bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 918: A secondary RET mutation allosterically conferring resistance to vandetanib
Authors: Nakaoku Takashi , Kohno Takashi , Araki Mitsugu , Nino Seiji , Chauhan Rakhee , Knowles Phillip P. , Tsuchihara Katsuya , Matsumoto Shingo , Shimada Yoko , Mimaki Sachiyo , Ishii Genichiro , Ichikawa Hitoshi , Okuno Yasushi , Yoh Kiyotaka , McDonald Neil Q. , Goto Koichi 
Published: August 2018

Abstract
Targeted therapy against oncogenic ALK and ROS1 fusion using type I tyrosine kinase inhibitors (TKIs), which bind to the ATP-binding cleft of kinases, is highly effective in lung adenocarcinoma (LADC); however, such cancers inevitably acquire resistance, which severely limits the efficacy of cancer treatments. The identification of these resistance mutations led to the development of novel TKIs to overcome acquired resistance. Here we report resistance to vandetanib, a type I RET kinase inhibitor, developed in a patient with metastatic LADC harboring a CCDC6-RET fusion that initially exhibited a response to treatment. The resistant tumor acquired a secondary mutation resulting in substitution of an amino acid located outside the nucleotide binding cleft. The mutation conferred resistance to vandetanib by increasing the ATP affinity and auto-phosphorylation activity of RET kinase. A crystal structure of the mutant revealed a small hydrophobic core around the mutated amino acid likely to enhance basal kinase activity by stabilizing an active conformer. In addition, a thermal shift assay suggested that the mutation was less able to bind vandetanib. Molecular dynamics simulation supported the mutant underwent conformational changes decreasing the binding affinity of vandetanib. Our findings indicate that the missense mutation is able to increase kinase activity and confers drug resistance through allosteric effects.
Citation Format: Takashi Nakaoku, Takashi Kohno, Mitsugu Araki, Seiji Nino, Rakhee Chauhan, Phillip P. Knowles, Katsuya Tsuchihara, Shingo Matsumoto, Yoko Shimada, Sachiyo Mimaki, Genichiro Ishii, Hitoshi Ichikawa, Yasushi Okuno, Kiyotaka Yoh, Neil Q. McDonald, Koichi Goto. A secondary RET mutation allosterically conferring resistance to vandetanib [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 918.
Abstract 920: COP1 E3 ligase regulates response to oncogenic MAPK pathway inhibition
Authors: Mayekar Manasi K. , Lin Luping , Bivona Trever G. 
Published: August 2018

Abstract
Oncogenically activated RAS-MAPK pathway is the driver of several cancers including the majority of non-small cell lung adenocarcinomas (NSCLC). RAS-MAPK pathway is activated in NSCLC tumors via diverse genetic alterations in upstream receptor tyrosine kinases such as EGFR and ALK as well as in RAS, BRAF, MEK and RAS GTPase activating protein (GAP) and tumor suppressor, NF1. Molecular targeting of players of RAS-MAPK pathway can elicit an initial tumor response in many patients. However, most patients show an incomplete response and some fail to respond despite the presence of RAS-MAPK pathway activating genetic lesion in the tumor. Hence, it is important to understand the molecular basis of response and resistance to targeted therapies inhibiting the RAS-MAPK pathway in lung adenocarcinomas in order to improve patient survival. We conducted a genetic screen to identify regulators of response to MAPK pathway inhibition in lung adenocarcinomas. Our genetic screen uncovered the E3 ubiquitin ligase COP1/RFWD2 as a novel modulator of response to inhibition of RAS-MAPK pathway. We found that depletion of COP1 and members of its complex, as well as proteasomal subunits, confers resistance to RAS-MAPK pathway inhibition in human lung adenocarcinoma cells with oncogenically activated RAS-MAPK pathway. Interestingly, oncogenic targets of COP1 include MAPK pathway effectors, presence of which has been shown to support the survival of cancer cells with oncogenically activated MAPK upon inhibition of the RAS-MAPK pathway. Hence, we tested if depletion of COP1 alters the levels of those oncogenic substrates. Excitingly, we observed a substantial impact of COP1 depletion on the levels of certain effectors in the presence of RAS-MAPK inhibitors in genetically diverse NSCLC cells and also in oncogenic-BRAF driven melanoma cells. Our studies suggests that depletion of COP1 confers resistance to MAPK pathway inhibition in RAS-MAPK pathway driven cancers through accumulation of specific MAPK pathway effectors. This work has improved our understanding of the molecular basis of tumor cell resilience during initial treatment as well as of primary treatment resistance. Additionally, we are examining if levels of COP1 could be a biomarker for predicting response to RAS-MAPK pathway inhibitor therapy. We will also determine if the resistance-conferring COP1 substrate could be cotargeted along with RAS-MAPK pathway to improve the patient response in RAS-MAPK pathway driven lung adenocarcinomas and other cancers with low levels of COP1.
Citation Format: Manasi K. Mayekar, Luping Lin, Trever G. Bivona. COP1 E3 ligase regulates response to oncogenic MAPK pathway inhibition [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 920.
Abstract 928: Regulatory heterogeneity in glioblastoma multiforme informs novel drug target discovery
Authors: Liu Yunpeng , He Shan , Hemann Michael T. , Regev Aviv 
Published: August 2018

Abstract
Glioblastoma multiforme (GBM) is one of the most malignant forms of cancer. Its heterogeneity has been assessed at multiple levels, including bulk and single-cell transcriptome profiling. The disease has been stratified into four molecular subtypes - Classical, Neural, Proneural and Mesenchymal according to their gene expression profiles, and each of these subtypes display distinct mutational signatures and histological features reflective of their nomenclature. However, the underlying regulatory circuitry that gave rise to such heterogeneity and its implications for specialized therapeutic options are unclear. To dissect subtype-specific regulatory programs, we have developed a nonlinear regression model to unveil key transcriptional rewiring across the four GBM subtypes. Using a backbone network of potential transcription factor (TF) - target gene pairs, we applied nonlinear regression using expression profiles of each subtype to derive subtype-specific regulatory parameters for each TF-gene pair. Coupled with a novel analysis pipeline, the model revealed a set of transcription regulators whose regulatory capacities for target genes are unique to each subtype. The target genes of these signature TFs are enriched for expression signature genes for the corresponding subtype, implying that subtype-specific rewiring of TFs play a significant role in shaping differential transcription landscapes. The model was also able to capture known physical and functional interactions between TFs, as well as identify potential new co-regulatory relationships. Detailed examination of both expression and co-regulatory profiles of signature TFs showed that altered regulatory behavior could be a result of differential expression of the TF itself, differential functional partnering of the TF with other TFs, or a combination of both mechanisms. Importantly, our model also demonstrates that differential regulatory programs could provide new options for targeted therapy in GBM. We simulated the effects of knockdown/inhibition of these co-regulatory partners by propagating changes in expression to the corresponding target genes and then to the protein signaling layer using a novel random walk-based algorithm. Using the apoptosis pathway as readout, we show that targeting the retinoic acid receptor RXRA may be specifically beneficial for killing tumor populations of the Neural subtype, whereas the HNF4A gene is a potentially beneficial drug target for cells of the Mesenchymal subtype.
Citation Format: Yunpeng Liu, Shan He, Michael T. Hemann, Aviv Regev. Regulatory heterogeneity in glioblastoma multiforme informs novel drug target discovery [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 928.
Abstract 94: DDX31 cooperates with mutant p53 and EGFR to promote the multistep progression of invasive bladder cancer
Authors: Katagiri Toyomasa , Daizumoto Kei , Yoshimaru Tetsuro , Matsushita Yosuke , Fukawa Tomoya , Ono Masaya , Kanayama Hiro-omi 
Published: August 2018

Abstract
Bladder cancer is the most common malignancy of the urinary tract worldwide. Approximately 70% of cases are diagnosed as non-muscle-invasive bladder cancer (NMIBC), while the remaining 30% of cases are classified as muscle-invasive bladder cancer (MIBC). Evidence based on molecular biology has highlighted that the aggressiveness of MIBC advances through a multistep mechanism due to many genomic alterations. Notably, alterations of TP53 and EGFR pathways frequently occur in bladder cancers and are associated with poor prognosis, respectively. However, the connection between the overexpression of EGFR and the p53 mutation in multistep carcinogenesis and the progression of MIBC remains unknown. Here we report the distinct critical roles of DEAD box polypeptide 31 (DDX31) in the multistep progression of muscle invasive bladder cancer (MIBC) through its sequential interaction with mutant p53 (mutp53) and EGFR. In early MIBC cells, nuclear DDX31 acts as a transcriptional co-activator that binds to mutp53/SP1 and enhances mutp53 transcriptional activation, thereby upregulating the EPB41L4B gene, which plays a critical role in metastatic behavior and promotes the invasion and migration of MIBC. Notably, in advanced MIBC, cytoplasmic DDX31, which is transported from the nucleus, functions as an adaptor scaffold protein that forms a complex with EGFR via its interaction with phosho-nucleolin (NCL), leading to constitutive activation of EGFR-Akt signaling. Significantly, high expression of both cytoplasmic DDX31 and p53 proteins is correlated with a poor prognosis in MIBC patients. More importantly, blocking the DDX31-NCL interaction via a dominant-negative peptide led to downregulation of EGFR-Akt signaling, resulting in a significant anti-tumoral effect of bladder cancer in vivo. Our findings reveal that DDX31 cooperates with mutp53 and EGFR to promote the multistep progression of MIBC and that inhibition of DDX31-NCL formation may lead to potential treatment strategies for advanced MIBC.
Citation Format: Toyomasa Katagiri, Kei Daizumoto, Tetsuro Yoshimaru, Yosuke Matsushita, Tomoya Fukawa, Masaya Ono, Hiro-omi Kanayama. DDX31 cooperates with mutant p53 and EGFR to promote the multistep progression of invasive bladder 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 94.
Abstract 948: Preventing estrogen receptor alpha-positive breast cancer outgrowth with the use of hormone replacement therapy
Authors: Dembo Anna G. , Aledort Emily S. , Greene Geoffrey L. 
Published: August 2018

Abstract
Menopause occurs in all women, usually between the ages of 45 and 55. As a result of menopause, women often experience undesirable vasomotor symptoms, which can be alleviated by hormone replacement therapy (HRT). The Women's Health Initiative (WHI) trial concluded that PremPro, a HRT formulation that combines conjugated equine estrogens (CE) with medroxyprogesterone acetate, increases the risk of breast cancer. Over the years, the number of women taking HRT has dramatically decreased due to the perceived risk based largely on the results of the WHI trial. Follow-up sudies suggest that breast cancer cases from PremPro treatment were primarily due to the outgrowth of occult tumors, not the formation of new disease. Duavee, a more recent form of HRT that combines CE and bazedoxifene (BZA), a selective estrogen receptor modulator (SERM) and degrader (SERD), has been approved by the FDA for treatment of moderate to severe hot flashes and to reduce the risk of osteoporosis. More importantly, this CE+BZA mixture not only relieves symptoms associated with menopause, but it also does not stimulate the breast or uterus. Several preclinical studies suggest that CE+BZA might be protective in the breast, however the mechanism of action of this new combination therapy is not known. Our goal, therefore, is to elucidate the underlying molecular mechanisms by which CE+BZA differentially affects estrogen receptor alpha (ERα) action in the mammary gland, using transcriptome and whole genome occupancy analysis in breast cancer cell lines. RNA-Seq and ChIP-Seq studies suggest that CE+BZA decreases pathways related to S-phase entry, cell cycle regulation and BRCA1. We are also studying the effects of CE+BZA on early mammary cancer progression in the estrogen-sensitive polyoma middle T antigen (PyMT) transgenic mouse model and have observed that treatment with CE+BZA delayed the onset of tumors and decreased their rate of growth. Mice treated with CE+BZA also survived longer. In addition, CE+BZA was able to decrease the rate of tumor growth in an ERα-positive patient-derived xenograft (PDX) mouse model. An improved understanding of the molecular mechanisms of CE+BZA action in hormone sensitive breast cancer cell and animal models should have important implications for women considering HRT.
Citation Format: Anna G. Dembo, Emily S. Aledort, Geoffrey L. Greene. Preventing estrogen receptor alpha-positive breast cancer outgrowth with the use of hormone replacement therapy [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 948.
Abstract 972: Defining the molecular context of MYC and WDR5 at chromatin
Authors: Guarnaccia Alissa D. , Tansey William P. 
Published: August 2018

Abstract
MYC is an oncoprotein transcription factor that is overexpressed in the majority of malignancies and contributes to the deaths of ~100,000 Americans each year. The tumorigenic functions of MYC stem from its influence on the transcriptional program of a cell, promoting the expression of thousands of genes involved in cell cycle progression, growth, and metabolism. In order to understand how MYC promotes cancer, we must understand the mechanisms by which MYC selects its target genes. Epigenetic signatures, DNA sequence motifs, and protein-protein interactions have all been implicated to play a role in MYC target gene selection, but a deep molecular understanding of the determinants of target gene recognition by MYC is missing. Our laboratory discovered that the chromatin-associated scaffolding protein WDR5 directly interacts with MYC and co-localizes on chromatin at a majority of loci (Thomas et al., Mol. Cell, 58: 440-452, 2015). The MYC-WDR5 interaction is disrupted by point mutation of three charged residues in MYC. While this MYC mutant retains the ability to bind to naked DNA, the mutant does not bind target loci in the context of chromatin and is unable to form tumors in mice. From these findings we propose that WDR5 is a crucial factor for enabling MYC activity in cancer. Both MYC and WDR5 are known to be highly networked proteins with multiple simultaneous interactions. Our aim is to tease apart this complicated network and define the molecular context specifically for the MYC-WDR5 interaction. To do this, we are employing our WDR5-binding deficient MYC mutant as a tool to genetically distinguish MYC interactions that are dependent upon WDR5. Our approach is to use Stable Isotope Labeling of Amino acids in Cell Culture (SILAC) because it enables us to quantitatively compare wild-type and mutant MYC and reduces background noise common to non-quantitative MYC-centered proteomics. Once identified by SILAC, interacting proteins are validated with biochemical methods and by proximity ligation assay in cells. This dual validation confirms the interaction in two ways, and provides information on the sub-cellular localization of the interaction. Thus far we have identified a preliminary set of ~25 interacting proteins that are currently undergoing validation. Characterization of these new factors by genetic, genomic, and biochemical approaches will expand our understanding of MYC biology, and potentially identify new factors that can be therapeutically targeted in cancer.
Citation Format: Alissa D. Guarnaccia, William P. Tansey. Defining the molecular context of MYC and WDR5 at chromatin [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 972.
Abstract 973: MEKK3 sustains EMT and stemness in pancreatic cancer by regulating YAP and TAZ transcriptional activity
Authors: Piro Geny , Santoro Raffaela , Zanotto Marco , Carbone Carmine , Tortora Giampaolo , Melisi Davide 
Published: August 2018

Abstract
Background: Pancreatic cancer (PC) is one of the most threatening and poorly understood human malignancies. MEKK3 (MAP3K3) is an intracellular serine/threonine kinase activated by different signaling pathways, including IL1, TNFα and TLR8, which regulates in turn NF-κB, JNK and p38 activation.The transcriptional regulators Yes Associated Protein (YAP) and transcriptional coactivator with a PDZ binding domain (TAZ) are central determinants of malignancy and have been identified as a critical oncogenic effectors of KRAS in pancreatic cancer. We hypothesized that MEKK3 could sustain pancreatic cancer by inducing YAP/TAZ oncogenic activities. Methods: MEKK3 was knocked-out (KO) in AsPC1, Panc1, and MDA-Panc28 PC cell lines by CRISPR/Cas9. The expression of MEKK3, E-cadherin, YAP/TAZ and their target genes was measured by both Western blot and qPCR. Cell migration was assessed by transwell and wound healing assays. Stemness was measured by spheroid formation and percentage of CD44+/CD24+/EpCAM+ cancer stem cells (CSC). Effects of MEKK3 KO was evaluated in vivo in an orthotopic nude mouse model with GFP-expressing Panc1 PC cells. Expression of YAP/TAZ and their target genes in tumor samples was measured by IHC. Results: MEKK3 KO resulted in the reversion of both Epithelial-to-Mesenchymal Transition (EMT) and cell migration, as well as in the impairment of cell proliferation. More interestingly, the size of 3D colonies arising from MEKK3 KO cell lines was smaller than the ones formed by their respective controls, due to a reduced percentage of CD44+/CD24+/EpCAM+ CSC. In MEKK3 KO cells, the recruitment of YAP/TAZ onto the promoters of their target genes was significantly impaired and this paired with a reduction of the expression of the same genes. In nude mice, MEKK3 KO significantly reduced tumor growth and prolonged overall survival. Conclusions: Our study is the first to demonstrate that genetic silencing of MEKK3 is a valid approach to revert in vivo the aggressiveness of PC by modulating YAP and TAZ transcriptional activities. Inhibition of MEKK3 could represent an exciting therapeutic strategy for the treatment of PC, which should be warranted further development.
Citation Format: Geny Piro, Raffaela Santoro, Marco Zanotto, Carmine Carbone, Giampaolo Tortora, Davide Melisi. MEKK3 sustains EMT and stemness in pancreatic cancer by regulating YAP and TAZ transcriptional activity [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 973.
Abstract 987: Organoid-based characterization of patient tumors and microenvironments at single cell resolution
Authors: Salahudeen Ameen A. , Zhu Junjie , Ju Jihang , Batish Arpit , Sutha Ken , Neal James T. , Giangarra Valeria , Montesclaros Luz , Sapida Jerald , Sharifi Osman , Lee Josephine , Zheng Grace X. , Wagh Dhananjay A. , Coller John A. , Neal Joel W. , Padda Sukhmani K. , Sabatti Chiara , Kuo Calvin J. 
Published: August 2018

Abstract
The advent of microenvironment directed cancer treatments such as antiangiogenic agents and recent immunotherapies have produced a pressing need for robust and systematic characterization of patient tumors and corresponding stromal populations. However, in vitro cultures of tumor biopsies do not typically preserve both the tumor epithelium and tumor microenvironment as an intact syngeneic unit. To address these limitations, we developed organoid cultures of surgically resected patient cancer biopsies that intrinsically retain diverse tumor microenvironmental cellular components without requiring reconstitution. We compared transcriptome profiles of fresh tumor cell populations to organoid cultures by droplet based single cell 5' RNA sequencing (scRNA-seq). Analysis of &gt;50k single cell transcriptome profiles revealed tumor and stromal cell populations including tumor epithelia, fibroblasts and immune cells in fresh tumors. scRNA-seq of organoid cultures revealed a similar composition of native cancer cells and stromal components in both immune and non immune populations. In particular, 5' scRNA-seq enabled simultaneous characterization of paired T cell receptor alpha and beta chains as well as generalized gene expression in individual cells. We observed clonotype expansion of cytotoxic T cells in both fresh tumors and organoid cultures. The faithful recapitulation of tumor microenvironmental diversity within human organoid cultures should facilitate the in vitro exploration of immunotherapeutic agents and modeling of associated patient-specific responses.
Citation Format: Ameen A. Salahudeen, Junjie Zhu, Jihang Ju, Arpit Batish, Ken Sutha, James T. Neal, Valeria Giangarra, Luz Montesclaros, Jerald Sapida, Osman Sharifi, Josephine Lee, Grace X. Zheng, Dhananjay A. Wagh, John A. Coller, Joel W. Neal, Sukhmani K. Padda, Chiara Sabatti, Calvin J. Kuo. Organoid-based characterization of patient tumors and microenvironments at single cell resolution [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 987.