, George Sai-Wah Tsao, Ken Hung-On Yu, Joanna Hung-Man Tong, Kwok-Wai Lo, Ka-Fai To. Epstein-Barr virus-encoded microRNAs regulate the expression of BRCA1 in nasopharyngeal carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2462.
Abstract 2464: Divergent lncRNA MYMLR regulates MYC by eliciting DNA looping and promoter-enhancer interaction
Authors: Kajino Taisuke , Shimamura Teppei , Gong Shuyi , Yanagisawa Kiyoshi , Nakatochi Masahiro , Griesing Sebastian , Shimada Yukako , Kano Keiko , Suzuki Motoshi , Miyano Satoru , Takahashi Takashi
Published: August 2018

Long non-coding RNAs (lncRNAs), longer than 200 nucleotides in length, function in a wide range of processes by diverse mechanisms. lncRNAs are attracting research interest in the field of cancer research though their roles in regulation of oncogenes and/or tumor suppressors remain rather elusive. In order to search for MYC-modulating lncRNA, we performed a global search for lncRNAs affecting MYC activity using a systems biology-based approach with a K supercomputer and the GIMLET algorism based on local distance correlations. Consequently, MYMLR was identified and experimentally shown to maintain MYC transcriptional activity despite its low levels of expression and cell cycle progression. A proteomic search for MYMLR-binding proteins identified PCBP2, which transcriptionally regulates MYC expression in cooperation with MYMLR. Mechanistically, MYMLR places a 557-kb upstream enhancer region to make the MYC promoter and enhancer regions reside in the proximity. These findings implicate a crucial role for MYMLR in regulation of the archetypical oncogene MYC, and warrant future studies regarding the involvement of low copy number lncRNAs in regulation of other crucial oncogenes and tumor suppressor genes in cancer development.

Citation Format: Taisuke Kajino, Teppei Shimamura, Shuyi Gong, Kiyoshi Yanagisawa, Masahiro Nakatochi, Sebastian Griesing, Yukako Shimada, Keiko Kano, Motoshi Suzuki, Satoru Miyano, Takashi Takahashi. Divergent lncRNA MYMLR regulates MYC by eliciting DNA looping and promoter-enhancer interaction [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2464.
Abstract 2475: Long noncoding RNA NNT-AS1 sponges miR-424 to promote the progression and metastasis of gastric cancer
Authors: Chen Beibei , Zhao Qingfang , Guan Lulu , Lv Huifang , Bie Liangyu , Huang Jinxi , Li Jitian , Zhang Jianying , Chen Xiaobing
Published: August 2018

Background: Long noncoding RNAs (lncRNAs) have been illustrated to function as important regulator in carcinogenesis and cancer progression. However, the roles of lncRNA NNT-AS1 in gastric cancer remain unclear. In present study, we investigate the expression level of NNT-AS1 in gastric cancer tissue and the role on gastric cancer cells tumorigenesis.

Methods: NNT-AS1 expression level was measured using RT-PCR. The prognosis and survival rate of gastric cancer patients with high/low expression of NNT-AS1 was tracked and analyzed. Cellular experiments were performed to test the role of NNT-AS1 on gastric cancer phenotype, including proliferation analysis, transwell assay, EMT-related marker blots and xenograft mice assay. Bioinformatics online program and luciferase assay were performed to predict and verify the potential miRNAs targeting NNT-AS1.

Results: NNT-AS1 expression level was significantly upregulated in 55 cases of gastric cancer tissue samples compared with adjacent normal tissue. Besides, the aberrantly enhanced NNT-AS1 expression predicted poor prognosis and lower survival rate. In vitro, NNT-AS1 knockdown suppressed the gastric cancer cells proliferation, invasion and EMT-related marker (N-cadherin and vimentin) expression. In vivo, lentivirus mediated NNT-AS1 silencing decreased the tumor growth. MiR-503 was verified to be the target miRNA of NNT-AS1 using bioinformatics online program and luciferase assay. Furthermore, miR-424 could reverse the role of NNT-AS1 on gastric cancer cells.

Conclusion: In conclusion, our study indicates that NNT-AS1 sponges miR-424 to facilitate gastric cancer cells invasion and metastasis, revealing the oncogenic role of NNT-AS1 on gastric cancer cells.

Citation Format: Beibei Chen, Qingfang Zhao, Lulu Guan, Huifang Lv, Liangyu Bie, Jinxi Huang, Jitian Li, Jianying Zhang, Xiaobing Chen. Long noncoding RNA NNT-AS1 sponges miR-424 to promote the progression and metastasis of gastric cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2475.
Abstract 2480: Olig2-dependent reciprocal shift in PDGF and EGF receptor signaling regulates tumor phenotype and mitotic growth in malignant glioma
Authors: Lu Fanghui , Xin Mei , Lu Qing Richard
Published: August 2018

Malignant gliomas exhibit extensive heterogeneity and poor prognosis. Diverse molecular characteristics in gliomas represent a significant hurdle for effective therapy. We uncover that a population of Olig2+ cells function as glioma-propagating cells and is critical for tumor initiation of primary gliomas in mice. Elimination of Olig2+ mitotic progenitors blocks tumor initiation and progression. Intriguingly, deletion of Olig2 resulted in tumors that grow, albeit at a decelerated rate. Genome occupancy and expression profiling analyses reveal that OLIG2 directly activates cell proliferation machinery to promote tumorigenesis. Olig2 deletion causes a tumor phenotypic shift from an oligodendrocyte precursor-correlated proneural toward an astrocyte-associated gene expression pattern, manifest in downregulation of PDGF receptor-alpha and reciprocal upregulation of EGFR. Olig2 deletion further sensitizes glioma cells to EGFR inhibitors and extends animal lifespans. Our observations reveal that OLIG2 is a molecular arbiter of tumor phenotype plasticity that may underlie drug resistance, suggesting new strategies for enhancing EGFR drug sensitivity in glioma treatment.

Citation Format: Fanghui Lu, Mei Xin, Qing Richard Lu. Olig2-dependent reciprocal shift in PDGF and EGF receptor signaling regulates tumor phenotype and mitotic growth in malignant glioma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2480.
Abstract 2481: Loss of FUBP1 impairs terminal neuronal differentiation and predisposes neural progenitors for transformation
Authors: Hwang Inah , Cao Dongqing , Kim Do-Yeon , Zhang Tuo , Hu Jian , Yao Yu , Paik Jihye
Published: August 2018

Loss of terminal differentiation capacity through genetic mutations is a selected genetic event in tumorigenesis. 1p19q co-deletion associated recurrent mutations of far upstream element-binding protein 1 (FUBP1) have been reported from genomic analysis of low- grade oligodendroglioma. It is frequently overexpressed in many human cancers and strongly correlated with disease progression. However, left unanswered is how FUBP1 serves uniquely as a tumor suppressor in the central nervous system. Here we show that expression of FUBP1 is dynamically regulated during neurogenesis, marking specific stages of neuronal differentiation. Loss of FUBP1 in neural stem/progenitor cells (NPC) increased the number of cells fail to terminally differentiate. Knockdown of FUBP1 further blocks differentiation and promotes tumorigenesis collaboratively with the expression of neomorphic isocitrate dehydrorgenase 1 mutant IDH1R132H. Mechanistically FUBP1 is necessary for mini exon 8a splicing of neurospecific isoform of histone demethylase LSD1 (nLSD1). It binds to intron 8 of LSD1 together with a neuron-specific splicing complex containing NOVA1 and 2 and works synergistically with SRRM4 for the inclusion of mini exon 8a. The expression level of nLSD1 is decreased upon loss of FUBP1 in neural progenitors, impairing the terminal neuronal differentiation and maturation. Reinforcing nLSD1 expression in FUBP1-downregulated NPC restores terminal differentiation, establishing nLSD1 as an obligatory effector of FUBP1-dependent neuronal differentiation. Together, these findings establish a direct role for FUBP1 in neuronal differentiation and also uncover the mechanism for its tumor suppressor function in the nervous system.

Citation Format: Inah Hwang, Dongqing Cao, Do-Yeon Kim, Tuo Zhang, Jian Hu, Yu Yao, Jihye Paik. Loss of FUBP1 impairs terminal neuronal differentiation and predisposes neural progenitors for transformation [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2481.
Abstract 2493: Inactivation of ARID1A-SWI/SNF complex alters chromatin compactness at enhancer regions and affects transcription of key tumor signaling circuitry
Authors: Rahmanto Yohan Suryo , Shi Xu , Shen Wenjing , Miyamoto Tsutomu , Yu Yu , Chen Xi , Lee Meng-Horng , Singh Vivek , Vitolo Michele I. , Wirtz Denis , Drapkin Ronny , Xuan Jianhua , Shih Ie-Ming , Wang Tian-Li
Published: August 2018

Somatic mutations in ARID1A, a SWI/SNF chromatin remodeling gene, are prevalent in human cancer and represent an emerging mechanism by which a molecular genetic alteration reprograms epigenomes and propels tumorigenesis. Through comprehensive sequencing of chromatin immunoprecipitation and chromatin accessibility, we found chromatin binding regions for ARID1A/BRG1-containing SWI/SNF remodeling complexes, which were enriched at enhancers and corresponded to euchromatin state. ARID1A deletion caused global re-distribution of BRG1-containing complexes in chromatin. Integrative analyses of ATAC-seq, ChIP-seq, and transcriptome data obtained from endometrial epithelium and human endometrioid carcinomas identified high-confidence ARID1A-regulated genes that participate in myriad key tumor and developmental signaling circuitry tissue. Deletion of Arid1a was found to inactivate the TGF-β pathway and to accelerate tumor progression from pre-cancerous lesions to endometrioid carcinomas. This study provides compelling evidence that Arid1a loss is required for developing endometrial cancer from its precursor. Collectively, targeting epigenomic modifications may hold promise for suppressing invasive behaviors of neoplasms carrying ARID1A mutations.

Citation Format: Yohan Suryo Rahmanto, Xu Shi, Wenjing Shen, Tsutomu Miyamoto, Yu Yu, Xi Chen, Meng-Horng Lee, Vivek Singh, Michele I. Vitolo, Denis Wirtz, Ronny Drapkin, Jianhua Xuan, Ie-Ming Shih, Tian-Li Wang. Inactivation of ARID1A-SWI/SNF complex alters chromatin compactness at enhancer regions and affects transcription of key tumor signaling circuitry [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2493.
Abstract 2499: Identification of functional proteins interacting with NSD2 in multiple myeloma
Authors: Chooi Jing Yuan , Xie Zhigang , Swa Hannah Lee-Foon , Gunaratne Jayantha , Kappei Dennis , Chng Wee Joo
Published: August 2018

Multiple myeloma (MM), characterized by the uncontrolled proliferation of malignant plasma cells, occurs mainly in the elderly population. Recurrent chromosomal translocations are central to the pathogenesis of MM, with t(4;14) being the second most common and associated with poor prognosis. The histone methyltransferase (HMTase) NSD2 is overexpressed in MM due to the t(4;14) translocation and has been suggested to play an important tumorigenic role in t(4;14) MM. However, the detailed molecular mechanism or signaling pathways describing how deregulation of NDS2 contributes to MM cell growth and survival are still uncertain. In this study, stable isotope labeling of amino acid in cell culture (SILAC)-based mass spectrometry analysis was used to determine NSD2-interacting proteins. Mass spectrometry analysis indicated that there were 75 proteins identified in the immunoprecipitation of NSD2 protein complexes. Gene ontology (GO) enrichment analysis showed that these proteins were enriched in processes related to chromatin organization, RNA processing and translation. Five high potential MMSET-interacting proteins from the most enriched functions were selected and verified by Immunoprecipitation and Western blot assays. The results indicated that there were interactions between NSD2 and SMARCA2, topoisomerase IIa, ADAR1, DDX5 and RPS6. In silico analysis with STRING database showed that SMARCA2 interacts with NSD2. SMARCA2 is the ATPase subunit of the SWI/SNF chromatin remodeling complex, which harnesses the energy from ATP to remodel the position of nucleosomes, making the DNA accessible during transcription, replication and DNA repair. Double immunofluorescence showed NSD2 and SMARCA2 co-localized in the cell nucleus. SMARCA2 was knocked down (KD) by shRNAs in t(4;14) MM cells. CellTiter-Glo Luminescent Cell Viability Assay (CTG assay) indicated that SMARCA2 KD by shRNA reduced t(4;14) MM cell growth. SMARCA2 KD also significantly inhibited the capacity to form colonies in t(4;14) MM cells on methylcellulose colony formation assay. Inhibiting SMARCA2 with active DNA-dependent ATPase A domain inhibitor (ADAADi) also reduced t(4;14) MM cell growth. In addition, SMARCA2 KD reduced cell cycle S phase. Western blot analysis showed downregulation of PRL3 and CCND1 protein level upon NSD2 or SMARCA2 KD. This study reveals a protein-protein interaction between NSD2 and SMARCA2. SMARCA2 KD showed SMARCA2 might be a novel therapeutic target for t(4;14) MM.

Citation Format: Jing Yuan Chooi, Zhigang Xie, Hannah Lee-Foon Swa, Jayantha Gunaratne, Dennis Kappei, Wee Joo Chng. Identification of functional proteins interacting with NSD2 in multiple myeloma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2499.
Abstract 2517: The role of endocytic traffic regulator EHD1 in EGFR traffic and breast cancer
Authors: Mushtaq Insha , Tom Eric C. , Arya Priyanka , Bielecki Timothy , Mohapatra Bhopal , Mirza Sameer , Storck Matthew D. , Ahmad Dena , Ansari Rokaya El , Rakha Emad , Band Vimla , Band Hamid
Published: August 2018

Epidermal growth factor receptor (EGFR) is a prototype receptor tyrosine kinase and serves as an oncogene in a variety of solid tumors. Its surface expression is dynamically regulated, and display of an activation-competent cell surface pool is an essential pre-requisite for cellular responses to EGF and other ligands, as well as for its oncogenic function. While mechanisms that regulate the post-activation endocytic fate of EGFR have received much attention, little is known about the mechanisms that control the basal, pre-activation, surface display of EGFR. Here, we identify a novel role of the endocytic recycling regulator EHD1 in the cell surface display of EGFR and EGF-driven functional responses. We demonstrate that inducible knockdown of EHD1 in human mammary epithelial cells impairs the EGFR delivery to the cell surface, resulting in reduced EGFR cell surface expression and accumulation in the Golgi, a phenotype rescued by exogenous EHD1. Reduced surface display of EGFR by depletion of EHD1 impaired EGF-induced proliferation mammary epithelial cells and a breast cancer cell line, demonstrating that the new molecular pathway we describe is functionally important. Given the role of EGFR and its family members in breast cancer, we carried out IHC screening of EHD1 expression in human breast cancer using tissue microarrays from a large (>800 samples) and well-annotated breast cancer cohort. Of the 757 evaluable samples, EHD1 was overexpressed in 115 (15%) patients. Notably, a substantially higher percentage of HER2/ErbB2+ patients (25%) showed EHD1 overexpression. Survival analysis revealed that EHD1 overexpression was associated with a significantly shorter overall survival over 15 years of follow up. These studies reveal novel roles of EHD1 in regulating EGFR traffic and suggest its potential roles in regulating other EGFR family members, especially HER2/ErbB2. Our patient sample analyses support a role for EHD1 overexpression in promoting breast tumorigenesis. Future studies will be directed at directly testing the role of EHD1, and its family members, in HER2 traffic and the role of EHD1 in breast tumorigenesis. As EHD proteins possess ATPase activity, which is required for their function, our studies raise the prospect of developing inhibitors of these enzymes as potential anti-cancer agents.

Citation Format: Insha Mushtaq, Eric C. Tom, Priyanka Arya, Timothy Bielecki, Bhopal Mohapatra, Sameer Mirza, Matthew D. Storck, Dena Ahmad, Rokaya El Ansari, Emad Rakha, Vimla Band, Hamid Band. The role of endocytic traffic regulator EHD1 in EGFR traffic and breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2517.