tbuckley/cabot-search huggingface dataset:
Abstract 5507: Investigation of the effects of alterations in the glutamate receptor, GRIK2 on osteosarcoma tumorigenesis
Authors: Justin G. Mayers, Nalan Gokgoz, Jay S. Wunder, Irene L. Andrulis
Journal: Cancer Research (2017)

Abstract Osteosarcoma is a primary, malignant bone tumour mainly affecting young adults with a five-year survival rate of 60-70% depending on presentation of metastasis at diagnosis. Tumours are marked by genetic instability and heterogeneity and for this reason, molecular subtypes have yet to be characterized. Survival rates have remained consistent over the past few decades and novel molecular targets for treatment are needed. Current genomic strategies have identified recurrent copy number alterations. In a study of 44 flash frozen osteosarcoma tumours which were obtained at the time of biopsy and 25 blood-matched samples we identified recurrent copy number losses including a region at 6q16.3 in 14% of tumours. Focal deletions were observed in the 5’ intergenic space and first intron of the GRIK2 gene and do not overlap with any coding sequence. The relationship between alterations in this region and osteosarcoma tumourigenesis has yet to be explored in depth. GRIK2 encodes an ionotropic glutamate receptor that has been implicated as a tumour suppressor in gastric cancer. An interesting feature of the tumours was the overlap of focal deletions with a SETDB1 histone methyltransferase binding site indicating a potential connection with epigenetic regulation of GRIK2. The goal of this study is to examine the effects of non-coding, focal deletions on GRIK2 gene expression, function and regulation in osteosarcoma cells. GRIK2 transcript levels were measured in osteosarcoma tumours and cell lines using qRT-PCR. Functional assays were performed to characterize the role of GRIK2 in osteosarcoma cell proliferation, migration and apoptosis in vitro. Gene editing with CRISPR/cas9 was performed to examine the link between non-coding deletions and GRIK2 expression. GRIK2 transcript levels varied in tumours; several tumours with focal deletions had increased transcript levels relative to cell lines which demonstrated low expression levels. Due to the observation of low transcript levels, a gain of function approach was employed to examine GRIK2 function in vitro. Overexpression of GRIK2 decreased proliferation, migration and increased apoptosis in osteosarcoma cells. Gene editing of the SETDB1 binding site resulted in increased GRIK2 transcript levels relative to untreated cells. This study suggests that non-coding focal deletions are linked to high expression levels of GRIK2 which may confer a less aggressive phenotype and are involved in epigenetic regulation of the gene. Citation Format: Justin G. Mayers, Nalan Gokgoz, Jay S. Wunder, Irene L. Andrulis. Investigation of the effects of alterations in the glutamate receptor, GRIK2 on osteosarcoma tumorigenesis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5507. doi:10.1158/1538-7445.AM2017-5507
Clinical research platform into molecular testing, treatment and outcome of non-small cell lung carcinoma patients (CRISP): A prospective German registry in stage IV NSCLC AIO-TRK-0315.
Authors: Frank Griesinger, Wilfried Ernst Erich Eberhardt, Norbert Marschner, Martina Jänicke, Lisa Spring, Joerg Sahlmann, Aysun Karatas, Annette Hipper, Martin Sebastian, Michael Thomas
Journal: Journal of Clinical Oncology (2016)

TPS9108 Background: Treatment in NSCLC is quickly evolving. Whether outcome and PRO data generated in clinical trials with narrow inclusion and exclusion criteria will hold up in the routine practice is of high interest, especially due to the increasing costs of new drugs. Therefore registry data are of increasing importance to patients, physicians and third parties. This is why we have started a prospective, clinical registry for patients with metastatic non-small cell lung cancer. Methods: The purpose of CRISP is to set up a national clinical research platform to document representative data on molecular testing, sequences of therapies and other treatment modalities, course of disease in patients with advanced or metastatic NSCLC not amenable to curative treatment. A particular focus is on molecular biomarker testing of patients before the start of first-line treatment. PRO assessment will provide large-scale data on quality of life and anxiety/depression for real-life patients in routine practice. In addition, two questionnaires (concerning individual quality of life and patient-caregiver communication) will be validated in German patients with metastatic NSCLC. Furthermore CRISP will set up a decentral tissue annotation for future collaborative, investigational scientific biomarker testing. This study will be carried out in up to 150 representative cancer centers in all therapeutic sectors in Germany. More than 5000 patients will be recruited and followed up to a maximum of 3 years, respectively until death. The first patients have been included as of December 2015. Preliminary data will be presented at the meeting in terms of molecular test rates, demographic data as well as treatment stratification in the 1st line setting. In conclusion: The registry CRISP will be the first to present representative real life data, covering all treatment settings of patients with NSCLC in Germany. ClinicalTrials.gov Identifier: NCT02622581. CRISP is supported by Grants from AstraZeneca, Boehringer Ingelheim, Bristol-Myers Squibb, Celgene, Merck Sharp & Dohme, Novartis, and Pfizer. Clinical trial information: NCT02622581.
Abstract 5066: Combination treatment with SAHA and 5-Azacytidine (Decitabine) induces apoptosis and suppresses tumor growth in preclinical models of chondrosarcoma
Authors: Tahir Sheikh, Parag Patwardhan, Gary K. Schwartz
Journal: Cancer Research (2017)

Abstract Chondrosarcomas are the second most frequently occurring type of bone malignancy, and account for approximately 25% of all bone sarcomas. They are often highly aggressive neoplasms that rapidly progress and eventually recur and give distant metastases. They are largely considered to be resistant to conventional chemotherapy and radiotherapy. Several studies have reported that targeting epigenetic mechanisms including DNA methylation or histone acetylation are novel approaches for the treatment of some human cancers. Previous reports have shown that the interaction of DNA methylation and histone modification regulates gene expression. In the present study, we hypothesized that concurrent inhibition of histone acetylation and DNA methylation could result in decreased viability of chondrosarcoma cells both in vitro and in vivo. To test this, we used a panel of chondrosarcoma cell lines including IDH wild type (CH2879), IDH1 mutant (JJ012) and IDH2 mutant (CS1) cell line. Results from our in vitro proliferation assay showed that combination of sub-IC50 concentrations of the DNA methyltransferase (DNMT) inhibitor Decitabine (5-AZA-dC) and histone deacetylase (HDAC) inhibitor (SAHA) resulted in decreased cell viability of all the three chondrosarcoma cell lines tested when compared to either drug alone. Western blot analysis showed induction of cleaved Poly-ADP Ribose Polymerase (PARP), a known marker of apoptosis. Consistent with augmented DNA damage, combination of Decitabine and SAHA markedly increased the levels of phospho-H2AX, a DNA damage marker, and pro-apoptotic BH3-only proteins such as Bim. Combination treatment also resulted in increased induction of histone acetylation (AcH3) and increased expression of E-Cadherin. Previous reports have shown that E-cadherin is critical for apoptosis and depletion and inhibition of E-Cadherin impairs apoptosis induction via DR4 and DR5 death receptors. To this end, we showed that induction of cleaved PARP by Apo2L/TRAIL stimulation decreased over time when E-Cadherin was knocked down by siRNA. Xenograft studies using IDH2 mutant (CS1) tumor model showed a significant suppression of tumor volume when animals were treated in combination with SAHA and Decitabine compared to single agent treatments. Taken together, our data strongly suggests that combination treatment with SAHA and Decitabine is a novel treatment approach and merits evaluation in the treatment of chondrosarcoma. Citation Format: Tahir Sheikh, Parag Patwardhan, Gary K. Schwartz. Combination treatment with SAHA and 5-Azacytidine (Decitabine) induces apoptosis and suppresses tumor growth in preclinical models of chondrosarcoma [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 5066. doi:10.1158/1538-7445.AM2017-5066
Abstract 2544: The lncRNA Meg3 acts as an epigenetic determinant of oncogenic signaling in multiple endocrine neoplasia type 1
Authors: Sucharitha Iyer, Sunita Agarwal
Journal: Cancer Research (2017)

Abstract Loss of tumor suppressors and gain of oncogenic properties is a hallmark of cancer. But the pathways leading to tumor formation are poorly understood. A good example is the multiple endocrine neoplasia type 1 (MEN1) syndrome, in which patients inherit germline mutations in the MEN1 gene, predisposing to tissue-specific loss of the encoded tumor suppressor protein menin. Consequently, tumors develop in multiple endocrine organs - the pituitary, the parathyroids, and the duodeno-pancreatic tissues, including pancreatic neuroendocrine tumors (PNETs). Insulinomas are the most common type of functioning PNETs that also occur in MEN1 patients. We investigated the molecular pathways associated with insulinomas. We previously showed that menin loss downregulated Maternally Expressed Gene 3 (MEG3), a long non-coding RNA (LncRNA), by eliciting promoter hypermethylation along with the loss of Histone H3 lysine 4 trimethylation (H3K4me3). Gene expression microarray analyses and RT-PCR, of mouse insulinoma MIN6 cells stably transfected with Meg3, showed a 5-fold decrease in the proto-oncogenic signaling receptor c-Met, suggesting a tumor suppressor function for Meg3. We also found MEG3 downregulation with concurrent upregulation of c-MET in PNETs. However, the molecular underpinnings of MEG3 governed c-MET repression remain elusive. To identify the mechanisms by which MEG3 inhibits oncogenic c-MET signaling to suppress tumorigenesis, we examined the effect of various Meg3 isoforms, explored Meg3 association with the epigenetic regulatory machinery, and RNA-DNA triplex formation. We provide direct evidence for the first time that ectopically expressed Meg3 isoforms could attenuate the highly abundant c-Met transcript in MIN6 insulinoma cells. Meg3 also interacted with components of the epigenetic machinery, such as the Polycomb Repressive Complex 2 (PRC2) protein conglomerate, to regulate c-Met RNA expression. Additionally, analyses of triplex forming oligos (TFOs) in MIN6 cells revealed that triple helix formation between Meg3 and dsDNA could potentially disrupt c-Met transcription. Combined, these data offer mechanistic insight into the dysregulation of c-MET repression in PNETs, and support the conclusion that MEG3 acts as an important determinant of oncogenic signaling in MEN1-associated endocrine tumor cells (insulinoma). These findings warrant further investigation into the tumorigenic pathways that may result from the loss of tumor suppressor MEG3 and gain of oncogenic c-MET signaling in other MEN1-associated endocrine tumors. Citation Format: Sucharitha Iyer, Sunita Agarwal. The lncRNA Meg3 acts as an epigenetic determinant of oncogenic signaling in multiple endocrine neoplasia type 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 2544. doi:10.1158/1538-7445.AM2017-2544
Abstract 5368: Comparative analysis of multiple copy number alteration tools in the detection of amplifications and deletions on both whole-exome and targeted NGS panel platforms
Authors: Selene M. Virk, Sean Michael Boyle, Ravi Alla, Jennifer Yen, Richard Chen
Journal: Cancer Research (2017)

Abstract Somatic copy number alterations, or CNAs, are frequent occurrences in the tumor landscape and can present in the form of focal alterations or as chromosome level events. Reliable detection of CNAs is crucial to understanding the impact of these events on a wide range of factors including tumor progression and treatment outcomes. The clinical use of NGS panels, and more recently exomes, continues to expand in cancer but the reliable detection of CNAs remains a challenge. A major factor contributing to the challenge is the availability of reliable tools that have been well tested and validated. We sought to characterize the sensitivity and specificity of multiple CNA detection tools with a focus on clinically relevant genes in NGS panel and whole-exome. Our approach utilized a variety of publicly available CNA tools to identify whole gene amplifications and deletions in a set clinically relevant genes identified in the Catalogue of Somatic Mutations in Cancer (COSMIC) database. The tested CNA tools included two that supported both whole exome and panel NGS data, allowing cross platform in addition to cross tool comparisons. This work involved more than 20 well characterized cell lines derived from a broad spectrum of tumor types, including breast, lung, melanoma, and prostate cancers. The cell lines were analyzed in both tumor/normal and tumor only (which utilizes a proxy normal) modes. Analyses of patient-matched and proxy-normal data were performed with both assays. Using our approach, we were able to identify clinically relevant CNAs on both platforms. The performance of the tools tested varied, with some tools performing best on either amplification or deletion events. These results represent a comprehensive comparison of recent copy number alteration tools and provides data that can be utilized to make the tools even more robust and reliable. Citation Format: Selene M. Virk, Sean Michael Boyle, Ravi Alla, Jennifer Yen, Richard Chen. Comparative analysis of multiple copy number alteration tools in the detection of amplifications and deletions on both whole-exome and targeted NGS panel platforms [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 5368. doi:10.1158/1538-7445.AM2017-5368
Abstract 5748: Roles of miR29c-ID2 axis in tumor initiating cells of breast ductal carcinomain situ
Authors: Yin Liu, Puspa R. Pandey, Sambad Sharma, Kerui Wu, Fei Xing, Kounosuke Watabe
Journal: Cancer Research (2017)

Abstract Ductal carcinoma in situ (DCIS) is an early-stage form of breast cancer that accounts for over 20% of all breast cancers in the US. Therefore, prevention of DCIS is a major goal for reducing breast cancer incidence. However, the underlying molecular and pathological mechanisms of DCIS remain poorly understood. It is believed that tumor-initiating cells are formed at a very early stage of tumorigenesis, which then leads to the progression of DCIS. Our recent work that focused on tumor-initiating cells of DCIS revealed that the expression of miR29c in tumor-initiating cells was significantly down-regulated in DCIS cells compared to that in normal cells. Furthermore, we found that the ID2 gene is one of the targets of miR29c in tumor-initiating cells and that miR29c suppresses the ID2 gene by directly binding to the 3’-UTR sequence. ID2 is a well-known dedifferentiation factor in embryonic development, and the ID family is involved in progression of cancer by affecting cell differentiation and proliferation. We also found that ectopic expression of ID2 in premalignant cells accelerated tumor growth and promoted self-renewal of tumor-initiating cells in DCIS, suggesting that ID2 also controls cancer cell dedifferentiation and promotes tumor-initiating cells formation. These results indicate that the miR29c-ID2 axis plays a critical role in self-renewal of DICS in vivo and that ID2 is a potential biomarker for tumor-initiating cells in DCIS. ID2 is thought to sequester E-protein transcription factors and thus regulates a wide range of gene expression. Our data suggest that ID2 upregulates expression of several cancers stem cell genes including SOX2, which is a well- known self-renewal regulator of stem cells. ID2 also upregulates the fatty acid synthase gene (FASN), which promotes cancer cell proliferation and survival. We also found that FASN expression was significantly suppressed by pterostilbene, indicating potential utility of this natural compound for preventing DCIS formation. Taken together, these results suggest that miR29c-ID2 functions as master regulators in forming DCIS. ID2 promotes self-renewal of tumor-initiating cells by regulating expression of the SOX2 and FASN genes. Note: This abstract was not presented at the meeting. Citation Format: Yin Liu, Puspa R. Pandey, Sambad Sharma, Kerui Wu, Fei Xing, Kounosuke Watabe. Roles of miR29c-ID2 axis in tumor initiating cells of breast ductal carcinoma in situ [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 5748. doi:10.1158/1538-7445.AM2017-5748
Abstract LB-080: The histone methyltransferase DOT1L promotes neuroblastoma by regulating gene transcription
Authors: Matthew Wong, Andrew Tee, Giorgio Milazzo, Jessica Bell, Stefan Hüttelmaier, Patsie Polly, Giovanni Perini, Christopher J. Scarlett, Tao Liu
Journal: Cancer Research (2017)

Abstract Myc oncoproteins exert tumorigenic effects by regulating the expression of target oncogenes. Histone H3 lysine 79 (H3K79) methylation at Myc-responsive elements of target gene promoters is a strict prerequisite for Myc-induced transcriptional activation. DOT1L is the only known histone methyltransferase that catalyses H3K79 methylation. Here, we showed that N-Myc up-regulated DOT1L mRNA and protein expression by binding to the DOT1L gene promoter. Knocking down DOT1L reduced mRNA and protein expression of the N-Myc target genes ODC1 and E2F2. DOT1L bound to the Myc Box II domain of N-Myc protein, and knocking down DOT1L reduced histone H3K79 methylation and N-Myc protein binding at the ODC1 and E2F2 gene promoters and reduced neuroblastoma cell proliferation. Treatment with the small molecule DOT1L inhibitor SGC0946 reduced H3K79 methylation and proliferation of MYCN gene-amplified neuroblastoma cells. In mice xenografted with neuroblastoma cells stably expressing doxycycline-inducible DOT1L small hair-pin RNA, ablating DOT1L expression with doxycycline significantly reduced ODC1 and E2F2 expression, reduced tumor progression and improved overall survival. In addition, high levels of DOT1L gene expression in human neuroblastoma tissues correlated with high levels of MYCN, ODC1 and E2F2 gene expression, and independently correlated with poor patient survival. Taken together, our data identify DOT1L as a novel co-factor in N-Myc-mediated transcriptional activation of target genes and neuroblastoma oncogenesis, and DOT1L inhibitors as novel anticancer agents against MYCN-amplified neuroblastoma. Citation Format: Matthew Wong, Andrew Tee, Giorgio Milazzo, Jessica Bell, Stefan Hüttelmaier, Patsie Polly, Giovanni Perini, Christopher J. Scarlett, Tao Liu. The histone methyltransferase DOT1L promotes neuroblastoma by regulating gene transcription [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 LB-080. doi:10.1158/1538-7445.AM2017-LB-080
Abstract 612: Methylation changes in DNA of CD8 T cells following CD137 costimulation
Authors: M. Angela Aznar, Sara Labiano, Angel Diaz-Lagares, Manel Esteller, Juan Sandoval, Ignacio Melero
Journal: Cancer Research (2017)

Abstract Introduction: CD137 ligation imprints long term changes in the behavior of costimulated T-cells (1). There is not a satisfactory mechanistic explanation yet. Experimental procedures: to determine the specific DNA methylation changes occurring upon CD137 costimulation, purified human CD8+ T cells from three healthy donors were activated in vitro for 5 days with anti-CD3 monoclonal antibody and either with an anti-CD137 monoclonal antibody or its corresponding isotype (huIgG4). Activated lymphocytes were left 5 days in culture with huIL-7 without further stimulation. Such back-to-resting CD8+ lymphocytes were reestimulated with anti-CD3 for 12, 24 and 36h to validate the expression of the genes differentially methylated upon primary stimulation at mRNA and protein levels. DNA methylation profiles of both activated and resting cell subsets were characterized with Infinium 450K DNA methylation array (Illumina). To further confirm our observations, identical experimental procedure was performed with a different anti-CD137 agonist antibody (mIgG1 isotype) in a CD8+ T-cell donor. Differentially methylated genes between anti-CD3+anti-CD137 versus their corresponding control counterparts were validated by pyrosequencing on activated and resting CD8+ from independent group of healthy donors (n=8 for hIgG anti-CD137 and n= 11 for mIgG anti-CD137). Expression changes were confirmed by qRT-PCR and flow cytometry in activated, rested and reestimulated CD8+ lymphocytes. Results: 853 genes were differentially methylated in hIgG4 anti-CD137-treated CD8+ T cells as compared with their controls, 52 of which were shared with mIgG1 anti-CD137-costimulated CD8+ T lymphocytes. A number of differentially methylated genes are involved in i) T cell migration, ii) T cell activation, survival and homeostasis and iii) regulation of gene expression including key T-cell transcription factors. Conclusions: CD137 costimulation induces CD8+ T lymphocytes that are poised to respond more effectively to a second antigen exposure. These acquired functions are imprinted in the genomic DNA of the CD8+ T cells by DNA methylation changes upon CD137 co-stimulation, and involve key genes for CD8+ T cells. References: 1. Hendriks, J., Y. Xiao, J.W. Rossen, K.F. van der Sluijs, K. Sugamura, N. Ishii, and J. Borst, During viral infection of the respiratory tract, CD27, 4-1BB, and OX40 collectively determine formation of CD8+ memory T cells and their capacity for secondary expansion. J Immunol 2005, 175: p. 1665-76. Citation Format: M. Angela Aznar, Sara Labiano, Angel Diaz-Lagares, Manel Esteller, Juan Sandoval, Ignacio Melero. Methylation changes in DNA of CD8 T cells following CD137 costimulation [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 612. doi:10.1158/1538-7445.AM2017-612