bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract IA13: It takes two to tango: The PVT1-MYC alliance in human cancer
Authors: Bagchi Anindya 
Published: May 2016

Abstract
Though gain of 8q24.21 is a common mutation in human cancers, its functional annotation is limited to studying myelocytomatosis (MYC), the prominent oncogene in the amplicon. However, MYC is co-gained with an adjacent long non-coding RNA gene plasmacytoma variant translocation 1 (PVT1), the CCDC26 gene candidate and gasdermin C GSDMC. Whether copy number gain of one or more of these genes drives neoplasia is not known. We developed chromosome engineered mouse strains with an extra copy of 1) Myc, 2) Pvt1, Ccdc26, Gsdmc, and 3) Myc, Pvt1, Ccdc26, Gsdmc. When rat Neu was introduced to test the change in the latency in mammary tumor development, only the mice with an extra copy of Myc, Pvt1, Ccdc26, Gsdmc (but not with an extra copy of Myc or Pvt1, Ccdc26, Gsdmc) developed adenocarcinomas with reduced latency, suggesting that while an extra copy of Myc gene failed to measurably advance cancer, it may co-operate with Pvt1, Ccdc26 or Gsdmc to promote cancer. Si-RNA mediated knockdown of Pvt1/PVT1 reduced the proliferation rates in the tumors, and in SK-BR-3 and MDA-MB-231, two human breast cancer cell lines with 8q24 amplification. Ablation of PVT1 markedly decreased MYC protein levels, suggesting a PVT1-dependence of MYC protein in MYC amplified cancer cells. Analysis of the cancer genome atlas suggested 99% of tumors with increased MYC copy-number also harbor co-gain of PVT1. Tissue microarray analysis revealed that PVT1 RNA and MYC protein expression are correlated in primary human tumors. These data suggests that PVT1 can potentiate MYC in human cancers. CRISPR mediated deletion of PVT1 in colorectal cell line HCT116 impaired tumor formation in xenografts, and significantly reduced MYC levels. We further confirmed the oncogenic potential of PVT1 in cancers even without supernumerary 8q24. Additionally, we have identified the putative functional domain of PVT1 which confers its oncogenic potential. We propose that the dependence of high levels of MYC on lncRNA PVT1 provides a much-needed therapeutic window against MYC protein, known to be refractory to small molecule inhibition.
Citation Format: Anindya Bagchi. It takes two to tango: The PVT1-MYC alliance in human cancer. [abstract]. In: Proceedings of the AACR Special Conference on Noncoding RNAs and Cancer: Mechanisms to Medicines ; 2015 Dec 4-7; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2016;76(6 Suppl):Abstract nr IA13.
Abstract PR03: A lncRNA regulates DNA repair by homologous recombination
Authors: Sharma Vivek , Khurana Simran , Kubben Nard , Abdelmohsen Kotb , Oberdoerffer Philipp , Gorospe Myriam , Misteli Tom 
Published: May 2016

Abstract
Introduction: Long non-coding RNAs (lncRNAs) have been shown to contribute to DNA damage response (DDR) by regulating gene expression. However, very little is known about the role that lncRNAs play in regulating DNA repair. In this study we characterized a lncRNA that regulates DNA repair by Homologous recombination (HR) by modulating recruitment of DNA repair factors at the sites of DNA damage.
Experimental procedures: Control or DNA damage treated cells were processed for gene expression analysis, qPCR, live cell imaging, Immunochemistry, Western blotting, FISH and RNA Immunoprecipitation.
Results: Using a genome-wide microarray screen we identified a novel ubiquitously expressed lncRNA, DDSR1 (DNA damage-sensitive RNA 1), which is induced upon DNA damage by several DNA double-strand break (DSB) agents. DDSR1 induction upon DNA damage is dependent on the ATM-NF-kB pathway. Loss of DDSR1 impairs cell proliferation, DDR signaling and reduces DNA repair capacity by homologous recombination (HR). The HR defect upon DDSR1 knockdown is characterized by aberrant BRCA1 and RAP80 accumulation at DSB sites. DDSR1 interacts with hnRNPUL1, an RNA-binding protein involved in HR. Loss of hnRNPUL1 also results in aberrant BRCA1 and RAP80 recruitment at DSB sites. Our results indicate that DDSR1/hnRNPUL1 depletion results in HR inhibition due to reduced end resection caused by aberrant BRCA1 and RAP80 at DSBs.
Conclusions: Our results reveal a previously unknown lncRNA involved in regulation of DDR by contributing DNA repair by HR. Our findings highlight the importance of DDSR1 in maintaining genome stability.
Citation Format: Vivek Sharma, Simran Khurana, Nard Kubben, Kotb Abdelmohsen, Philipp Oberdoerffer, Myriam Gorospe, Tom Misteli. A lncRNA regulates DNA repair by homologous recombination. [abstract]. In: Proceedings of the AACR Special Conference on Noncoding RNAs and Cancer: Mechanisms to Medicines ; 2015 Dec 4-7; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2016;76(6 Suppl):Abstract nr PR03.
Abstract PR07: Precise let-7 expression levels balance organ regeneration against tumor suppression
Authors: Nguyen Liem Hieu , Wu Linwei , Zhu Hao 
Published: May 2016

Abstract
The in vivo roles for even the most intensely studied microRNAs remain poorly defined. We interrogated the physiological functions of let-7, a large and ancient microRNA family that is well-known for regulating developmental timing, metabolism, and cancer. Analysis of mouse models revealed that let-7 performs tumor suppressive roles at the expense of regeneration. Too little or too much let-7 resulted in compromised protection against cancer or tissue damage, respectively. Modest let-7 overexpression, achieved by genetic induction or by lipid nanoparticle delivery, abrogated the development of aggressive MYC-driven liver cancer and provided a robust survival benefit by antagonizing let-7 sensitive oncogenes (Cdc25a, Cdc34, E2f2, E2f5, and Map4k4). However, the same level of overexpression blocked liver regeneration, while deletion of two let-7 family members significantly enhanced it, demonstrating that distinct levels of this microRNA can mediate desirable phenotypes. The observed let-7 dependent regeneration phenotypes resulted from influences on the insulin-PI3K-mTOR pathway. We found that chronic high-dose let-7 overexpression caused liver damage and degeneration, paradoxically leading to tumorigenesis. These dose-dependent roles for let-7 in tissue repair and tumorigenesis rationalize the tight regulation of this microRNA family in development, and have important implications for let-7 based therapeutics.
Citation Format: Liem Hieu Nguyen, Linwei Wu, Hao Zhu. Precise let-7 expression levels balance organ regeneration against tumor suppression. [abstract]. In: Proceedings of the AACR Special Conference on Noncoding RNAs and Cancer: Mechanisms to Medicines ; 2015 Dec 4-7; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2016;76(6 Suppl):Abstract nr PR07.
Abstract A15: Epigenetic regulators maintain neuroblastoma cancer stem cells: Model to treatment
Authors: Agarwal Saurabh , Chen Zaowen , Vasudevan Sanjeev , Shohet Jason M. 
Published: May 2016

Abstract
High risk neuroblastoma (NB) represents a major clinical challenge in pediatric oncology and accounts for 15% of pediatric cancer deaths. Our recent studies suggest that neuroblastoma tumors are heterogeneous and composed of multiple subpopulations including cancer stem cells (CSCs), marked by Granulocyte Colony Stimulating Factor Receptor (G-CSFR or CD114) positive cells. These CD114+ cells are shown to be highly tumorigenic, metastatic, self-renewing and can differentiate into non-tumorigenic progeny.
As tumor subpopulations typically demonstrate distinct epigenetic modifications at histone H3K4 and H3K27, we evaluate these epigenetic marks at the CSF3R locus (gene encoding G-CSFR) by ChIP-qPCR. Results suggest that the CSF3R gene is switched ‘on’ in NB CSCs via reversible epigenetic histone modifications. The CSF3R promoter in CD114+ NB CSCs, shows increased activating H3K4me3 marks and reduced repressive H3K27me3 marks. In the CD114- bulk tumor population, we found the opposite pattern of increased H3K27me3 marks and reduced H3K4me3 marks. In addition, knockdown of EZH2 (the PRC2 methyltransferase responsible for H3K27me3 marks) increases CD114+ expression in both cell culture and murine xenograft models of neuroblastoma.
Furthermore, gene expression studies revealed high levels of MLL1 (encoded by KMT2A), and Jumonji D3 (JMJD3, encoded by KDM6B) in CD114+ cells. MLL1 is a histone methyltransferase that catalyzes mono-, di- and tri-methylation on H3K4, while JMJD3 is an H3K27me3 demethylase.
Blocking MLL1 and JMJD3 with specific small molecule inhibitors, MM-102 and GSK-J4 reduces overall survival of NB cells and also reduces the percentage of CD114+ cells in vitro. Importantly, targeting these epigenetic regulators rapidly down-regulate the G-CSF receptor expression and induces apoptosis specifically in CD114+ cells but not in CD114- cells, suggesting maintenance of NB CSCs by these epigenetic modifiers. In vivo studies of these epigenetic inhibitors in neuroblastoma murine xenograft models validate our in vitro studies and demonstrate highly significant reduction in overall tumor size and metastasis with correlated reduction of total CD114+ cells in resected tumors.
Overall, we demonstrate that histone modifications play a key role in maintaining the NB cancer stem cells, and that specific epigenetic inhibitors are highly potent anti-tumor agents for high risk neuroblastoma. Our findings have direct translational impact and support the development of epigenetic stem cell targeted therapies for neuroblastoma.
Citation Format: Saurabh Agarwal, Zaowen Chen, Sanjeev Vasudevan, Jason M. Shohet. Epigenetic regulators maintain neuroblastoma cancer stem cells: Model to treatment. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Pediatric Cancer Research: From Mechanisms and Models to Treatment and Survivorship; 2015 Nov 9-12; Fort Lauderdale, FL. Philadelphia (PA): AACR; Cancer Res 2016;76(5 Suppl):Abstract nr A15.
Abstract A22: The histone demethylase KDM3A in Ewing sarcoma metastasis
Authors: Sechler Marybeth , Parrish Janet , Jedlicka Paul 
Published: May 2016

Abstract
This study aims to explore the roles and mechanisms of new candidates for therapeutic targeting in Ewing Sarcoma. Ewing Sarcoma is an aggressive pediatric malignancy of the bone and soft tissue, driven by EWS/Ets oncogenic fusions and characterized by high propensity for metastasis and poor clinical outcomes. We have identified the histone demethylase KDM3A as a novel tumor and metastasis promoter downstream of EWS/Fli1, the most common driver in this disease. Moreover, we have identified the cell surface protein, Melanoma Cell Adhesion Molecule (MCAM), as a potential important mediator of KDM3A action. Our data show that both KDM3A and MCAM depletion can inhibit growth and metastatic phenotypes. Additionally we explore the regulation of MCAM, showing that KDM3A may upregulate MCAM expression both through a direct as well as an indirect mechanism via the Ets1 transcription factor. Since both KDM3A and MCAM are pharmacologically targetable, understanding of this pathway could provide at least two new therapeutic targets in Ewing Sarcoma, and, importantly alternatives to drugging of EWS/Ets fusions, which to date has proven very difficult.
Citation Format: Marybeth Sechler, Janet Parrish, Paul Jedlicka. The histone demethylase KDM3A in Ewing sarcoma metastasis. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Pediatric Cancer Research: From Mechanisms and Models to Treatment and Survivorship; 2015 Nov 9-12; Fort Lauderdale, FL. Philadelphia (PA): AACR; Cancer Res 2016;76(5 Suppl):Abstract nr A22.
Abstract A36: Validation of candidate cancer genes using the CRISPR system
Authors: Wolf Natalie , Smeester Branden , Weg Madison , Largaespada David A. , Moriarity Branden Scott 
Published: May 2016

Abstract
We have used Sleeping Beauty (SB) transposon mutagenesis to study the development of several types of sarcomas including osteosarcoma (OS) and malignant peripheral nerve sheath tumors (MPNST). This work has revealed the power of SB mutagenesis to identify critical genes and genetic pathways that, when altered, can cooperate to cause these tumors. We have discovered specific novel oncogenes, such as FOXR2 in MPNST and SEMA4D in OS, recurrent alterations in certain pathways, such as the Wnt/β−catenin pathway in MPNST, and information about what genetic alterations can cooperate in sarcomagenesis, such as loss of NF1 and PTEN in MPNST. We have functionally validated these genetic alterations in several ways, including the use of genetically engineered mouse (GEM) models and TAL effector nucleases (TALEN) or CRISPR RNA-guided Cas9 nuclease modified human cell lines. However, these studies typically analyzed only single candidates of great interest due to the alteration observed in comparative genomics analyses or novelty in the cancer field. In an attempt to further study our candidate cancer genes (CCGs) we have implemented the CRISPR nuclease system to perform a medium throughput screen of all candidate tumor suppressor genes (TSGs). To this end, we are generating and validating CRISPR gRNAs to target all TSGs identified in our MPNST and OS SB screens (~300 genes). Using immortalized human cell lines we have targeted these candidate TSGs and screened for their ability to increase colony formation in soft agar, migration, and xenograft tumor formation. We have identified numerous genes that when mutated by CRISPR resulted in increased tumorigenic properties. These genes are currently being tested for their ability to induce xenograft formation in immunocompromised mice. This CRISPR screen for MPNST and OS CCGs is ongoing and new results will be reported.
Citation Format: Natalie Wolf, Branden Smeester, Madison Weg, David A. Largaespada, Branden Scott Moriarity. Validation of candidate cancer genes using the CRISPR system. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Pediatric Cancer Research: From Mechanisms and Models to Treatment and Survivorship; 2015 Nov 9-12; Fort Lauderdale, FL. Philadelphia (PA): AACR; Cancer Res 2016;76(5 Suppl):Abstract nr A36.
Abstract B12: The ALK inhibitor PF-06463922 shows significant response as a single agent in ALK/MYCN driven models of neuroblastoma
Authors: Guan J. , Danielson L. , Chand D. , Jamin Y. , Ruuth K. , Tucker E. , Umapathy G. , Wakil A. El , Witek B. , Johnson T. W. , Smeal T. , Chesler L. , Palmer R. H. , Hallberg B. 
Published: May 2016

Abstract
ALK inhibitors such as the ALK/MET/ROS1 inhibitor crizotinib (Xalkori) have shown clinical efficacy in a number of tumour types. However, in ALK positive neuroblastoma treatment with the ALK inhibitor crizotinib has proved more difficult, highlighting the exploration of new drugs as a clinical priority. A recent report of an increased percentage of ALK positive cases in the relapsed neuroblastoma patient population, together with the increased repertoire of ALK inhibitors now available, led to the investigation of alternative ALK inhibitors with potential for use in treatment of neuroblastoma. Here we report an investigation of the activity of a next generation ALK inhibitor in a range of in vitro and pre-clinical ALK driven neuroblastoma models.
Initially PF-06463922 was tested in various neuroblastoma cell lines and a range of gain-of-function ALK neuroblastoma mutations were subsequently analyzed in more detail in engineered Ba/F3 and PC12 cell models and by in vitro kinase assays, comparing the effect of PF-06463922 in abrogating cell growth and induced pharmacodynamics markers of response with the ALK inhibitor crizotinib. These results clearly show PF-06463922 to be a superior inhibitor of ALK kinase activity inhibiting all neuroblastoma mutant ALK forms assayed. Finally, single agent oral administration of PF-06463922 lead to induction of apoptosis and a dramatic reduction in tumour volume in a genetically engineered mouse model of treatment-resistant high-risk neuroblastoma driven by aberrant expression of MYCN and activated ALK. Taken together, our results suggest that PF-06463922 represents an important potential step forward in the treatment of relapsed neuroblastoma with mutated ALK.
Statement of significance: Our results together with PK/PD analysis of PF-06463922 suggest future clinical trial investigation of ALK positive neuroblastoma
Citation Format: J. Guan, L. Danielson, D. Chand, Y. Jamin, K. Ruuth, E. Tucker, G. Umapathy, A. El Wakil, B. Witek, T. W. Johnson, T. Smeal, L. Chesler, R. H. Palmer, B. Hallberg. The ALK inhibitor PF-06463922 shows significant response as a single agent in ALK/MYCN driven models of neuroblastoma. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Pediatric Cancer Research: From Mechanisms and Models to Treatment and Survivorship; 2015 Nov 9-12; Fort Lauderdale, FL. Philadelphia (PA): AACR; Cancer Res 2016;76(5 Suppl):Abstract nr B12.
Abstract B28: Genomic analysis of osteosarcoma for identification of targeted therapies
Authors: Sayles Leanne , Breese Marcus , Sweet-Cordero E. Alejandro 
Published: May 2016

Abstract
Osteosarcoma (OS) is an aggressive pediatric bone malignancy that affects 400 children per year in the United States. OS is characterized by genomic instability and numerous copy number alterations (CNA). We hypothesized that CNA may be drivers of OS and that targeting cancer genes with CNAs may be a novel approach for treatment of OS. We have established a robust approach for generation of patient-derived xenografts (PDX) from patients with OS. To date, 15 PDX have been established from OS patients. Using whole-genome sequencing (WGS), we have identified possible target CNAs for individual patients and are currently testing them in their corresponding PDX. In two patients, an amplification in c-myc suggested possible susceptibility to the BRD4 inhibitor JQ1 or the CDK9 inhibitor AT7519. In a third patient sample, amplification of Cyclin D and Cyclin E in the setting of wild-type Rb suggested responsiveness to a CDK inhibitor. A fourth patient had a FOXM1 amplification which suggests a vulnerability to Palbociclib, a CDK4/6 specific inhibitor. This patient sample also had an Aurora kinase B amplification, suggesting susceptibility to inhibition of this kinase as a therapeutic approach. We treated the corresponding PDX with the drug predicted to target the patient sample based on CNA. In all cases, treatment of the PDX with the drugs predicted show a significant reduction in tumor growth compared to vehicle alone or to the drugs predicted for the other patient CNAs. As a follow up we are currently submitting several more patient samples and paired PDX for WGS as well as RNAseq to determine other potential targeted therapeutics based on CNA. In summary, our work suggests that WGS can be used to identify potential novel therapies for patients with OS. Further work will be needed to determine whether response in PDX models correlates with clinical response in patients.
Citation Format: Leanne Sayles, Marcus Breese, E. Alejandro Sweet-Cordero. Genomic analysis of osteosarcoma for identification of targeted therapies. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Pediatric Cancer Research: From Mechanisms and Models to Treatment and Survivorship; 2015 Nov 9-12; Fort Lauderdale, FL. Philadelphia (PA): AACR; Cancer Res 2016;76(5 Suppl):Abstract nr B28.
Abstract B29: MDM4 is a major p53 regulator in hepatoblastoma
Authors: Shi Yan , Patel Roma , Hollingsworth Emporia , Sarabia Stephen , Jin Jingling , Lopez-Terrada Dolores , Vasudevan Sanjeev 
Published: May 2016

Abstract
Purpose: Unresectable or metastatic hepatoblastoma generally confers a poor survival. MDM4 and MDM2 are the major negative regulators of p53, which has a predominantly wild type status in hepatoblastoma. Having previously shown that MDM4 has copy gain/amplification associated with the 1q32.1 amplicon in hepatoblastoma, we hypothesize that MDM4 is the predominant negative regulator of p53 function in hepatoblastoma and that blocking MDM4 will cause tumor cell death due to uninhibited p53 tumor suppressor activity.
Methods: An MTT assay was used to measure NSC207895 (MDM4 inhibitor) and Nutlin-3a (MDM2 inhibitor) cytotoxicity on hepatoblastoma cell lines (HepG2, HepT1, and Huh-6) as well as a patient-derived hepatoblastoma cell line (PDCL-1). CCK-8 was used to assess effects of low dose NSC207895 on HB cell line proliferation. Soft agar was used to assess the effect of NSC207895 on hepatoblastoma colony formation. Immunoblotting and quantitative RT-PCR was used to measure expression of p53 downstream targets in hepatoblastoma after treatment with NSC207895. P53 knockdowns were created to assess the effect of NSC207895 in hepatoblastoma in the absence of p53. Cell cycle analysis was performed using BRDU.
Results: Huh-6, HepG2, and HepT1 were all tested with Nutlin-3a and did not show significant cell death (IC50 &gt;10μΜ) inhibition with NSC207895 caused significant cell death in Huh-6 (IC50=1.27μΜ), HepG2 (1.62μΜ), and HepT1 (2.05μΜ). A decrease in cell proliferation was noted with concentrations of NSC207895 as low as 0.05μΜ, 0.1μΜ and 0.3μΜ in HepG2, HepT1, and Huh-6 respectively. An increase in IC50 was seen in the p53 knockdowns compared to each respective control (HepG2: 12.6μΜ vs 3.38μΜ; HepT1: &gt;50μΜ vs 1.45μΜ; Huh-6: 20.2μΜ vs 7.52μΜ). Increased PARP cleavage products and decreased MDM4 expression were seen on immunoblotting after treatment with NSC207895. By both immunoblotting and qPCR, the p53 downstream transcriptional targets, p21, BAX and PUMA, were increased after exposure to NSC207895 in all three cell lines. Cell cycle analysis showed an increased percentage of cells in G1/G0-phase and decreased percentage of actively replicating S-phase cells in HepG2 with NSC207895 treatment.
Conclusion: Our data supports the hypothesis that in hepatoblastoma, MDM4 may be a dominant inhibitor of p53 and inhibition of MDM4 causes p53-mediated cell death and growth inhibition. Therefore, inhibition of MDM4 may be a viable drug target for treating hepatoblastoma.
Citation Format: Yan Shi, Roma Patel, Emporia Hollingsworth, Stephen Sarabia, Jingling Jin, Dolores Lopez-Terrada, Sanjeev Vasudevan. MDM4 is a major p53 regulator in hepatoblastoma. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Pediatric Cancer Research: From Mechanisms and Models to Treatment and Survivorship; 2015 Nov 9-12; Fort Lauderdale, FL. Philadelphia (PA): AACR; Cancer Res 2016;76(5 Suppl):Abstract nr B29.