bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 281: Identifying genetic variation and cellular heterogeneity with a comprehensive cancer analysis toolkit
Authors: Garcia Sarah , Bharadwaj Rajiv , Boutet Stéphane , Catalanotti Claudia , Giangerra Valeria , Lee Josephine , Terry Jessica , Williams Stephen , Zheng Grace X. , Mikkelsen Tarjei , Schnall-Levin Michael , Hindson Ben , Church Deanna M.
Published: August 2018

Understanding disease development, progression and response to treatment remains elusive for most types of cancer. This is due both to the genetic complexity seen in tumors as well as differences in how the surrounding cells and immune system respond to the developing tumor. To fully understand all aspects of disease progression and response to treatment, a systems level approach is needed. We have developed a platform that allows for high resolution multi-omics analysis of the tumor and its microenvironment. This platform is built upon a microfluidic system that enables the production of hundreds of thousands to millions of partitioned barcoded reactions. On this platform we generate Linked-Reads that allow for the detailed resolution of complex structural variant events. To obtain more detailed information about tumor heterogeneity and clonal structure, we also perform single cell DNA analysis that allows for the detection of sub-megabase copy number variants at the single cell level.The platform also provides detailed resolution of the cells occupying the microenvironment surrounding the tumor. Using a combination of single cell gene expression and enriched V(D)J B and T cell repertoire analysis, we identify cells constituting a tumor, as well as the immune and nonimmune cells surrounding the tumor. We also provide single cell profiling of the paired antigen receptor chains for both B and T cells. As a demonstration, we have performed this analysis on three types of tumor samples: metastatic melanoma (MM), primary colorectal cancer (CRC) and primary clear cell renal carcinoma (CCRC). We are able to identify a clonal expansion in the CCRC sample and determine there is no expansion in the CRC sample. The combination of these approaches allows for unparalleled characterization of disease development, progression and response.

Citation Format: Sarah Garcia, Rajiv Bharadwaj, Stéphane Boutet, Claudia Catalanotti, Valeria Giangerra, Josephine Lee, Jessica Terry, Stephen Williams, Grace X. Zheng, Tarjei Mikkelsen, Michael Schnall-Levin, Ben Hindson, Deanna M. Church. Identifying genetic variation and cellular heterogeneity with a comprehensive cancer analysis toolkit [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 281.
Abstract 2836: Spatially resolved single-cell analysis of cellular plasticity and mechanisms of drug resistance
Authors: Pitchiaya Sethuramasundaram , D'silva Jeremy , Lee Nicole , Narayanan Sathiyapandi , Jiang Xia , Dhanasekaran Saravana M. , Chinnaiyan Arul M.
Published: August 2018

Cellular heterogeneity adversely affects clinical stratification, treatment decisions, and development of therapeutic resistance in cancer. Heterogeneity manifests as variability in gene expression and scales with the number of unique cell types and/or the extent of phenotypic plasticity. Therefore, an incisive tool that effectively quantifies heterogeneity, robustly identifies rare cell populations, efficiently predicts cell state transitions, and preserves the associated phenotypic manifestations will provide key insights into the mechanisms of plasticity and development of drug resistance. To this end, we developed High-Throughput Single-cell analysis using single-molecule Fluorescence In Situ Hybridization (HITS-FISH) - a completely automated imaging-based tool that provides absolute quantification of gene expression (mature and immature transcripts that are coding or non-coding), while still preserving spatial and morphological information. Using a combination of HITS-FISH and single cell RNAseq, which provides a high-throughput readout of gene expression signatures, we find that multiple, potentially plastic cell states (genetic, epigenetic, and cell cycle) coexist within a seemingly homogeneous population of cancer cells from various tissues. HITS-FISH suggests that one of the major contributors of such heterogeneity is pervasive aneuploidy, which is accentuated during treatment of cancer cells with chemotherapeutic agents and subsequent development of resistance against such drugs. Currently, we are further characterizing these plastic cells via lineage tracing and single-cell analysis to identify pre-resistant cell states and drug-induced gene-expression reprogramming.

Citation Format: Sethuramasundaram Pitchiaya, Jeremy D'silva, Nicole Lee, Sathiyapandi Narayanan, Xia Jiang, Saravana M. Dhanasekaran, Arul M. Chinnaiyan. Spatially resolved single-cell analysis of cellular plasticity and mechanisms of drug resistance [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 2836.
Abstract 2839: Notch3-dependent beta-catenin signaling mediates EGFR TKI drug persistence in EGFR mutant NSCLC
Authors: Arasada Rajeswara Rao , Shilo Konstantin , Zhang Jianying , Ghanem Rashelle , Yamada Tadaaki , Yano Seiji , Carbone David
Published: August 2018

EGFR tyrosine kinase inhibitors (EGFR-TKIs) usually cause dramatic responses in EGFR-mutant lung cancer, but different patients with identical drivers have widely different progression-free intervals, and resistance universally develops. In those cases without pre-existing resistant clones, even though every cell expresses the driver, some tumor clonogens survive in order to acquire target reactivation or bypass resistance mechanisms. The involvement of β-catenin in EGFR TKI resistance has been previously reported however the precise mechanism by which β-catenin activation contributes to EGFR TKI resistance is not clear. Our transcriptome analysis identified that EGFR inhibition results in the activation of β-catenin signaling in a Notch3-dependent manner, which facilitates the survival of a subset of cells that we call “adaptive persisters”. We have previously reported that EGFR-TKI treatment rapidly activates Notch3, and here our co-immunoprecipitation studies identified a physical association of Notch3 with β-catenin, which in turn leads to increased stability and activation of β-catenin. In vitro pulmosphere formation assays and in vivo limiting dilution assays reveled that adaptive persisters display characteristics of stem-like cells. Furthermore, tumor xenograft studies using HCC827 and HCC4006 demonstrate that the combination of EGFR-TKI and the β-catenin inhibitor, ICG-001 inhibits the development of these adaptive persisters, decreases tumor burden, improves recurrence free survival, and overall survival. Overall, Notch3 plays a pivotal role in the maintenance of lung cancer stem cells (CSCs) and the induction of EGFR TKI mediated drug persisters with cancer stem cell like characteristics, but is difficult to selectively target. Our study finds that this effect is driven by the Notch3-dependent activation of β-catenin signaling in a non-canonical fashion. A combination of EGFR TKI and β-catenin inhibitors decreases tumor take, delays tumor recurrence and increases overall survival in EGFR mutant models. Thus, our findings provide novel insights on role of drug persistence early after EGFR TKI therapy and presents a rationale for clinical testing of EGFR TKIs with β-catenin inhibitors for the treatment of EGFR mutant NSCLC.

Citation Format: Rajeswara Rao Arasada, Konstantin Shilo, Jianying Zhang, Rashelle Ghanem, Tadaaki Yamada, Seiji Yano, David Carbone. Notch3-dependent beta-catenin signaling mediates EGFR TKI drug persistence in EGFR mutant NSCLC [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 2839.
Abstract 2842: The biological effects and therapeutic potential of directly targeting K-Ras
Authors: Wolfe Andrew L.
Published: August 2018

K-Ras is a small GTPase that is among the most frequently mutated oncoproteins in cancer, with alterations common in lung adenocarcinoma, colorectal cancer, and up to 90% of pancreatic cancers. Tumors with mutant K-Ras often become addicted to its presence and in inducible genetic mouse models the sudden removal of mutant K-Ras can trigger cancer regressions. However, these cancers remain among the most refractory to therapy and pharmacological agents capable of inhibiting many common K-Ras mutants have remained elusive. Here, we set out to evaluate the efficacy of recently developed inhibitors that directly target K-Ras in cancer and understand potential mechanisms of resistance to K-Ras based therapies. Treatment of K-Ras mutant cells with K-Ras inhibitors led to mutant-specific halting of cell growth. Upon extended treatment a subpopulation of drug-resistant cells emerged that displayed adaptation patterns leading to reversible drug resistance. To identify cooperating factors that modulate sensitivity to K-Ras inhibition, screens were performed in wild-type and isogenic K-Ras mutant cells using a genome-wide CRISPRi library and a pharmacological compound library in the presence or absence of K-Ras inhibitors. These strategies identified synthetically lethal pathways and favorable combination therapies, moving toward the goals of identifying the optimal patient populations that can most benefit from K-Ras inhibitors and enabling a personalized medicine approach to cancer therapy.

Citation Format: Andrew L. Wolfe. The biological effects and therapeutic potential of directly targeting K-Ras [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 2842.
Abstract 2861: PUMA induction by p73 mediates response and resistance of colorectal cancer to anti-EGFR antibody therapy
Authors: Knickelbein Kyle , Tong Jingshan , Chen Dongshi , Wang Yi-Jun , Misale Sandra , Bardelli Alberto , Yu Jian , Zhang Lin
Published: August 2018

Intrinsic and acquired resistance to anti-EGFR antibody therapy, frequently mediated by mutant or amplified KRAS oncogene, is a significant challenge in the treatment of colorectal cancer (CRC), the second-leading cause of cancer-related death in the United States. However, the mechanism of KRAS-mediated therapeutic resistance is not well understood. In this study, we found that clinically used anti-EGFR antibodies, including cetuximab and panitumumab, induce killing of sensitive CRC cells through p73-dependent transcriptional activation of the pro-apoptotic Bcl-2 family protein PUMA. Inhibition of EGFR and downstream AKT by cetuximab and panitumumab promotes Tyr99 phosphorylation of p73, which then binds to PUMA promoter to activate its transcription, resulting in cell death via the mitochondrial pathway. PUMA induction and p73 phosphorylation are abrogated in CRC cells with acquired resistance to anti-EGFR antibodies due to KRAS alterations and residual AKT activity. Upon screening a panel of anticancer drugs, we found that inhibition of aurora kinases preferentially kills mutant KRAS CRC cells. A combination with aurora kinase inhibitor overcomes KRAS-mediated resistance to anti-EGFR antibodies in vitro and in vivo by restoring PUMA induction and eliminating the residual AKT activity. Collectively, our results suggest that p73-dependent PUMA induction plays a critical role in mediating the sensitivity of CRC cells to anti-EGFR antibodies, and that restoration of PUMA induction and apoptosis is a promising approach to improve the efficacy of EGFR-targeted therapy.

Citation Format: Kyle Knickelbein, Jingshan Tong, Dongshi Chen, Yi-Jun Wang, Sandra Misale, Alberto Bardelli, Jian Yu, Lin Zhang. PUMA induction by p73 mediates response and resistance of colorectal cancer to anti-EGFR antibody 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 2861.
Abstract 2889: Aitongxiao (ATX) induces apoptosis and blocks exosomes release in human liver carcinoma cells
Authors: Huang Ming B. , Leng Jiang
Published: August 2018

Background: The role of exosomes in cancer development has become the focus of much

research, due to the many emerging roles possessed by exosomes. These contents of exosomes

could contribute to tumorigenesis. We discovered Aitongxiao (ATX), a group of 80% alcohol

extracts from 15 plants, has been shown to have an anti-tumor effect on liver carcinoma; however,

the mechanism for the anti-cancer effect of ATX on human liver carcinoma cells is still unclear.

Objective: Due its inhibitory effects on chemical carcinogenesis and inflammation, Aitongxiao

(ATX) has been proposed as an effective agent for the prevention or treatment of human

carcinoma. In this study, we aimed to explore the effect of ATX on human liver carcinoma cells.

Methods: The inhibitory effect of Aitongxiao (ATX) on proliferation of HepG2 and HKCL-C3 cells

was assessed by CCK-8 assay. The cell cycle distribution and cell apoptosis were determined by

flow cytometry. The expression of Alix and CD63 exosomes marker proteins, were detected by

Western Blotting. The exosomes protein concentration was measured by and fluorescent

antibody assays. Exosomes size and particle number were measured by NanoSight analysis.

Results: Aitongxiao (TAX) inhibited the growth of human liver carcinoma cells in a dose and time-

dependent manner. Flow cytometry analysis showed that ATX induced G2/M phase arrest and

cell apoptosis. ATX treatment promoted the cleavage of caspase 3. In addition, the ATX reduced

exosomes release from HepG2 cells, and lose-dose ATX significantly enhanced the growth

inhibition induced by 5-Fu.

Conclusions: Aitongxiao (ATX) could inhibit the growth of human liver carcinoma cells in vitro.

ATX induced both apoptosis and cell cycle arrest and blocked exosomes release, probably

through the inhibition of STAT3 function. Lose-dose ATX significantly enhanced the growth

inhibitory effect of 5-FU on breast cancer cells, further indicating the potential clinical values of

ATX for the prevention or treatment of human liver carcinoma.

Keywords: Aitongxiao, liver carcinoma, HepG2 cells, apoptosis, exosomes

Citation Format: Ming B. Huang, Jiang Leng. Aitongxiao (ATX) induces apoptosis and blocks exosomes release in human liver carcinoma cells [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 2889.
Abstract 2896: A genome-wide CRISPR/Cas9 pooled screen identifies EML4-ALK variant-specific synthetic lethal partners of HSP90 inhibitors
Authors: Licciardello Marco P. , Clarke Paul A. , Workman Paul
Published: August 2018

The chromosomal rearrangement generating the EML4-ALK fusion protein occurs in 5–7% of patients with non-small-cell lung cancer (NSCLC). Distinct breakpoints give rise to variants with different EML4 fragments and an invariable ALK kinase domain. Patients treated with ALK tyrosine kinase inhibitors, such as crizotinib or alectinib, inevitably develop resistance to the drugs and need alternative therapies. EML4-ALK v1 and v3a/b, the most common variants of the fusion oncogene, display distinct cellular localization and different sensitivity to the inhibition of HSP90 chaperoning activity. In the clinic, HSP90 inhibitors have shown encouraging results in EML4-ALK+ NSCLC patients, but the responses have been heterogeneous. Currently, there is no EML4-ALK variant-based classification of patients and this might have contributed to confounding results in clinical trials. Moreover, the identification of additional biomarkers of sensitivity could further improve patient stratification and suggest potential combinatorial regimes. As chaperones are molecular hubs enriched for synthetic lethal partners, we performed a CRISPR/Cas9-based pooled screen in human NSCLC cell lines carrying different EML4-ALK variants in the presence of non-lethal concentrations of an HSP90 inhibitor. In the screen, we found already described as well as previously unreported EML4-ALK variant-specific synthetic lethal interactions. We are currently dissecting the mechanism behind these interactions, and evaluating their therapeutic potential for EML4-ALK+ NSCLC patients.

Citation Format: Marco P. Licciardello, Paul A. Clarke, Paul Workman. A genome-wide CRISPR/Cas9 pooled screen identifies EML4-ALK variant-specific synthetic lethal partners of HSP90 inhibitors [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 2896.
Abstract 2906: eEF1A2 interacts with and inhibits PKR to enhance cancer cell survival
Authors: Martínez-Leal Juan F. , Losada Alejandro , Muñoz Maria Jose , Martinez-Diez Marta , Dominguez Juan Manuel , Galmarini Carlos M.
Published: August 2018

Human translation elongation factor 1α2, encoded by the eEF1A2 gene, is a pro-oncogenic protein absent from the majority of body tissues (with exception of brain, heart and skeletal muscle1), but expressed in many cancers1-3, where it provides tumor cells with improved fitness and survival. Though its canonical function is delivering aminoacyl-tRNAs to the ribosome, other “moonlighting” functions such as enhancing sphingosine kinase4,5 or antioxidant (most probably through peroxiredoxin-1 stimulation) activities6 have been described for the elongation factor. Recently, we have reported that eEF1A2 is the target for plitidepsin, a marine-derived cyclic depsipeptide currently under development for the treatment of relapsed or refractory multiple myeloma patients7. We have also confirmed that eEF1A2 interacted with previously described partners as PRDX1 and SPHK and enhanced their pro-survival activities8. Here we investigated the role of new “moonlighting functions” of eEF1A2 in the maintenance of the tumor phenotype and survival of cancer cells. Through co-immunoprecipitation and HPLC/MS we have uncovered the interaction between eEF1A2 and dsRNA-activated protein kinase (PKR, EIF2AK2). We have analyzed the kinase activity of PKR in the presence of eEF1A2, demonstrating that PKR activity is inhibited when complexed with eEF1A2. This complex is disrupted after plitidepsin binding to eEF1A2, rendering PKR active. Once activated, the kinase triggers a MAPK cascade and the NF-κB signaling pathway, leading to the activation of the extrinsic apoptotic pathway and the death of the tumor cell. Taken together, these results show that the fitness boost that the moonlighting functions of eEF1A2 provide to cancer cells, which are important for their growth and survival, constitutes an Achilles heel that can be purposely exploited in anticancer therapy. 1 Abbas, W., Kumar, A. & Herbein, G. Front Oncol 5, 75 (2015). 2 Anand, N. et al. Nature genetics 31, 301-305 (2002). 3 Li, Z. et al. PloS one 5, e10755 (2010). 4 Leclercq, T. M., Moretti, P. A., Vadas, M. A. & Pitson, S. M. J Biol Chem 283, 9606-9614 (2008). 5 Leclercq, T. M., Moretti, P. A. & Pitson, S. M. Oncogene 30, 372-378 (2011). 6 Chang, R. & Wang, E. J Cell Biochem 100, 267-278 (2007). 7 Losada, A. et al. Sci Rep 6, 35100 (2016) 8 Losada, A. et al. Abstract #1165, AACR Annual Meeting (2017)

Citation Format: Juan F. Martínez-Leal, Alejandro Losada, Maria Jose Muñoz, Marta Martinez-Diez, Juan Manuel Dominguez, Carlos M. Galmarini. eEF1A2 interacts with and inhibits PKR to enhance cancer cell survival [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 2906.
Abstract 2910: Identification of URST1 as a novel prognostic biomarker and therapeutic target for various subtypes of breast cancer
Authors: Nakamura Masako , Takano Atsushi , Thang Phung Manh , Miyagi Yohei , Daigo Yataro
Published: August 2018

Breast cancer is one of the most common causes of cancer death for women worldwide. To identify diagnostic and therapeutic targets for breast cancer, we screened molecules that were highly expressed in the majority of breast cancers by our gene expression profile database. During this process, we identified URST1 (up-regulated in solid tumor 1) as a candidate. Immunohistochemical analysis showed that URST1 was expressed in 195 of 257 (75%) breast cancer cases (69% in luminal type, 88% in HER2-positive cancer, 86% in Triple-negative cancer) that had undergone curative surgery, whereas no staining was observed in adjacent normal breast tissues. URST1 expression was significantly related to poor clinical outcome for breast cancer patients (P = 0.01, Log-rank test) and multivariate analysis showed that it was an independent prognostic factor. Knockdown of endogenous URST1 expression by siRNAs against URST1 or treatment with URST1 inhibitor significantly inhibited the growth of breast cancer cells through cell cycle arrest at G2/M phase. Our data suggest that URST1 is likely to be a prognostic biomarker and therapeutic target for various subtypes of breast cancers.

Citation Format: Masako Nakamura, Atsushi Takano, Phung Manh Thang, Yohei Miyagi, Yataro Daigo. Identification of URST1 as a novel prognostic biomarker and therapeutic target for various subtypes of 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 2910.
Abstract 2918: Decursin from Angelica gigas Nakai regulates CXCR7 expression and its downstream signaling in gastric cancer cells
Authors: Kim Solbi , Kim Nayoung , Ryu Hyewon , Song Gyu-Yong , Lee Hyo Jin
Published: August 2018

Background: C-X-C motif chemokine receptor 7 (CXCR7) is a member of the G protein-coupled receptor family and is reported to be involved in the invasion, migration and tumor progression of various cancers. However, few compounds regulate CXCR7 expression. Therefore, compounds that negatively regulate CXCR7 may inhibit tumor progression and thus serve as candidates for effective anti-cancer drugs. In this study, we investigated the regulation of CXCR7 by decursin derived from Angelica gigas and its downstream signaling.

Methods: A CXCR7-overexpressing stable cell line was established in gastric cancer cells, and the expression of membrane CXCR7 was confirmed by flow cytometry and immunocytochemistry. Cell viability was examined using the CCK-8 assay. We investigated the potential of decursin to inhibit cell migration and invasion using a Transwell system. We also examined the mechanism of CXCR7 regulation by decursin by performing Western blot analysis of downstream proteins using phospho-specific antibodies.

Results: CXCR7 overexpression significantly increased the proliferation, invasion and migration of gastric cancer cells. In addition, spheres were well formed under anchorage-independent conditions in CXCR7-expressing gastric cancer cells. Levels of phospho-Stat3 and -Akt, positive regulators of cancer progression, were significantly increased. Decursin treatment reduced CXCR7 expression at the cellular membrane, and significantly decreased cancer cell invasion and migration. When treated with decursin, the sphere formation capacity decreased in a dose-dependent manner. In addition, decursin decreased the phosphorylation of Stat3 and its downstream target, c-Myc; however, it had no effect on Akt phosphorylation.

Conclusion: Decursin reduces the invasion, migration and tumor progression of cancer cells by inhibiting CXCR7. Decursin could be proposed as a new anti-cancer drug by decreasing the expression of CXCR7, which is believed to be a therapeutic target in gastric cancer.

Citation Format: Solbi Kim, Nayoung Kim, Hyewon Ryu, Gyu-Yong Song, Hyo Jin Lee. Decursin from Angelica gigas Nakai regulates CXCR7 expression and its downstream signaling in gastric cancer cells [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 2918.
Abstract 2919: Discovery of small-molecule compounds targeting c-MYC using a novel cell-based screen
Authors: Mangatt Biju , Pietra Anthony D. , Waszkiewicz Anna , Jaworski Jon-Paul , Ghidelli-Disse Sonja , Berrodin Thomas J. , Sherk Christian S. , Meinhold Derrick W. , Rutkowska-Klute Anna , Sundaram Shanker K. , Ganji Gopinath , Halsey Wendy S. , Livi George P. , Li William , Mack James , Romeril Stuart P. , Minthorn Elisabeth A. , Kumar Rakesh , Drewes Gerard C. , Heerding Dirk A. , Kallal Lorena A. , Buser Carolyn A. , Medina Jesus R.
Published: August 2018

Elevated expression of the c-MYC oncogene (either due to gene amplification, translocation, abnormality in upstream signaling pathways and/or protein stabilization) is one of the most common abnormalities in human cancers. Efforts to identify direct pharmacological inhibitors of c-MYC function have not yet yielded drug-like molecules. Therefore, we sought to pursue alternative screening strategies for this classically “undruggable” transcription factor. We developed a novel antibody-based high-throughput HTRF screening assay that specifically detects endogenous c-MYC protein levels in a MYC amplified cancer cell line. Taking advantage of the short half-life of c-MYC, both at the protein and mRNA level, we conducted a cell-based screen of the GSK screening collection to identify compounds that can rapidly decrease c-MYC protein levels. Elimination of false positive hits using stringent triage assays successfully identified two valid hit series exemplified by GSK970 and GSK417. Molecular mode of action studies revealed these molecules inhibit MYC transcription by binding to the minor groove of DNA with AT sequence specificity. Unfortunately, this mechanism of c-MYC inhibition demonstrated poor in vivo translatability as tissue DNA acts as a molecular sink, effectively sequestering compound, and limiting its pharmacodnyamic response.

Citation Format: Biju Mangatt, Anthony D. Pietra, Anna Waszkiewicz, Jon-Paul Jaworski, Sonja Ghidelli-Disse, Thomas J. Berrodin, Christian S. Sherk, Derrick W. Meinhold, Anna Rutkowska-Klute, Shanker K. Sundaram, Gopinath Ganji, Wendy S. Halsey, George P. Livi, William Li, James Mack, Stuart P. Romeril, Elisabeth A. Minthorn, Rakesh Kumar, Gerard C. Drewes, Dirk A. Heerding, Lorena A. Kallal, Carolyn A. Buser, Jesus R. Medina. Discovery of small-molecule compounds targeting c-MYC using a novel cell-based screen [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 2919.
Abstract 2921: Co-inhibition of BET and proteasome enhances ER stress and Bim-dependent apoptosis with augmented cancer therapeutic efficacy
Authors: Qian Guoqing , Yao Weilong , Hall Williams D. , Shanmugam Mala , Lonial Sagar , Sun Shi-Yong
Published: August 2018

Background: Agents that inhibit bromodomain and extra-terminal domain (BET) protein, a promising cancer therapeutic target which imposes epigenetic modulation of gene expression, have been actively tested in the clinic as potential anticancer drugs. Some proteasome inhibitors such as carfilzomib (CFZ) are FDA-approved drugs for the treatment of patients with advanced multiple myeloma. The current study focuses on studying the combination of a BET inhibitor (e.g., JQ1) and a proteasome inhibitor (e.g., CFZ) as a novel cancer therapeutic strategy.

Methods: Diverse solid and hematologic cancer cell lines were used to test the effects of the combinations on cell survival and apoptosis via SRB assay, colony formation assay, flow cytometric analysis, and Western blotting. Bim knockout cell lines were generated using a CRISPR-based method for mechanistic study. Transcriptional regulation of target genes was examined by quantitative RT-PCR. The anti-tumor effects were also examined in a xenograft tumor model.

Results: The tested combinations (e.g., JQ1 with CFZ) synergistically decreased cancer cell survival and enhanced apoptosis in vitro and inhibited tumor growth in vivo. The combinations dramatically induced apoptosis accompanying with enhanced elevation of Bim and several ER stress marker proteins. Bim knockout significantly blocked apoptosis induced by the combinations in both HCT116 and L363 cells. Transcriptional upregulation of Bim by the combinations was observed.

Conclusions: The enhanced anti-tumor effects of dual inhibition of BET and proteasome is likely due to augmented induction of ER stress and Bim-dependent apoptosis. Our findings warrant further investigation of this combinatorial strategy as an effective regimen against cancer in the clinic.

Citation Format: Guoqing Qian, Weilong Yao, Williams D. Hall, Mala Shanmugam, Sagar Lonial, Shi-Yong Sun. Co-inhibition of BET and proteasome enhances ER stress and Bim-dependent apoptosis with augmented cancer therapeutic efficacy [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 2921.
Abstract 2981: Clonal deletion of tumor-specific T cells by combination checkpoint blockade compromises antitumor efficacy in low tumor burden states
Authors: Pai Chien-Chun Steven , Lu Xiaoqing , Simons Donald , DuPage Michel , Roybal Kole T. , Chen Mingyi , Kwek Serena , Casbon Amy-Jo , Kinsbury Gillian A. , Fong Lawrence
Published: August 2018

A myriad of combination immunotherapies is being developed as cancer treatments with the goal of enhancing antitumor immunity. We found that depending on the disease setting, combined immune checkpoint blockade may not always lead to synergistic antitumor effects. While combined anti-CTLA-4 and anti-PD-1 improves control of established tumors, this combination can paradoxically compromise antitumor immunity in the low tumor burden state in preclinical models as well as in melanoma patients. This paradoxical outcome results from treatment-induced apoptosis of tumor-specific T cells. These changes further alter the overall T-cell receptor repertoire. Activated tumor-specific T cells express higher levels of IFN-γ receptor and are more susceptible to apoptosis. Deficiency of IFN-γ receptor on immune cells rescues this phenotype and restores antitumor activity. Additionally, tumor-specific T cells lacking the IFN-γ receptor demonstrate a significant survival advantage compared to their wild-type counterparts in tumor-bearing mice receiving combination therapy. Finally, combination therapy induces significantly higher levels of IFN-γ in the low versus high tumor burden state on a per cell basis, reflecting their less exhausted immune status. Thus, the optimal immunotherapy strategy may depend on disease context, and may not always favor more potent combination immunotherapies.

Citation Format: Chien-Chun Steven Pai, Xiaoqing Lu, Donald Simons, Michel DuPage, Kole T. Roybal, Mingyi Chen, Serena Kwek, Amy-Jo Casbon, Gillian A. Kinsbury, Lawrence Fong. Clonal deletion of tumor-specific T cells by combination checkpoint blockade compromises antitumor efficacy in low tumor burden states [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 2981.
Abstract 2998: Dynamic 3d chromosomal landscapes in acute leukemia
Authors: Thandapani Palaniraja , Kloetgen Andreas , Lazaris Charalampos , Chen Xufeng , Ntziachristos Panagiotis , Tsirigos Aristotelis , Aifantis Iannis
Published: August 2018

T-cell acute lymphoblastic leukemia (T-ALL) accounts for approximately 10-15% of pediatric and 25% of adult ALL cases. Despite improved prognosis driven by the significant advances in the molecular understanding of T-ALL, the outcome of T-ALL patients with primary resistant and relapsed leukemia remains poor. Recent evidences have highlighted a role for changes in 3D chromatin architecture in cancer progression. Herein, for the first time we explored genomewide changes in chromatin organization in primary T-ALL samples relative to T cells from healthy donors. We show how the organization of topologically associated domains (TADs) influences key oncogenic and tumor-suppressive loci by modifying the promoter-enhancer landscape, deregulating the transcriptional program and ultimately causing disease progression.

To comprehensively characterize the chromatin landscape of clinically relevant loci in T-ALL, we sought to identify changes in intra-TAD activity and TAD disruptions on a genome-wide scale. We developed and implemented new computational approaches for Hi-C data analysis with a focus on Hi-C data integration with ChIP-Seq and RNA-Seq. We found significant correlations of TAD activity with CTCF occupancy, super-enhancer activity and gene expression of leukemia relevant loci. Furthermore, among the dozens of TAD disruptions we identified, we found a novel TAD “fusion” event around the MYC locus, which allows for chromatin interactions between a recently reported Notch-dependent MYC super-enhancer and promoter to drive overexpression of MYC. This particular TAD fusion is accompanied by a complete CTCF loss in the TAD boundary and increased MYC expression in T-ALL samples. Overall, this study sheds new light into how changes in chromatin architecture influence disease progression by restructuring oncogene and tumor suppressor landscapes.

Citation Format: Palaniraja Thandapani, Andreas Kloetgen, Charalampos Lazaris, Xufeng Chen, Panagiotis Ntziachristos, Aristotelis Tsirigos, Iannis Aifantis. Dynamic 3d chromosomal landscapes in acute leukemia [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 2998.
Abstract 3011: Determinants and prognostic value of quality of life in patients with pancreatic ductal adenocarcinoma
Authors: Deng Yang , Tu Huakang , Pierzynski Jeanne A. , Miller Ethan , Huang Maosheng , Gu Xiangjun , Chang David W. , Ye Yuanqing , Hildebrandt Michelle A. , Klein Alison P. , Lippman Scott M. , Wu Xifeng
Published: August 2018

Background Quality of life (QOL) is impaired in pancreatic cancer patients. Our aim was to investigate the determinants and prognostic value of QOL after diagnosis in a hospital-based cohort of racially/ethnically diverse patients with pancreatic ductal adenocarcinoma (PDAC). Patients and methods QOL was prospectively assessed using the Short Form-12 version 1 in 2478 PDAC patients. The Physical Component Summary (PCS) and Mental Component Summary (MCS) were categorized into tertiles based on their distribution. Ordered logistic regression was adopted to compare the risk of having lower PCS and MCS by patient sociodemographic and clinical characteristics. The association of PCS and MCS with mortality was assessed by Cox regression. Results Compared with non-Hispanic whites, Hispanics were at significantly higher risk of having lower PCS (odds ratio [95%CI], 1.69 [1.26-2.26]; P < .001) and lower MCS (1.66 [1.24-2.23]; P < .001). Patients diagnosed with stage III (1.80 [1.10-2.94]; P = .02) and stage IV (2.32 [1.50-3.59]; P < .001) were more likely to have lower PCS than were patients diagnosed with stage I. Other determinants included sex, age, drinking, smoking, education level, and comorbidities. The low tertile of PCS (hazard ratio [95%CI], 1.94 [1.72-2.18]; P < .001) and MCS (1.42 [1.26-1.59]; P < .001) were each related to poor prognosis. Similar results were found for non-Hispanic Whites as compared to African Americans/Hispanics/others. Conclusion QOL after diagnosis is a significant prognostic indicator for patients with PDAC, and multiple factors determine QOL, suggesting possible means of intervention to improve QOL and outcomes of PDAC patients.

Citation Format: Yang Deng, Huakang Tu, Jeanne A. Pierzynski, Ethan Miller, Maosheng Huang, Xiangjun Gu, David W. Chang, Yuanqing Ye, Michelle A. Hildebrandt, Alison P. Klein, Scott M. Lippman, Xifeng Wu. Determinants and prognostic value of quality of life in patients with pancreatic ductal adenocarcinoma [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 3011.
Abstract 3015: Precise investigation of cancer stem cells in mouse glioblastoma
Authors: Xie Xuanhua P. , Laks Dan R. , Sun Daochun , Poran Asaf , Laughney Ashley M. , Belenguer German , Massague Joan , Zhou Xiuping , Farinas Isabel , Elemento Olivier , Parada Luis F.
Published: August 2018

In this study, we employ mouse models to investigate features and roles of cancer stem cells (CSCs) in glioblastoma (GBM). A nestin-TK-GFP transgene is firstly used to label CSCs in a fully penetrant mouse model of GBM (M7: hGFAP-Cre; Nf1fl/+; p53fl/fl; Ptenfl/+). Food-mediated ganciclovir (GCV) delivery kills proliferative transgene positive cells and significantly prolongs the lives of the transgene bearing mice. Isolation and transplantation of the tumor cells indicates the GFP+ cells are more tumorigenic than the GFP- cells. We then generate and characterize a novel transgene (CGD: nestin-CreERT2-H2BeGFP-hDTR) that labels all the neural stem/progenitor cells in the subventricular zone (SVZ). This transgene efficiently promotes brain tumors by eliminating tumor suppressor genes (CGD-M4: CGD; Nf1fl/+; p53fl/+; Ptenfl/+) in the corresponding cells. The CGD-GFP+ tumor cells are quiescent in vivo, yet form more spheres in vitro than the GFP- cells. The GFP+ cells are competent to develop tumors in a serial transplantation assay and constantly maintain a quiescent subpopulation pool in the newly formed tumors. Diphtheria toxin treatment ablates the CGD-GFP+ tumor cells and greatly reduces the tumor bulk. Temozolomide, the conventional chemotherapy for human GBM patients, benefits only mice transplanted with GFP- but not CGD-GFP+ tumor cells. Our study demonstrates the essential role of CSCs in GBM initiation, recurrence, and drug resistance. Further analysis of the CGD-GFP+ cells might delineate novel treatments for this deadly disease.

Citation Format: Xuanhua P. Xie, Dan R. Laks, Daochun Sun, Asaf Poran, Ashley M. Laughney, German Belenguer, Joan Massague, Xiuping Zhou, Isabel Farinas, Olivier Elemento, Luis F. Parada. Precise investigation of cancer stem cells in mouse glioblastoma [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 3015.
Abstract 3058: Data and resource sharing: Advancing our understanding of glioblastoma
Authors: Luchman Hema A. , Coutinho Fiona , Weiss Samuel , Consortium Stand Up to Cancer Stem Cell Dream Team , Dirks Peter
Published: August 2018

Glioblastoma multiforme (GBM), characterized by an aggressive clinical course, therapeutic resistance, and striking molecular heterogeneity, remains incurable. GBM has a median survival of only 12-15 months post-surgery in adults even with standard of care chemotherapy and radiation. Through a collaborative pan-Canadian Stand up to Cancer (SU2C) Stem Cell Dream Team effort, our group is focusing on brain tumour stem cells (BTSCs), a subpopulation of cells within tumours, which are hypothesized to drive tumour growth, relapse, and resistance to conventional chemotherapies. We are completing large-scale phenotypic cell biology, tumourigenicity, drug screening, and multi-platform ‘omic studies (genomics, bulk and single cell transcriptomics, epigenomics, metabolomics, proteomics, ATACseq) on a large number of adult GBM patient-derived BTSC cultures. Using both in vitro and in vivo approaches and the above multi-platform approaches, we are investigating the unique growth and stem cell characteristics of the BTSCs. In addition, we are using BTSC cultures to investigate drug response and genetic targeting approaches to identify new therapeutic strategies for clinical translation and understand mechanisms of resistance and recurrence. The wealth of information derived from this project is being integrated using systems biology approaches and will be shared in the public domain via data visualization and big data sharing platforms. Contemporaneously, we are depositing a number of well-characterized BTSC cultures in the American Type Culture Collection repository for unrestricted access to the scientific community. Our cross-Canada multi-disciplinary Cancer Stem Cell Dream Team, comprised of scientists, clinicians and patient advocates supports the ideal of data and resource sharing to help improve patient outcome for this devastating disease. Our goal is to provide the broader community of scientists, clinicians and patient groups an enduring resource and data sharing model to advance our understanding of glioblastoma.

Citation Format: Hema A. Luchman, Fiona Coutinho, Samuel Weiss, Stand Up to Cancer Stem Cell Dream Team Consortium, Peter Dirks. Data and resource sharing: Advancing our understanding of glioblastoma [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 3058.
Abstract 3060: EGFR-mediated interleukin enhancer-binding factor 3 contributes to formation and survival of cancer stem-like tumorspheres through regulating HER3/ERBB3 expression as a therapeutic target against EGFR-positive non-small cell lung cancer
Authors: Cheng Chun-Chia , Chou Kuei-Fang , Wu Cheng-Wen , Su Nai-Wen , Peng Cheng-Liang , Su Ying-Wen , Chang Jungshan , Ho Ai-Sheng , Lin Huan-Chau , Chen Caleb Gon-Shen , Chang Yu-Cheng , Lim Ken-Hong , Chang Yi-Fang
Published: August 2018

Objectives: YM155, an inhibitor of interleukin enhancer-binding factor 3 (ILF3), significantly suppresses cancer stemness property, implying that ILF3 contributes to cell survival of cancer stem cells. However, the molecular function of ILF3 inhibiting cancer stemness remain unclear. This study aimed to uncover the potential function of ILF3 involving in cell survival of epidermal growth factor receptor (EGFR)-positive lung stem-like cancer, and investigate the potential role to improve the efficacy of anti-EGFR therapeutics.

Materials and Methods: The regulated association of EGFR and ILF3 was investigated at first. ILF3 was knockdowned and RNAseq was utilized to search for the putative genes regulated by ILF3. Meanwhile, HCC827- and A549-derived cancer stem-like cells were used to investigate the role of ILF3 in the formation of cancer stem-like tumorspheres.

Results: We found that EGFR induced ILF3 expression, and YM155 reduced EGFR expression. The knockdown of ILF3 reduced not only EGFR expression in mRNA and protein levels, but also cell proliferation in vitro and in vivo, demonstrating that ILF3 was an oncoprotein contributing to cancer cell survival. Moreover, the knockdown and inhibition of ILF3 by shRNA and YM155, respectively, reduced the formation and survival of HCC827- and A549-derived tumorspheres through inhibiting HER3/ERBB3 expression, and synergized the therapeutic efficacy of afatinib, a tyrosine kinase inhibitor, against EGFR-positive A549 lung cells.

Conclusion: This study demonstrated that ILF3 played an oncogenic role maintaining the EGFR-mediated cellular pathway as a therapeutic target to improve the therapeutic efficacy of afatinib. Therefore, we suggested that YM155, an ILF3 inhibitor, was potential for utilization in cancer therapy against the EGFR-positive cancers.

Citation Format: Chun-Chia Cheng, Kuei-Fang Chou, Cheng-Wen Wu, Nai-Wen Su, Cheng-Liang Peng, Ying-Wen Su, Jungshan Chang, Ai-Sheng Ho, Huan-Chau Lin, Caleb Gon-Shen Chen, Yu-Cheng Chang, Ken-Hong Lim, Yi-Fang Chang. EGFR-mediated interleukin enhancer-binding factor 3 contributes to formation and survival of cancer stem-like tumorspheres through regulating HER3/ERBB3 expression as a therapeutic target against EGFR-positive non-small cell lung 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 3060.
Abstract 3068: Chronic alcohol exposure induces malignant transformation of pancreatic ductal epithelial cells and generates stem cell characteristics
Authors: Yu We , Ma Yiming , Shankar Sharmila , Srivastava Rakesh K.
Published: August 2018

Findings from epidemiologic studies and research with experimental animal models provide insights into alcohol toxicity-related disease pathogeneses. Epidemiologic data indicate that heavy drinking is associated with high risk of pancreatic cancer. However the molecular mechanisms by which chronic ethanol exposure changes pathophysiology of human pancreatic ductal epithelial (HPNE) cells is not well understood. Cancer stem cells (CSCs) play significant role in cellular transformation, and their emergence is responsible for cancer initiation, progression and metastasis. SATB2 is required for normal mammalian development; however, it is not expressed in normal adult cells. Inappropriate activation of SATB2 gene may cause malignant cellular transformation. SATB2 regulates transcription of pluripotency maintaining factors which are required for sustaining the stem cells capacity for self-renewal. The main goal of the paper is to examine the molecular mechanisms by which chronic alcohol consumption induces cellular transformation of HPNE cells. To investigate the role of SATB2 at an early step of cell transformation, we utilized HPNE cells to generate progenitor cells either by chronic ethanol exposure or overexpression with SATB2. Our data demonstrate that chronic exposure of HPNE cells to ethanol induces cellular transformation by upregulating SATB2. Furthermore, during ethanol-induced cell transformation, cells gain the phenotype of progenitor cells / CSCs and express pluripotency maintaining factors and epithelial-mesenchymal transition (EMT) markers. Suppression of SATB2 expression in ethanol-transformed HPNE cells inhibits stemness and EMT. SATB2 is highly expressed in pancreatic cancer tissues derived from human and KrasG12D mice. In conclusion, chronic ethanol exposure may contribute in pancreatic carcinogenesis by inducing the expression of SATB2 gene.

Citation Format: We Yu, Yiming Ma, Sharmila Shankar, Rakesh K. Srivastava. Chronic alcohol exposure induces malignant transformation of pancreatic ductal epithelial cells and generates stem cell characteristics [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 3068.