bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 2986: E-cadherin/ROS1 inhibitor synthetic lethality in breast cancer
Authors: Bajrami Ilirjana , Marlow Rebecca , Ven Marieke van de , Brough Rachel , Pemberton Helen N. , Frankum Jessica , Song Fei Fei , Rafiq Rumana , Konde Asha , Menon Malini , Campbell James , Gulati Aditi , Kumar Rahul , Pettitt Stephen J. , Gurden Mark D. , Cardenosa Marta Llorca , Chong Irene , Gazinska Patrycja , Wallberg Fredrik , Sawyer Elinor J. , Martin Lesley-Ann , Dowsett Mitch , Linardopoulos Spiros , Ryan Colm , Derksen Patrick W. , Jonkers Jos , Tutt Andrew N.J. , Ashworth Alan , Lord Christopher J. 
Published: August 2018

Abstract
The E-cadherin (CDH1) tumour suppressor gene encodes a calcium-dependent cell-cell adhesion glycoprotein, which has roles in maintaining cell polarity, differentiation, cell migration and survival. E-cadherin dysfunction is a feature common to many epithelial tumours, with the highest incidence occurring in diffuse gastric cancer (50%) and lobular breast cancer (63%) and can occur via CDH1 mutation, deletion or epigenetic silencing. Although E-cadherin dysfunction is relatively common, precision medicine approaches that exploit this pathogenic alteration are not yet available. Using genetic and small-molecule perturbation screens in breast tumour cells with CRISPR-Cas9 engineered CDH1 mutations, we identified a synthetic lethal interaction between E-cadherin deficiency and inhibition of the tyrosine kinase ROS1. Using data from large-scale genetic screens in molecularly diverse breast tumour cell lines, we found that the E-cadherin/ROS1 synthetic lethality was not only robust in the face of considerable molecular heterogeneity but was also elicited with clinical ROS1 inhibitors including foretinib and crizotinib. ROS1 inhibitors induced mitotic abnormalities and multinucleation in E-cadherin defective cells, phenotypes that were associated with a defect in cytokinesis and aberrant p120-catenin phosphorylation and localisation. In vivo, ROS1 inhibitors produced profound anti-tumour effects in multiple, distinct, models of E-cadherin defective breast cancer. This data therefore provides the pre-clinical rationale for assessing ROS1 inhibitors such as the licensed drug crizotinib in appropriately stratified patients.
Citation Format: Ilirjana Bajrami, Rebecca Marlow, Marieke van de Ven, Rachel Brough, Helen N. Pemberton, Jessica Frankum, Fei Fei Song, Rumana Rafiq, Asha Konde, Malini Menon, James Campbell, Aditi Gulati, Rahul Kumar, Stephen J. Pettitt, Mark D. Gurden, Marta Llorca Cardenosa, Irene Chong, Patrycja Gazinska, Fredrik Wallberg, Elinor J. Sawyer, Lesley-Ann Martin, Mitch Dowsett, Spiros Linardopoulos, Colm Ryan, Patrick W. Derksen, Jos Jonkers, Andrew N.J. Tutt, Alan Ashworth, Christopher J. Lord. E-cadherin/ROS1 inhibitor synthetic lethality in breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2986.
Abstract 2987: Identification of new combination therapies for lung tumors harboring KRAS mutations
Authors: Molina-Arcas Miriam , Moore Christopher , Rana Sareena , Maldegem Febe van , Horswell Stuart , Hancock David , Downward Julian 
Published: August 2018

Abstract
Oncogenic mutations in KRAS are frequent in non-small cell lung cancer (NSCLC) and have been associated with poor prognosis and resistance to existing therapies. Thus, new therapeutic strategies are needed to treat these tumors. We have previously shown that NSCLC cells harboring KRAS mutations are more sensitive to inhibition of KRAS downstream effectors MEK and RAF and to treatment with IGF1R inhibitors than their wild-type counterparts. In order to identify complementary targets for the improvement of IGF1R and/or MEK targeting therapies, we performed a whole-genome shRNA screen in KRAS-mutant NSCLC cells. Interestingly, the list of sensitizers to IGF1R inhibitors included several genes encoding components of the mTOR pathway. Viability assays in a panel of lung cancer cell lines confirmed that combinations of IGF1R inhibitors with mTOR inhibitors, both rapalogs and kinase inhibitors, resulted in a synergistic anti-proliferative effect in KRAS-mutant NSCLC cells. Mechanistic investigations demonstrated some differences between the effects of rapalogs and mTOR kinase inhibitors although, in both cases, mTOR inhibitors increased IGF1R and AKT phosphorylation. Combination with IGF1R inhibitors blocked the reactivation of the PI3K pathway resulting in a robust suppression of PI3K and mTORC1 signaling. Notably, the inhibition of these signaling pathways was stronger in KRAS-mutant cells than in wild-type cells. Addition of a MEK inhibitor to the combination produced a more profound and durable suppression of cell proliferation and a stronger induction of apoptosis. Finally, we validated the different drug combinations in mouse models of KRAS-induced NSCLC. Results showed that the three-drug combination produced a marked tumor regression in a NSCLC mouse model driven by mutant Kras and p53 loss-of-function and also in urethane-induced lung tumors. These findings suggest potential novel therapeutic strategies for NSCLC tumors harboring KRAS mutations.
Citation Format: Miriam Molina-Arcas, Christopher Moore, Sareena Rana, Febe van Maldegem, Stuart Horswell, David Hancock, Julian Downward. Identification of new combination therapies for lung tumors harboring KRAS mutations [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2987.
Abstract 299: A susceptible-quiescent model can describe biphasic cell-kill by MCL1 inhibitor AZD5991 in vitro
Authors: Gibbons Francis D. , Belmonte Matthew , Secrist Paul , Schuller Alwin 
Published: August 2018

Abstract
AZD5991 is a potent and selective inhibitor of Mcl-1, now in phase 1 clinical development. Mcl-1 is an anti-apoptotic Bcl2-family protein that is up-regulated by cancer cells in order to avoid apoptosis. Disruption of binding of Mcl-1 to pro-apoptotic BH3-only proteins such as Bax and Bak results in loss in cellular viability of several cell-line models of multiple myeloma (MM). As a function of time, many cell lines display a biphasic response, with an initial period of rapid cell kill, followed by a period of slower kill. Such biphasic kill curves are not uncommonly seen in bacteria. As a function of concentration, cell lines display a range of efficacy (extent of cell kill) and potency (concentration of half-maximal cell kill). Here we apply a model originally developed for bacterial cell-kill to parameterize the in vitro cell kill over time and across several orders of magnitude in concentration. Cells from 10 MM cell lines were grown in culture, then plated at uniform density in microtiter plates where they were incubated at concentrations of AZD5991 ranging from 0.3nM to 30µM (with DMSO control), each plate for a duration of 0.5h to 72h. After the desired incubation period, Cell-Titer Glo® was used to assess cellular viability by luminescence. Plates were run in duplicate. A model of cell survival was implemented in MATLAB, in which cells can be in one of two states: a proliferating state ‘S' in which they are susceptible to a saturable concentration-dependent drug-induced cell death, or a quiescent state ‘Q' in which they don't proliferate and have only a constitutive death rate independent of drug concentration. Transition between the two states is possible in either direction. By fitting the model to the data across time and over a wide range of concentrations, we can succinctly and precisely describe the rate of growth and drug-induced cell death, as well as transition between the susceptible and quiescent states. To our knowledge, this represents the first application of such a model to a BH3 mimetic such as AZD5991. We find that the cell lines show much greater variation in efficacy (i.e., maximum inducible cell kill rate) than in potency, suggesting that the main difference between these lines lies in their dependence on Mcl-1 for survival.
Citation Format: Francis D. Gibbons, Matthew Belmonte, Paul Secrist, Alwin Schuller. A susceptible-quiescent model can describe biphasic cell-kill by MCL1 inhibitor AZD5991 in vitro [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 299.
Abstract 2990: Attenuation of RNA polymerase II pausing mitigates BRCA1-associated R-loop accumulation and tumorigenesis
Authors: Zhang Xiaowen , Chiang Huai-Chin , Wang Yao , Zhang Chi , Jin Victor X. , Hu Yanfen , Li Rong 
Published: August 2018

Abstract
Most BRCA1-associated breast tumours are basal-like yet originate from luminal progenitors. BRCA1 is best known for its functions in double-strand break repair and resolution of DNA replication stress. However, it is unclear whether loss of these ubiquitously important functions fully explains the cell lineage-specific tumorigenesis. In vitro studies implicate BRCA1 in elimination of R-loops, DNA-RNA hybrid structures involved in transcription and genetic instability. Here we show that R-loops accumulate preferentially in breast luminal epithelial cells, not in basal epithelial or stromal cells, of BRCA1 mutation carriers. Furthermore, R-loops are enriched at the 5′ end of those genes with promoter-proximal RNA polymerase II (Pol II) pausing. Genetic ablation of Cobra1, which encodes a Pol II-pausing and BRCA1-binding protein, ameliorates R-loop accumulation and reduces tumorigenesis in Brca1-knockout mouse mammary epithelium. Our studies show that Pol II pausing is an important contributor to BRCA1-associated R-loop accumulation and breast cancer development.
Citation Format: Xiaowen Zhang, Huai-Chin Chiang, Yao Wang, Chi Zhang, Victor X. Jin, Yanfen Hu, Rong Li. Attenuation of RNA polymerase II pausing mitigates BRCA1-associated R-loop accumulation and tumorigenesis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2990.
Abstract 2995: CDK9 phosphorylates BRG1 chromatin remodeler
Authors: Pandey Somnath , Zhang Hanghang , Barrero Carlos A. , Merali Salim , Graña Xavier , Issa Jean-Pierre 
Published: August 2018

Abstract
Cyclin-dependent kinase 9 (CDK9) belongs to the class of CDKs involved in transcription regulation along with CDK7, 8, 10-13. Earlier works have established that CDK9 is the catalytic subunit of P-TEFb, and a transcriptional activator. CDK9 inhibition holds promise for patients belonging to Chronic Lymphocytic Leukemia (CLL) and BRD4-NUT-rearranged NUT midline carcinoma (NMC) groups. It is therefore fundamentally important to understand CDK9 mediated gene regulation. CDK9 in complex with its regulatory subunit, Cyclin T1 or T2, is known to promote RNAPII promoter-proximal pause release by phosphorylating negative elongation factors. Additionally, phosphorylation of the C-terminal domain (CTD) of RNAPII on Serine-2 allows recruitment of RNA processing factors, which work on the nascent RNA as it emerges from RNAPII. It is however not known whether CDK9 has any transcriptional repression activity. Earlier work from our lab demonstrated that long-term CDK9 inhibition leads to the activation of BRG1, an ATP-dependent nucleosome-remodeling complex from the SWI/SNF family of proteins. We therefore hypothesized that CDK9 directly phosphorylates BRG1 and regulates its activity. Using Co-immunoprecipitation (Co-IP) assay we discovered that CDK9 associates with BRG1 endogenously in colon cancer cells. We tested the association of these proteins more rigorously by transiently over-expressing either FLAG-tagged or GFP-tagged CDK9 in HEK293T cells and performed immunoprecipitation using BRG1 antibody. CDK9 was found to co-precipitate with BRG1. We validated this via reciprocal Co-IPs. We performed an in vitro kinase assay using purified CDK9 and BRG1 proteins to demonstrate that CDK9 directly phosphorylates BRG1 and that inhibition of CDK9 leads to reduced phosphorylation of BRG1. We validated these results in vivo in colon cancer cells. Furthermore, our LC-MS/MS data lead to the identification of novel phosphorylation sites in BRG1 following CDK9 inhibition. These findings provide a potential mechanism for the transcriptional repressor activity associated with CDK9 and may be relevant for developing therapies targeting this transcriptional regulator.
Citation Format: Somnath Pandey, Hanghang Zhang, Carlos A. Barrero, Salim Merali, Xavier Graña, Jean-Pierre Issa. CDK9 phosphorylates BRG1 chromatin remodeler [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2995.
Abstract 2999: Low-dose demethylation therapy for the treatment of cisplatin-resistant testicular cancer
Authors: Corbet Andrea , Albany Costantine , Bikorimana Emmanuel , Khan Ema , Rodriguez Jennifer , Christensen Brock C. , Sandusky George , Einhorn Lawrence H. , Freemantle Sarah J. , Spinella Michael J. 
Published: August 2018

Abstract
Testicular germ cell tumors (TGCTs) are the most common cancers of young males. A portion of TGCT patients are refractory to cisplatin. Only 30% of patients refractory to cisplatin respond to salvage therapies while to remainder die from progressive disease. Embryonal carcinoma (EC) are the stem cells of TGCTs. We have found that EC cells were highly sensitive to the DNA methyltransferase inhibitor, 5-aza deoxycytidine (5-aza). As an initial step in bringing demethylation therapy to the clinic for TGCT patients, we evaluated the effects of the clinically optimized, second generation demethylating agent guadecitabine (SGI-110) on EC cells in an animal model of cisplatin refractory testicular cancer. EC cells were exquisitely sensitive to guadecitabine and the hypersensitivity was dependent on high levels of DNA methyltransferase 3B. Guadecitabine mediated transcriptional reprogramming of EC cells included induction of p53 targets and repression of pluripotency genes. As a single agent, guadecitabine completely abolished progression and induced complete regression of cisplatin resistant EC xenografts even at doses well below those required to impact somatic solid tumors. Low dose guadecitabine also sensitized refractory EC cells to cisplatin in vivo. Genome-wide analysis indicated that in vivo antitumor activity was associated with activation of p53 and immune-related pathways and the antitumor effects of guadecitabine were dependent on p53, a gene rarely mutated in TGCTs. Together, these preclinical findings provided the rationale for our recently initiated and promising phase I clinical trial using SGI-110 to treat cisplatin refractory TGCT patients. We discuss our recent genome-wide molecular studies aimed to identify potential mechanism(s) to account for the hypersensitivity of TGCTs to 5-aza including promoter demethylation, p53 activation and dsRNA MDA5/MAVS/IRF7 viral mimicry. We also discuss preliminary findings from our ongoing trial. Our findings suggest that guadecitabine alone or in combination with cisplatin is a promising strategy to treat refractory TGCT patients.
Citation Format: Andrea Corbet, Costantine Albany, Emmanuel Bikorimana, Ema Khan, Jennifer Rodriguez, Brock C. Christensen, George Sandusky, Lawrence H. Einhorn, Sarah J. Freemantle, Michael J. Spinella. Low-dose demethylation therapy for the treatment of cisplatin-resistant testicular cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2999.
Abstract 3002: Genome engineering approaches to generate models of chromosome arm-level cancer aneuploidy
Authors: Taylor Alison Marie , Zhang Xiaoyang , Shih Juliann , Ha Gavin , Gao Galen F. , Berger Ashton C. , Cherniack Andrew D. , Beroukhim Rameen , Meyerson Matthew 
Published: August 2018

Abstract
Aneuploidy, whole chromosome or chromosome arm copy number imbalance, is a near-universal characteristic of human cancers. Although yeast and mammalian models of whole chromosome aneuploidies have been extensively investigated, chromosome arm-level aneuploidies have rarely been modeled. Cancer subtypes are often characterized by tumor-specific patterns of these arm-level copy number alterations; for example, squamous cell carcinomas (SCCs) from different tissues of origin (including lung, esophagus, and bladder) have a pattern of chromosome 3p loss and chromosome 3q gain. Our analysis of 495 lung SCCs found chromosome 3p deletion to be the most frequent genomic alteration, occurring in almost 80% of the tumors and covering the entire length of the chromosome arm. Over two-thirds of chromosome 3p genes showed significantly decreased expression in these samples. Without models of chromosome arm-level alterations, the phenotypic effects of specific aneuploidies in cancer, such as 3p deletion, remain unknown. However, recent advances in genome engineering and targeting of endonucleases allow new approaches to generate chromosomal alterations. Here, we used the CRISPR-Cas9 system to delete one copy of chromosome 3p in vitro. We successfully isolated almost 90 clones of immortalized lung epithelial cells with deletion of the 3p arm, with 8 validated by whole-genome sequencing. Consistent with patient data, expression of 3p genes was also decreased upon deletion. Phenotypic characterization revealed that cells with chromosome 3p deletion initially proliferated more slowly than their siblings. These chromosome 3p-deleted cells had increased G1 arrest, but did not undergo increased apoptosis or cell death. Interestingly, after several passages in culture, the proliferation defect was rescued in chromosome 3p-deleted cells; genome sequencing and karyotype analyses suggested that this was the result of chromosome 3 duplication. With our cellular model of chromosome arm-level aneuploidy, we uncovered a possible selection mechanism that allows aneuploidy tolerance in vitro. We used genome engineering to model chromosome arm-level deletions, providing a robust model that will address a gap in our understanding of aneuploidy in cancer.
Citation Format: Alison Marie Taylor, Xiaoyang Zhang, Juliann Shih, Gavin Ha, Galen F. Gao, Ashton C. Berger, Andrew D. Cherniack, Rameen Beroukhim, Matthew Meyerson. Genome engineering approaches to generate models of chromosome arm-level cancer aneuploidy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3002.
Abstract 3020: An essential role for Argonaute 2 in EGFR-KRAS signaling in pancreatic cancer development
Authors: Shankar Sunita , Tien Jean , Siebenaler Ronald F. , Dommeti Vijaya L. , Zelenka-Wang Sylvia , Juckette Kristin M. , Xu Alice , Mody Malay , Goodrum Andrew , Tsaloff Grace , Apel Ingrid J. , Wang Lisha , Siddiqui Javed , Shi Jiaqi , Kumar-Sinha Chandan , Chinnaiyan Arul 
Published: August 2018

Abstract
KRAS and EGFR have been shown to function as essential mediators of pancreatic cancer development. In addition, KRAS and EGFR have been separately shown to interact with and perturb the function of Argonaute 2 (AGO2), a key mediator of RNA-mediated gene silencing. Here, we employed a genetically engineered mouse model of pancreatic cancer to define the effects of conditional loss of AGO2 in KRASG12D driven pancreatic cancer. Genetic ablation of AGO2 does not interfere with development of the normal pancreas or KRASG12D driven early precursor pancreatic intraepithelial (PanIN) lesions. However, AGO2 loss prevents progression from early to late PanIN lesions, development of pancreatic ductal adenocarcinoma (PDAC), and metastatic progression. This results in a dramatic increase in survival of KRASG12D mutant mice deficient in AGO2 expression. In both mouse and human pancreatic tissues, increased AGO2 expression at the plasma membrane is associated with PDAC progression. Mechanistically, within early precursor PanIN lesions, loss of AGO2 elevates phospho-EGFR levels and activates wild-type RAS, antagonizing KRASG12D activation and PDAC development. Furthermore, we observe that phosphorylation of AGO2Y393 by EGFR disrupts the interaction of wild-type RAS with AGO2, but does not affect the interaction of mutant KRAS with AGO2. Taken together, our study supports a biphasic model of pancreatic cancer development: an AGO2-independent early phase of PanIN formation reliant on EGFR and wild-type RAS signaling, and an AGO2-dependent phase wherein the KRAS-AGO2 interaction is critical to the progression from PanIN to PDAC. A recent study by Phillip Sharp and Tyler Jacks describes a requirement for the oncogenic KRAS-AGO2 interaction in the development of a transplant mouse model of plasmablastic lymphoma, and together these studies substantiate the role of the interaction in KRAS oncogenesis.
Citation Format: Sunita Shankar, Jean Tien, Ronald F. Siebenaler, Vijaya L. Dommeti, Sylvia Zelenka-Wang, Kristin M. Juckette, Alice Xu, Malay Mody, Andrew Goodrum, Grace Tsaloff, Ingrid J. Apel, Lisha Wang, Javed Siddiqui, Jiaqi Shi, Chandan Kumar-Sinha, Arul Chinnaiyan. An essential role for Argonaute 2 in EGFR-KRAS signaling in pancreatic cancer development [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3020.