bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract LB-216: Stroma-induced up-regulation of discoidin domain receptor 1 enhances peritoneal metastasis of gastric carcinomas
Authors: Jin Hyejin , Ham In-Hye , Oh Hye Jung , Lee Dakeun , Han Sang-Uk , Brekken Rolf A. , Hur Hoon
Published: July 2017

Introduction: Discoidin domain receptor-1 (DDR1), a receptor tyrosine kinase, is expressed by about 50% of gastric tumor cells in previous our study and is activated by fibrillar collagens, which are major components of tumor stroma. Further, it has been proposed that peritoneal metastasis is associated with high stroma content in gastric carcinomas (GCs). In this study we investigated the contribution of DDR1 activity to peritoneal metastasis of GCs.

Methods: We performed the immunohistochemistry for DDR1 and Masson’s trichrome staining for accumulation of collagen bundles in 202 human GC tissues. The human GC cell lines (MKN-28 and KATO-III) were co-cultured with GCs-associated fibroblasts (CAFs), and the expression of DDR1 and signal transduction pathways were investigated by Western blot. We evaluated CAF-induced tumorigenesis of GCs cell lines and the effects of DDR1 specific inhibitor in 3D co-culture system and peritoneal seeding in xenograft animal models.

Results: High stromal collagen correlated with peritoneal recurrence (P=0.004) and was positively associated with expression of DDR1 in GC tissues (P<0.001). We confirmed that co-culture with CAFs elevated the expression of DDR1 in GC cell lines. CAFs also enhanced GC cell line spheroid formation in vitro in a tumor cell DDR1-dependent manner. Co-implantation of CAFs with GC cells enhanced peritoneal tumor formation in vivo, an effect that was sensitive to pharmacologic inhibition of DDR1.

Conclusion: Our findings suggest that CAF-induced elevation of tumor cells DDR1 enhances peritoneal tumorigenesis of GCs and the inhibition of DDR1 signaling is an attractive strategy for the treatment of GC peritoneal metastasis.

Citation Format: Hyejin Jin, In-Hye Ham, Hye Jung Oh, Dakeun Lee, Sang-Uk Han, Rolf A. Brekken, Hoon Hur. Stroma-induced up-regulation of discoidin domain receptor 1 enhances peritoneal metastasis of gastric carcinomas [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-216. doi:10.1158/1538-7445.AM2017-LB-216
Abstract LB-222: A nanoscale optical reporter implant for miRNA biomarkers in vivo
Authors: Heller Daniel A. , Harvey Jackson D. , Jena Prakrit V. , Williams Ryan M. , Galassi Thomas V. , Baker Hanan A. , Roxbury Daniel , Zerze Gül , Mittal Jeetain
Published: July 2017

MicroRNAs and other small oligonucleotides in biofluids are promising biomarkers, but conventional assays require complex processing steps unsuitable for point-of-care assays or implantable/wearable sensors. Single-walled carbon nanotubes are an ideal material for implantable sensors due to emission in the near-infrared spectral region, photostability, and exquisite sensitivity. We engineered a carbon nanotube-based platform capable of real-time optical quantification of hybridization events of microRNA and other oligonucleotides for use in vivo. The sensor mechanism derived from competitive effects between displacement of both oligonucleotide charge groups and water from the nanotube surface, resulting in a solvatochromism-like response. The platform allowed detection via single molecule sensor elements and multiplexing using multiple nanotube species. The sensor monitored toehold-based strand displacement events, reversing the sensor response and regenerating the sensor complex. The sensor functioned in whole urine and serum, and it non-invasively measured DNA and microRNA biomarkers after implantation into live mice.

Citation Format: Daniel A. Heller, Jackson D. Harvey, Prakrit V. Jena, Ryan M. Williams, Thomas V. Galassi, Hanan A. Baker, Daniel Roxbury, Gül Zerze, Jeetain Mittal. A nanoscale optical reporter implant for miRNA biomarkers in vivo [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-222. doi:10.1158/1538-7445.AM2017-LB-222
Abstract LB-227: Combined treatment with radiation and epigenetic regulation improve to targeting cancer stem cells in pancreatic cancer
Authors: Yi Joo Mi , Kwon Hyun-Mi , Kang Eun-Jin , Yang Kwangmo
Published: July 2017

Increasing evidences suggests that various cancer types contain a population of cells that display stem cell properties. These cells are called cancer stem cells (CSCs). They are virtually resistant to radiation, and may contribute to treatment resistance and recurrence. Therefore, therapies specifically targeting CSCs will likely be needed for complete tumor eradication. Exposure of cells to ionizing radiation (IR) induces, not only, activation of multiple signaling pathways that play critical roles in cell fate determination, but also alteration of molecular pathways involved in cell death or survival. Recently, DNA methylation has been established as a critical epigenetic process involved in the regulation of gene expression in cancer cells, suggesting that DNA methylation inhibition may be an effective cancer treatment strategy. We therefore investigated the combination effect of a DNA methyltransferase inhibitor, 5-aza-2’-deoxycytidine (5-aza-dC), and radiation treatment in pancreatic cancer. Pancreatic cancer cell lines were initially tested for radiation sensitivity by ionizing radiation (IR) in vitro and were treated with 5-aza-dC. The effects of 5-aza-dC along with irradiation on cell growth, cell cycle distribution, apoptosis, and apoptosis-related gene expression were examined. Combination irradiation treatment with 5-aza-dC significantly decreased growth activity compared with irradiation or 5-aza-dC treatment alone. To understand whether combination treatment can target to pancreatic cancer stem cells, we observed that combination treatment can significantly reduce Oct4, Nanog, Sox2, CD133, and CD44 levels which are key factors for self-renewal pathway or cancer stem cell surface markers in pancreatic cancer cells, respectively. Using transcriptome analysis, OCT4 target genes showed differential expression pattern between irradiation or 5-aza-dC treatment alone and combination treatment. In addition, sphere forming assay supports these data in vitro and in vivo, describing that combination effect of IR and 5-aza-dC can reduce significantly sphere forming ability and proportion of side population (putative CSCs) significantly decreased in combination treated cells compared to control or single treatment. Therefore combined treatment of IR and 5-aza-dC is capable of eliminating pancreatic CSCs. Further investigation of this useful approach may lead to the development of a novel intervention for the cancer therapeutic strategy.

Citation Format: Joo Mi Yi, Hyun-Mi Kwon, Eun-Jin Kang, Kwangmo Yang. Combined treatment with radiation and epigenetic regulation improve to targeting cancer stem cells in pancreatic cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr LB-227. doi:10.1158/1538-7445.AM2017-LB-227
Abstract LB-243: Precision medicine: Lung biomarkers
Authors: Harris Curtis C.
Published: July 2017

More than half of all new lung cancer diagnoses are made in patients with locally advanced or metastatic disease, at which point therapeutic options are scarce. It is anticipated, however, that the widespread use of Low-Dose Computed Tomography (LDCT) screening, will lead to a greater proportion of lung cancers being diagnosed at an early, operable, stage. Still, the overall rate of recurrence for surgically treated Stage I lung cancer patients is up to 30% within 5 years of diagnosis. Thus, the identification and clinical application of biomarkers of early stage lung cancer are a pressing medical need. The integrative analysis of "omic," clinical and epidemiological data for single patients is a core principle of precision medicine. Through rigorous bioinformatics and statistical analyses we have identified biomarkers of early-stage lung cancer based on DNA methylation, expression of mRNA and miRNA, inflammatory cytokines, and urinary metabolites. Beyond a more comprehensive understanding of the molecular taxonomy of lung cancer, these biomarkers can have very practical implications in the context of unmet clinical needs of early stage lung cancer patients: First, current guidelines for LDCT screening broadly include individuals based on age and history of heavy smoking. Tumor-derived circulating biomarkers in the blood and urine associated with lung cancer risk could narrow and prioritize individuals for LDCT screening. Second, a high number of nodules are identified by LDCT, of which fewer than 5% are finally diagnosed as lung cancer. Biomarkers may help discriminate malignant nodules from benign or indolent lesions. Third, the expected rise in the numbers of lung cancer patients diagnosed at an early stage will necessitate new treatment options. Circulating, urinary and tissue-based biomarkers that molecularly categorize Stage I patients after tumor resection can help identify high-risk patients who may benefit from adjuvant chemotherapy or innovative immunotherapy regimens.

References

1. Vargas, A.J. and C.C. Harris, Biomarker development in the precision medicine era: lung cancer as a case study. Nat Rev Cancer, 2016. 16(8): p. 525-37.

2. Robles, A.I. and C.C. Harris, Integration of multiple "OMIC" biomarkers: A precision medicine strategy for lung cancer. Lung Cancer, 14 June 2016: p. [Epub ahead of print].

3. Robles, A.I., et al., An Integrated Prognostic Classifier for Stage I Lung Adenocarcinoma Based on mRNA, microRNA, and DNA Methylation Biomarkers. J Thorac Oncol, 2015. 10(7): p. 1037-48.

Citation Format: Curtis C. Harris. Precision medicine: Lung biomarkers [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-243. doi:10.1158/1538-7445.AM2017-LB-243
Abstract LB-249: Examination of analytical factors impacting concordance of plasma-tumor testing by next-generation sequencing (NGS)
Authors: Stetson Daniel , Dougherty Brian , Ahmed Ambar , Lubinski Tristan , Markovets Aleksandra , Thress Kenneth , McEwen Robert , Schiavon Gaia , Whitston David , Nuttall Barrett , Barrett J. Carl
Published: July 2017

The increased usage of circulating tumor DNA (ctDNA) sequencing for oncology clinical research demonstrates a critical need for sensitive and specific testing. While we have observed a high degree of concordance between single tumor mutations in tumor and plasma, several recent studies have highlighted a lack of concordance between plasma and tumor panel NGS gene panel testing due to biological and technical factors. To explore further these factors and benchmark ctDNA NGS testing services, a set of matched plasma, tumor, and normal samples from 24 subjects were acquired from three biobanking companies. Replicate 2 ml-plasma samples were tested by four ctDNA sequencing companies, and matching tumor/normal samples were tested by two tumor sequencing companies. Concordance was measured by comparing plasma mutations to tumor mutations as well as comparing mutations among the same plasma tested by the ctDNA companies. While our experience with NGS of matched samples from clinical trials typically identifies ~30% of patients with no detectable mutation and therefore likely not shedding tumor DNA, with the retrospectively collected commercial samples ~60% lacked detectable high confidence mutations, likely due to quality control issues with sample collection. We also found variation in the concordance of ctDNA mutation detection rates among the four vendors, due to significant differences in DNA yield and assay sensitivity. While factors such as tumor heterogeneity and timing of plasma-tumor collection can lower concordance rates, the majority of discordance in our study was due to technical rather than biological variation. Assay analytical variance and the impact of reporting false positive variants are key factors that need to be addressed as plasma-based NGS testing is more widely incorporated into translational and clinical research. Examples illustrating the complexity of the analyses and giving support for confidence in ctDNA testing results will be given.

Citation Format: Daniel Stetson, Brian Dougherty, Ambar Ahmed, Tristan Lubinski, Aleksandra Markovets, Kenneth Thress, Robert McEwen, Gaia Schiavon, David Whitston, Barrett Nuttall, J. Carl Barrett. Examination of analytical factors impacting concordance of plasma-tumor testing by next-generation sequencing (NGS) [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-249. doi:10.1158/1538-7445.AM2017-LB-249
Abstract LB-262: A somatic-mutational process in breast cancer genomes recurrently duplicates germline susceptibility loci and tissue-specific super-enhancers
Authors: Glodzik Dominik , Morganella Sandro , Davies Helen , Nik-Zainal Serena ,   ICGC Breast Cancer Consortium
Published: July 2017

Somatic rearrangements are a part of mutational landscape of human cancer genomes. We systematically investigated the distribution of the somatic rearrangements in 560 breast cancer genomes and highlight 33 rearrangement hotspots associated with a signature of Homologous Recombinational repair deficiency, characterized mainly by large (>100kb) tandem duplications.

Remarkably, these tandem duplication hotspots are enriched for breast cancer germline susceptibility loci (OR 4.28) and breast-specific “super-enhancer” regulatory elements (OR 3.54). They likely represent sites of selective susceptibility to double-strand break damage due to high transcriptional activity. However, through incrementally increasing the number of copies of these functionally active loci, they could inadvertently come under some level of selective pressure. Indeed, transcriptomic consequences range from strong individual oncogene effects through to weak but quantifiable multigene expression effects.

We thus present a passenger somatic rearrangement mutational process that has the ability to create secondary driver events. It exerts its influence through coding sequences and non-coding regulatory elements, contributing a continuum of driver consequences, from modest through to strong effects, making this mutational process a particularly deleterious one.

Citation Format: Dominik Glodzik, Sandro Morganella, Helen Davies, Serena Nik-Zainal, ICGC Breast Cancer Consortium. A somatic-mutational process in breast cancer genomes recurrently duplicates germline susceptibility loci and tissue-specific super-enhancers [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-262. doi:10.1158/1538-7445.AM2017-LB-262
Abstract LB-265: 5’ gap-mediated long patch base excision repair
Authors: Woodrick Jordan , Camacho Sharon , Parvathaneni Swetha , Sharma Sudha , Roy Rabindra
Published: July 2017

The base excision repair (BER) pathway is one of the most frequently used DNA repair mechanisms in the cell and modulates many human pathophysiological conditions related to DNA damage. Through live cell and in vitro reconstitution experiments, we have discovered a novel step in a sub-pathway of the conventional long-patch BER that involves formation of a 9 nt gap 5’ to the lesion, which is mediated by RECQ1 DNA helicase and ERCC1-XPF endonuclease in cooperation with PARP1 and RPA. The novel step is employed during repair of a variety of DNA lesions, including oxidative and alkylation damage. Moreover, RECQ1 regulates the autoribosylation status of PARP1 and the choice between long-patch and single-nucleotide BER, which regulates cellular toxicity to DNA damage. Taken together, our results propose a revised model of the long-patch BER pathway and characterize a crucial regulation point for pathway choice in BER.

Citation Format: Jordan Woodrick, Sharon Camacho, Swetha Parvathaneni, Sudha Sharma, Rabindra Roy. 5’ gap-mediated long patch base excision repair [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-265. doi:10.1158/1538-7445.AM2017-LB-265
Abstract LB-266: DAXX promotes de novo lipogenesis in triple-negative breast cancer
Authors: Mahmud Iqbal , Garrett Timothy J. , Liao Daiqing
Published: July 2017

Triple-negative breast cancers (TNBCs), defined by the absence of ER and PR expression and the lack of HER2 amplification, have no targeted treatment options, are highly aggressive, and exhibit poor prognosis. Identification of drivers and associated signaling pathways, particularly for TNBCs, is needed to assist the development of targeted therapies, to prolong disease-free survival, and to improve clinical outcome for cancer patients. Using high-throughput microarray-based global transcriptome profiling, we found that transcriptional regulator DAXX depletion strikingly impaired while DAXX overexpression enhanced the expression of genes in the de novo lipogenesis pathways in TNBCs cell line. Consistently, unbiased global metabolomics and lipidomics profiling by Ultra-High performance Liquid Chromatography coupled High-Resolution Mass Spectrometry (UHPLC-HRMS) also revealed that DAXX promotes de novo lipogenesis in both TNBC cell line as well as in corresponding xenograft tumors. In analyzing large number of genomic datasets including The Cancer Genome Atlas (TCGA), MolEcular Taxonomy of BReast cancer International Consortium (METABRIC), and The Cancer Cell Line Encyclopedia (CCLE) dataset, we found that DAXX expression is significantly higher in TNBC tumor samples and cell lines, and also DAXX gene expression positively correlates with that of key lipogenesis enzymes. The role of DAXX in cancer metabolism is previously unknown. Our integrated OMICs data analysis thus indicates that DAXX promotes de novo lipogenesis in TNBC. The mechanism through which DAXX regulates lipid metabolism is being investigated in our laboratory. Overall, our study identifies a potentially important pathway driving TNBC progression and suggests potential therapeutic targets for treating this aggressive form of breast cancer that still lacks curative treatment options.

Citation Format: Iqbal Mahmud, Timothy J. Garrett, Daiqing Liao. DAXX promotes de novo lipogenesis in triple-negative breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr LB-266. doi:10.1158/1538-7445.AM2017-LB-266
Abstract LB-271: SplashRNA, a sequential classification algorithm for ultra-potent RNAi
Authors: Pelossof Raphael , Fairchild Lauren , Leslie Christina S. , Fellmann Christof
Published: July 2017

We present SplashRNA, a sequential classifier - analogous to face detection algorithms - to predict ultra-potent microRNA-based short hairpin RNAs (shRNAs) for virtually any gene. Trained on existing and novel large-scale datasets, SplashRNA outperforms previous algorithms and reliably predicts the most efficient shRNAs for a given gene. Combined with the optimized miR-E backbone, >90% of high-scoring SplashRNA predictions trigger >85% protein knockdown when expressed from a single genomic integration. SplashRNA can significantly improve the accuracy of loss-of-function genetics studies and facilitates the generation of compact shRNA libraries. The open source SplashRNA platform completes the RNAi toolkit to harness microRNA-based shRNAs for robust single-gene and multiplexed inducible and reversible target inhibition.

Citation Format: Raphael Pelossof, Lauren Fairchild, Christina S. Leslie, Christof Fellmann. SplashRNA, a sequential classification algorithm for ultra-potent RNAi [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-271. doi:10.1158/1538-7445.AM2017-LB-271
Abstract LB-280: The landscape of somatic microsatellite indels across cancer: detection and identification of driver events
Authors: Maruvka Yosef E. , Mouw Kent W. , Karlic Rosa , Parasuraman Rasanna , Kamburov Atanas , Polak Paz , Haradhvala Nicholas J. , Hess Julian M. , Rheinbay Esther , Brody Yehuda , Braunstein Lior Z. , D’Andrea Alan , Lawrence Michael S. , Bass Adam , Bernards Andre , Michor Franziska , Getz Gad
Published: July 2017

Microsatellites (MSs) are tracts of variable-length repeats of short DNA motifs that are abundant in the human genome and exhibit high rates of mutations in the form of insertions or deletions of the repeated motif (MS indels). Despite their prevalence, the contribution of somatic MS indels to cancer is largely unexplored due to difficulties in detecting them and assessing their significance. Here, we present a comprehensive analysis of MS indels across 20 tumor types. We characterize the overall MS indel landscape and detect genes with candidate driver MS indel events. We present two novel tools: MSMuTect for accurate detection of somatic MS indels and MSMutSig for identifying candidate cancer genes containing events at higher frequency than expected by chance. We observe high variability of the frequency of MS indels across tumors and demonstrate that the number and pattern of MS indels can accurately distinguish microsatellite stable (MSS) tumors from tumors with microsatellite instability (MSI). Applying MSMutSig across 6,788 tumors from 20 different tumor types identified 7 genes with significant MS indel hotspots: ACVR2A, RNF43, DOCK3, MSH3, ESRP1, PRDM2 and JAK1. In the four genes that have been previously implicated in cancer (ACVR2A, RNF43, JAK1 and MSH3), we identified previously unreported MS indels events. Three of the genes with significant loci - DOCK3, PRDM2 and ESRP1- had not been previously listed as cancer genes. MS indels in DOCK3, a negative regulator of the WNT pathway, were mutually exclusive with mutations in CTNNB1. MS indels in ESRP1, an RNA processing gene, correlated with alternative splicing of FGFR2, an event associated with the epithelial-to-mesenchymal transition. Overall, our comprehensive analysis of somatic MS indels across cancer highlights their importance, particularly in

MSI tumors, significantly contributes to the ongoing global efforts to detect cancer genes, and may improve classification of patients into clinically-relevant subgroups.

Citation Format: Yosef E. Maruvka, Kent W. Mouw, Rosa Karlic, Rasanna Parasuraman, Atanas Kamburov, Paz Polak, Nicholas J. Haradhvala, Julian M. Hess, Esther Rheinbay, Yehuda Brody, Lior Z. Braunstein, Alan D’Andrea, Michael S. Lawrence, Adam Bass, Andre Bernards, Franziska Michor, Gad Getz. The landscape of somatic microsatellite indels across cancer: detection and identification of driver events [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-280. doi:10.1158/1538-7445.AM2017-LB-280
Abstract LB-282: Two different strategies of delivery CRISPR/Cas9 system to gene edit rs4644 SNP in LGALS3 gene
Authors: Corrado Alda , Lepori Irene , Miglietta Simona , Batoni Simone , Vitiello Marianna , Evangelista Monica , Chisci Elisa , Giovannoni Roberto , Poliseno Laura , Gemignani Federica , Landi Stefano
Published: July 2017

Galectin-3 is a glycoprotein of 31KDa with a chimeric structure. It is encoded by a single gene, LGALS3, located on chromosome 14. Previous studies showed a relation between the single nucleotide polymorphism (SNP) (rs4644, c.191C>A, p.Pro64His) and the risk of cancer. In literature, some data show different results indicating that SNP could have different roles in base on the tissues. The aim of our study is to create isogenic cell lines that differ only for SNP permitting further studies about the function of SNP in different cancers. The “generation” of the cell lines is performed with a Clustered Regularly Interspaced Short Palindromic Repeats-associated Endonuclease 9 (CRISPR/Cas9) system. We have used two different strategies to deliver the system. In the first strategy, our aim was the reduction of the problem of efficiency of transfection that could depend on different cell lines. In fact, we have used the lentivirus method to deliver all components of the CRISPR/Cas9 on Nthy-Ori (normal thyroid tissue) and HCT 116 +/+ (colorectal cancer tissue) cells. Two different vectors (pCW-Cas9 and pLXgRNA) are used to build up the inducible CRISPR/Cas9 system and HR410PA-1 vector (transfected by Lipofectamine 3000) is used to knock-in. HR410PA-1 is a particular vector that facilities the homologous recombination (HR) to repair the double strand break. Moreover, to improve HR, we use also Scr7, which is an inhibitor of DNA IV ligase. In the second approach, we have used the double nickase system using two modified Cas9 vectors (SpCas9D10a) that produce only a single strand break. In this way, the problem of off-targets is notably reduced. In this approach, the knock-in is due to or single-stranded oligodeoxynucleotides (ssODNs) or HR410PA-1 vector. The first results show that some of the transfected cells are edited in a correct way. In the further steps, we will isolate the “positive clones” using the selection cassette in HR410PA-1 vector (GFP protein and/or puromycin) or the single cell dilution assay (1 cell/well) for the transfected cells with ssODNs.

Citation Format: Alda Corrado, Irene Lepori, Simona Miglietta, Simone Batoni, Marianna Vitiello, Monica Evangelista, Elisa Chisci, Roberto Giovannoni, Laura Poliseno, Federica Gemignani, Stefano Landi. Two different strategies of delivery CRISPR/Cas9 system to gene edit rs4644 SNP in LGALS3 gene [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-282. doi:10.1158/1538-7445.AM2017-LB-282
Abstract LB-286: ARID1A loss impairs enhancer-mediated gene regulation and drives colon cancer in mice
Authors: Mathur Radhika , Alver Burak H. , Roman Adrianna K. San , Wilson Boris G. , Wang Xiaofeng , Agoston Agoston T. , Park Peter , Shivdasani Ramesh , Roberts Charles W.
Published: July 2017

Genes encoding subunits of SWI/SNF (BAF) chromatin remodeling complexes are collectively mutated in ~20% of all human cancers, but the mechanism by which these mutations promote tumorigenesis is unclear. In this study, we investigate the tumor suppressor role of ARID1A, the subunit of SWI/SNF complexes that is the most frequent target of mutations. We develop an inducible Arid1a-knockout mouse model and find that mice develop invasive ARID1A-deficient colon adenocarcinoma. These cancers show prominent mucinous differentiation and tumor-infiltrating lymphocytes, features associated particularly with microsatellite-instable (MSI) human colorectal cancer - the subtype with the highest frequency of inactivating ARID1A mutations (37-39%). Although deregulation of Wnt signaling components (APC/β-catenin) is commonly utilized to model intestinal tumorigenesis, Arid1a-knockout mice reflect human colorectal cancer with greater accuracy. These mice do not show deregulation of Wnt signaling components, thus demonstrating a novel pathway to colon tumorigenesis that is independent of established models. Chromatin immunoprecipitation sequencing reveals that SWI/SNF complexes are targeted primarily to enhancers, where they function in coordination with transcription factors to activate gene expression. ARID1A loss impairs the targeting of SWI/SNF complexes to thousands of enhancers, which subsequently lose activity - showing reduced levels of H3K27ac and expression of nearest genes. Residual SWI/SNF complexes in ARID1A-deficient cells bind enhancers that remain active; these complexes contain ARID1B, the subunit that is mutually exclusive with ARID1A and has been identified as a therapeutic target in ARID1A-deficient cancers. Enhancers associated with developmental gene expression programs are most affected by ARID1A loss, both in the mouse colonic epithelium and in human colon cancer cells. Collectively, these findings represent an advance in colon cancer modeling and implicate enhancer-mediated gene regulation as the principal tumor suppressor function of ARID1A.

Citation Format: Radhika Mathur, Burak H. Alver, Adrianna K. San Roman, Boris G. Wilson, Xiaofeng Wang, Agoston T. Agoston, Peter Park, Ramesh Shivdasani, Charles W. Roberts. ARID1A loss impairs enhancer-mediated gene regulation and drives colon cancer in mice [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-286. doi:10.1158/1538-7445.AM2017-LB-286
Abstract LB-317: Identification of a novel preclinical candidate for CDK7 inhibition
Authors: Satyam Leena K. , Poddutoori Ramulu , Mukherjee Subhendu , Marappan Sivapriya , Gopinath Sreevalsam , Basavaraju Aravind , Kaza Lakshmi Narayana , Pothuganti Manoj Kumar , Nayak Shilpa , C Nandish , A Amith , MV Ravindra , Babu Dabbeeru Madhu , A Nagaraju , Tgore Suraj , Antony Thomas , Pandit Chetan , Ramachandra Murali , Chelur Shekar , Daginakatte Girish , Samajdar Susanta
Published: July 2017

Cyclin-dependent kinase 7 (CDK7) is an important constituent of the cellular transcriptional machinery, where it phosphorylates the C-terminal domain (CTD) of RNAP polymerase II (RNAPII). Because many tumor types are critically dependent on transcription for maintenance of their oncogenic state, pharmacological modulation of CDK7 kinase activity is considered as an approach to treat cancer. Multiple series of covalent CDK7 inhibitors were identified by iterative medicinal chemistry efforts and SAR based approach. These compounds were optimized towards attaining good physicochemical properties, high potency, good selectivity and desirable pharmacokinetic profile to achieve anti-tumor activity. We have now identified a pre-clinical candidate AU-BGB-002 which is highly potent in inhibiting CDK7 in biochemical as well as cellular assays while fully efficiently engaging the target. In a panel of kinases, AU-BGB-002 shows selectivity for CDK7. A panel of cell lines derived from a diverse set of indications are sensitive to AU-BGB-002. AU-BGB-002 exhibits excellent drug-like characteristics including solubility, permeability, metabolic stability and good oral bioavailability. When tested in a xenograft model, AU-BGB-002 treatment resulted in dose dependent tumor growth inhibition in AML xenograft model with tumor stasis at a dose of 10 mg/kg. Potent inhibiton of tumor growth was accompanied by complete target engagement and suppression of pS5RNAPII RNAPolII Ser5 phosphorylation in a parallel PK-PD study. Efficacy studies in additional xenograft models, advanced DMPK and toxicity studies are ongoing for this compound. In summary, we have identified a novel and selective CDK7 covalent inhibitor candidate with desirable drug-like properties that shows excellent efficacy in an AML xenograft model. Findings presented here support further development of AU-BGB-002 for the treatment of cancer.

Citation Format: Leena K. Satyam, Ramulu Poddutoori, Subhendu Mukherjee, Sivapriya Marappan, Sreevalsam Gopinath, Aravind Basavaraju, Lakshmi Narayana Kaza, Manoj Kumar Pothuganti, Shilpa Nayak, Nandish C, Amith A, Ravindra MV, Dabbeeru Madhu Babu, Nagaraju A, Suraj Tgore, Thomas Antony, Chetan Pandit, Murali Ramachandra, Shekar Chelur, Girish Daginakatte, Susanta Samajdar. Identification of a novel preclinical candidate for CDK7 inhibition [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-317. doi:10.1158/1538-7445.AM2017-LB-317
Abstract LB-321: Cytoplasmic DEDD promotes G1- to S-phase cell cycle transition
Authors: Schmidt Keon R. , Ni Yingjia , Zhang Siyuan
Published: July 2017

Death Effector Domain-Containing DNA-binding protein (DEDD), a highly conserved and ubiquitous protein, has been studied primarily for its role as a scaffold protein in cell death pathways. DEDD resides predominantly in the cytoplasm, but translocates to the nucleus to propagate the terminal apoptotic signal. Overexpression of nuclear DEDD, not cytoplasmic DEDD, has been shown to be sufficient to induce cytotoxic effects. This suggests that DEDD may have functional importance beyond directing apoptotic signals. Further, the cytoplasmic function of DEDD has yet to be characterized. Other DED-containing proteins, such as FADD, have been shown to interact with cyclin/cyclin-dependent kinase cell cycle regulatory molecules. Here, we show that DEDD is implicated in cell cycle regulation and can assume a pro- proliferative function when overexpressed in the cytoplasm. To glean phenotypic changes in cell cycle transitions, we utilized a two-dimensional approach with an EdU proliferation label and a propidium iodine DNA content label differentiated via flow cytometry analysis. Based on these labels, it can be determined whether a cell is in the G1-, S-, or G2-phase of the cell cycle. We have identified that overexpression of DEDD leads to an increase in S-phase cells when compared to control suggesting an easier transition through the G1/S checkpoint. Conversely, a knockdown of DEDD leads to a decrease in S-phase cells and an increase in G1-phase cells when compared to control indicating G1 arrest. Gain-of-function flow cytometry analysis was repeated by overexpressing a DEDD construct with disrupted nuclear localization sequences. The resulting phenotype mirrored that of the overexpressed wild-type DEDD construct. Thus, these results suggest that DEDD may be interacting with regulatory molecules regulating the G1/S checkpoint of the cell cycle and that the change in G1- to S-phase transition dynamics in response to manipulated DEDD expression is not attributable to the nuclear function of DEDD. Further studies will focus on elucidating the specific molecular interactions through which DEDD can carry out this novel cell cycle regulatory function.

Citation Format: Keon R. Schmidt, Yingjia Ni, Siyuan Zhang. Cytoplasmic DEDD promotes G1- to S-phase cell cycle transition [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-321. doi:10.1158/1538-7445.AM2017-LB-321
Abstract LB-322: MicroRNA-130a suppresses breast cancer cell migration and invasion by targeting FOSL1 and upregulating ZO-1
Authors: Chen Xiaowei , Zhao Min , Li Yuhuang , Dai Mushui
Published: July 2017

FOSL1 is frequently overexpressed in multiple types of human cancers including invasive breast cancers and implicated in cancer invasion and metastasis. However, how FOSL1 is overexpressed in cancers remains to be elucidated. Several microRNAs (miRNAs) have been shown to target FOSL1 and are downregulated in human cancers. Here, we report that miR-130a is a novel FOSL1 targeting miRNA. Using gene expression microarray analysis, we found that FOSL1 is among the most up-regulated genes in cells transfected with miR-130a inhibitors. Transient transfection-immunoblot, RNA-immunoprecipitation (IP) and luciferase reporter assays revealed that miR-130a directly targets FOSL1 mRNA at its 3’-UTR. Overexpression of miR-130a significantly reduced the levels of FOSL1 in invasive breast cancer MDA-MB-231 and Hs578T cell lines and suppresses their migration and invasion. This inhibition can be rescued by ectopic expression of miR-130a-resistant FOSL1. Interestingly, we show that overexpression of miR-130a increased the levels of tight-junction protein ZO-1 while inhibition of miR-130a reduced the levels of ZO-1, via regulating the expression of FOSL1. We further show that miR-130a expression is significantly reduced in cancer tissues from triple-negative breast cancer (TNBC) patients, correlating significantly with the upregulation of FOSL1 expression, compared to non-TNBC tissues. Together, our results reveal that miR-130a directly targets FOSL1 and suppresses FOSL1-mediated inhibition of ZO-1, thus inhibiting cancer cell migration and invasion, in TNBCs.

Note: This abstract was not presented at the meeting.

Citation Format: Xiaowei Chen, Min Zhao, Yuhuang Li, Mushui Dai. MicroRNA-130a suppresses breast cancer cell migration and invasion by targeting FOSL1 and upregulating ZO-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 LB-322. doi:10.1158/1538-7445.AM2017-LB-322
Abstract LB-325: Tumor suppressor effects of miR-17-92a cluster miRNAs on prostate cancer
Authors: Chakrabarti Ratna , Ottman Richard , Hasan Md Faqrul
Published: July 2017

MicroRNAs in miR-17-92a cluster are transcribed from a polycistronic transcription unit C13orf25 that generates six mature miRNAs, miR-17, miR-18a, miR-19a, miR- 19b, miR-20a. These miRNAs are reported to be overexpressed in colon and lung cancers, however, we noted a loss of expression of all members of this miR cluster in prostate cancer tissues compared to uninvolved tissues and in aggressive prostate cancer cells. In this study, we show that replenishment of miR-17-92a cluster as a whole showed antiproliferative effects, reduced activation of AKT and MAP kinases, delayed tumorigenicity and reduced tumor growth. Analysis of the expression of mRNA targets showed reduced expression of cell cycle regulatory proteins cyclin D1 and SSH1; and LIMK1 and FGD4 of RhoGTPase signaling pathway through direct targeting. miR-17-92 cluster expression also inhibited EMT via reduced cell migration and expression of mesenchymal markers while elevating expression and surface localization of the epithelial marker E-Cadherin. miR-17-92a miRNAs improved sensitivity of androgen dependent LNCaP 104-S prostate cancer cells to anti-androgen drug Casodex, AKT inhibitor MK-2206 2HCl, and docetaxel. The androgen refractory PC-3 cells also showed increased sensitivity to docetaxel, MK-2206 2HCl and Aurora kinase inhibitor VX680 upon ectopic expression of miR-17-92a cluster miRNAs. RNA seq analysis of prostate cancer cells expressing miR-17-92a cluster revealed altered expression of a number of oncogenic and tumor suppressor mRNAs, and noncoding RNAs, which may have implications in the altered phenotype of these cells. Our data demonstrate a tumor suppressor effect of miR-17-92a cluster miRNAs in prostate cancer cells and restoration of expression of these miRNAs has a therapeutic benefit for both androgen-dependent and -independent prostate cancer cells.

Note: This abstract was not presented at the meeting.

Citation Format: Ratna Chakrabarti, Richard Ottman, Md Faqrul Hasan. Tumor suppressor effects of miR-17-92a cluster miRNAs on prostate cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr LB-325. doi:10.1158/1538-7445.AM2017-LB-325
Abstract LB-334: xCT promotes malignant phenotypes in EGFR-expressing glioma
Authors: Tsuchihashi Kenji , Okazaki Shogo , Yoshikawa Momoko , Seishima Ryo , Sampetrean Oltea , Onishi Nobuyuki , Wakimoto Hiroaki , Furnari Frank , Baba Eishi , Akashi Koichi , Saya Hideyuki , Nagano Osamu
Published: July 2017

Malignant glioma such as glioblastoma is a cancer still difficult to treat. System xc(-) is composed of xCT and CD98hc subunits and functions as a plasma membrane antiporter for the uptake of extracellular cystine in exchange for intracellular glutamate, which has been reported to be involved in malignant phenotypes of glioma cells. However, the underlying mechanism of xCT regulation in glioma is not elucidated. Here we show that the epidermal growth factor receptor (EGFR) interacts with xCT and thereby promotes its cell surface expression and function in human glioma cells. EGFR-expressing glioma cells manifested both enhanced antioxidant capacity as a result of increased cystine uptake as well as increased extracellular glutamate which promotes glioma matrix invasion. Imaging mass spectrometry also revealed that brain tumors formed in mice by human glioma cells stably overexpressing EGFR contained higher levels of reduced glutathione compared with those formed by parental cells. Targeted inhibition of xCT suppressed the EGFR-dependent enhancement of antioxidant capacity in glioma cells as well as tumor growth and invasiveness. Our findings propose that xCT is a promising therapeutic target in EGFR-overexpressing malignant glioma.

Citation Format: Kenji Tsuchihashi, Shogo Okazaki, Momoko Yoshikawa, Ryo Seishima, Oltea Sampetrean, Nobuyuki Onishi, Hiroaki Wakimoto, Frank Furnari, Eishi Baba, Koichi Akashi, Hideyuki Saya, Osamu Nagano. xCT promotes malignant phenotypes in EGFR-expressing glioma [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-334. doi:10.1158/1538-7445.AM2017-LB-334
Abstract PL01-03: Earlier detection as a key to lower cancer death rates
Authors: Vogelstein Bert
Published: July 2017

Two disciplines within cancer research—secondary prevention and cancer therapeutics—have historically been viewed as distinct. I will argue that these two disciplines are intertwined and that their joint pursuit is the optimal way to reduce cancer deaths. At present, the preferred way to treat cancers, in fact the only way that generally cures patients, is surgery. It is therefore widely recognized that the detection of cancers prior to the onset of metastasis is vital to reducing cancer deaths. What is less widely recognized is that the detection of metastatic cancers can also be life-saving—as long as this detection occur priors to the formation of bulky metastatic disease. Therapies that only modestly extend life when administered to patients with measurable metastases can be curative when administered to patients with metastatic disease that is present but undetectable by imaging. Such therapies include conventional cytotoxic drugs as well as genome-targeted agents and immunotherapeutics. A new paradigm for designing clinical trials to test such agents in adjuvant settings will be described. Genome-based diagnostic approaches for detecting cancers earlier will be discussed, as these are integral to the design of the next generation of adjuvant trials. In aggregate, these issues support the importance of modulating the focus of cancer research and treatment from patients with advanced disease towards patients with less-advanced disease. They also highlight the importance of developing novel diagnostic approaches that will allow the detection of smaller tumors.

Citation Format: Bert Vogelstein. Earlier detection as a key to lower cancer death rates [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 PL01-03. doi:10.1158/1538-7445.AM2017-PL01-03
Abstract PL04-01: G-quadruplexes and DNA dynamics
Authors: Balasubramanian Shankar
Published: July 2017

DNA is structurally dynamic in ways that have a consequence for biologic processes. A class of four-stranded DNA structure, called the G-quadruplexes, can be formed from G-rich single-stranded DNA. There is now a good level of understanding of the structural biophysics of G-quadruplexes along with a large body of work on the design and synthesis of small organic molecules that can target such structures. Some such molecules have been found to have antiproliferative effects on human cancer cells along with specific effects on the activity of certain genes, raising intriguing hypotheses about their existence and function in cells. Recent results from my laboratory provide new insights into when and where such non-Watson-Crick structures may exist in cellular DNA, together with a perspective on whether this structural motif in DNA presents new opportunities to think about intervention and future therapeutics.

Citation Format: Shankar Balasubramanian. G-quadruplexes and DNA dynamics [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 PL04-01. doi:10.1158/1538-7445.AM2017-PL04-01
Abstract SY06-02: Macrophage-targeted cancer immunotherapy
Authors: Ries Carola
Published: July 2017

Combining immunotherapies that harness cytotoxic T cells to fight cancer has become a major effort in treating metastatic cancer patients. We present data on an example of cancer immunotherapy combination targeting innate immune cells, in particular tumor-associated macrophages (TAMs), that is currently being tested in the clinic. Combination of a TAM-depleting anti-CSF-1R antibody with an activating anti-CD40 agonist demonstrated synergistic antitumoral efficacy resulting in complete tumor remission in preclinical mouse cancer models. Ex vivo RNA sequencing of sorted TAM revealed that only the combination treatment induced a transient, profound repolarization of TAMs towards an immunostimulatory M1 phenotype. However, these TAM populations are ultimately eliminated. The central role of macrophages was further substantiated by complete loss of therapeutic benefit when TAMs were depleted prior to combinational treatment. Furthermore, rechallenge and depletion experiments demonstrated that tumor rejection is finally mediated by an antitumoral T-cell response. In colorectal cancer patients coexpression of human CSF1R and CD40 on TAMs was detected, providing the basis to explore this combination in the clinic.

Citation Format: Carola Ries. Macrophage-targeted cancer immunotherapy [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 SY06-02. doi:10.1158/1538-7445.AM2017-SY06-02