tbuckley/cabot-search huggingface dataset:
Abstract 2326: A high-throughput screen identified cancer selective small molecules that kill independent of mitochondrial apoptosis
Authors: Catriona M. Dowling, Micheal Hemann, James Bradner, Anthony Letai, Triona Ni Chonghaile
Journal: Cancer Research (2017)

Abstract Triple negative breast cancer (TNBC) lacks expression of oestrogen receptor (ER), progesterone receptor (PR) and human epidermal growth factor 2 (HER2). Importantly, there have been fewer advances in the treatment of TNBC with the mainstay of treatment being cytotoxic chemotherapy. All too often though tumor responds poorly to chemotherapy, or relapse and resistance follow an initial response. We previously found in a range of hematological and solid tumors that chemoresistant cancers are far from the mitochondrial apoptotic threshold. To identify novel therapeutics for the treatment of chemoresistant breast cancer, we performed a high-throughput screen to identify small molecules that are cancer selective but can kill independent of the mitochondrial pathway of apoptosis. To perform this screen we used TNBC line MDA-MB-231 in which the pro-death proteins BAX/BAK were knocked down. BAX/BAK are essential for mitochondrial apoptosis. To enrich for compounds that were not non-specifically toxic, we simultaneously counter-screened against the non-transformed breast epithelial cell line MCF10a. We screened a total of 30,000 compounds in duplicate across the two cell lines. There was a hit rate of 0.3% in the screen and 85 compounds were retested in the validation cherry pick screen. From the cherry pick screen 18 compounds were further validated with low-throughput assessment for mitochondrial independent killing and selectivity for cancer cells. To identify the mechanism of action of the lead compound we used a genetic approach to generate an RNAi signature for the compound. This signature enables classification of the compound into known or novel class of compounds. The lead compound signature was most like that of histone deacetylase inhibitors (HDAC). Using an in vitro HDAC inhibitor screen, we identified that the compound selectively inhibited HDAC6. Importantly, we validated that the lead compound caused an increase in acetylated tubulin in cells, a target of HDAC6. In conclusion, we have identified a novel HDAC6 specific inhibitor that selectively kills cancer cells independent of mitochondrial apoptosis. Citation Format: Catriona M. Dowling, Micheal Hemann, James Bradner, Anthony Letai, Triona Ni Chonghaile. A high-throughput screen identified cancer selective small molecules that kill independent of mitochondrial apoptosis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2326. doi:10.1158/1538-7445.AM2017-2326
Abstract LB-216: Stroma-induced up-regulation of discoidin domain receptor 1 enhances peritoneal metastasis of gastric carcinomas
Authors: Hyejin Jin, In-Hye Ham, Hye Jung Oh, Dakeun Lee, Sang-Uk Han, Rolf A. Brekken, Hoon Hur
Journal: Cancer Research (2017)

Abstract Introduction: Discoidin domain receptor-1 (DDR1), a receptor tyrosine kinase, is expressed by about 50% of gastric tumor cells in previous our study and is activated by fibrillar collagens, which are major components of tumor stroma. Further, it has been proposed that peritoneal metastasis is associated with high stroma content in gastric carcinomas (GCs). In this study we investigated the contribution of DDR1 activity to peritoneal metastasis of GCs. Methods: We performed the immunohistochemistry for DDR1 and Masson’s trichrome staining for accumulation of collagen bundles in 202 human GC tissues. The human GC cell lines (MKN-28 and KATO-III) were co-cultured with GCs-associated fibroblasts (CAFs), and the expression of DDR1 and signal transduction pathways were investigated by Western blot. We evaluated CAF-induced tumorigenesis of GCs cell lines and the effects of DDR1 specific inhibitor in 3D co-culture system and peritoneal seeding in xenograft animal models. Results: High stromal collagen correlated with peritoneal recurrence (P=0.004) and was positively associated with expression of DDR1 in GC tissues (P&amp;lt;0.001). We confirmed that co-culture with CAFs elevated the expression of DDR1 in GC cell lines. CAFs also enhanced GC cell line spheroid formation in vitro in a tumor cell DDR1-dependent manner. Co-implantation of CAFs with GC cells enhanced peritoneal tumor formation in vivo, an effect that was sensitive to pharmacologic inhibition of DDR1. Conclusion: Our findings suggest that CAF-induced elevation of tumor cells DDR1 enhances peritoneal tumorigenesis of GCs and the inhibition of DDR1 signaling is an attractive strategy for the treatment of GC peritoneal metastasis. Citation Format: Hyejin Jin, In-Hye Ham, Hye Jung Oh, Dakeun Lee, Sang-Uk Han, Rolf A. Brekken, Hoon Hur. Stroma-induced up-regulation of discoidin domain receptor 1 enhances peritoneal metastasis of gastric carcinomas [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr LB-216. doi:10.1158/1538-7445.AM2017-LB-216
Abstract 1514: A novel approach for targeting androgen receptor signaling axis in prostate cancer
Authors: Salma Kaochar, Christopher Foley, Cristian Coarfa, Nicholas Mitsiades
Journal: Cancer Research (2017)

Abstract Background and Objectives: The androgen receptor (AR) is a ligand-activated transcription factor (TF) that plays critical oncogenic roles. Medical castration therapy is the mainstay treatment for advanced PrCa, but the AR signaling axis frequently remains active in castration-resistant PrCa (CRPC). Despite advances in AR targeting with abiraterone and enzalutamide, disease progression re-occurs in the form of CRPCs that still express AR-dependent genes. This highlights the need for novel approaches to block AR signaling and CRPC growth. The GATA family of TFs contains six members in mammals, all of which bind a consensus DNA sequence (A/T)GATA(A/G) to regulate gene expression. GATA2 is the predominant family member in prostate luminal epithelial cells. In a search for TFs that control AR expression, we found that GATA2 induces AR gene expression as well as promotes the recruitment of coactivators to the AR transcriptional complex. We found that GATA2 protein expression was strongly correlated with AR protein expression (Spearman's correlation coefficient: 0.323, p-value &amp;lt;0.0001) in our PrCa specimens (n=383). The intensity of GATA2 immunostaining in our BCM patient cohort positively correlated with Gleason score (R=0.37, p-value &amp;lt;0.01) and was a significant predictor of biochemical recurrence (p-value &amp;lt;0.001). We also demonstrated that GATA2 directly promotes expression of both full-length and AR splice-variant, resulting in a strong positive correlation between GATA2 and AR expression in both PrCa cell lines and patient specimens. Conversely, GATA2 expression is repressed by androgen and AR, suggesting a negative feedback regulatory loop that, upon androgen deprivation, derepresses GATA2 to contribute to AR overexpression in CRPC. Simultaneously, GATA2 is necessary for optimal transcriptional activity of both full-length and AR splice-variants. Using ChIP-Seq we found that GATA2 colocalizes with AR and Forkhead box protein A1 (FOXA1) on chromatin to enhance recruitment of steroid receptor coactivators (SRC1, SRC2, and SRC3) and formation of the transcriptional holocomplex. Lastly, we identified a GATA2 small molecule inhibitor (SMI) that can suppress the expression and transcriptional function of both full-length and splice-variant AR and exerted potent anticancer activity against PrCa cell lines. We propose that the inhibition of GATA2 is a ‘first-in-field’ approach to target AR expression and function, including ligand-independent AR, for the treatment of CRPC. Citation Format: Salma Kaochar, Christopher Foley, Cristian Coarfa, Nicholas Mitsiades. A novel approach for targeting androgen receptor signaling axis in prostate cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1514. doi:10.1158/1538-7445.AM2017-1514
Number faculty is alive and kicking: On number discriminations and number neurons
Authors: Andreas Nieder
Journal: Behavioral and Brain Sciences (2017)

Abstract Leibovich et al. advocate for a single “sense of magnitude” to which a dedicated faculty for number could allegedly be reduced. This conclusion is unjustified as the authors adopt an unnecessarily narrow definition of “number sense,” neglect studies that demonstrate non-symbolic numerosity representation, and furthermore ignore abstract number representations in the brain.
Abstract 1208: Analysis of the combinatorial antiproliferative effect of pan RAF inhibitor AZ-628 and MEK1-inhibitor AZD-6244 on a large panel of tumor cell lines
Authors: Alokta Chakrabarti, Daniel Feger, Sarah Umber, Orysya Stus, Marianne Birkle, Oliver Siedentopf, Jan E. Ehlert
Journal: Cancer Research (2017)

Abstract Cancer is a highly complex, multigenic disease with tumor cells underlying constant transition. Single drug treatments against specific targets frequently result in only partial success because mutations and redundant pathways cause drug resistance. Therefore, drug combinations that effect different synergistically acting targets in the cancer cell in parallel have become a promising strategy to improve the success in many fields of cancer therapy. One example for such an approach is the co-treatment of B-Raf driven tumors with Raf and MEK1 inhibitors. In our study, we determined the combinatorial effect of the pan-Raf inhibitor AZ-628 and the MEK1 inhibitor AZD-6244 on the viability of a large panel of more than 100 tumor cell lines. Whittaker et al. (Mol.CancerTher, 2015) could already show that this drug combination has a significant synergistic effect in several melanoma and colon cancer cell lines. The authors showed evidence that synergistic activity was correlated with enhanced mutation-triggered RAS/RAF/MAPK signaling with a special role for C-Raf in resistance due to a negative feedback mechanism. We here applied the combination of AZD-6244 and AZ-628 in a broad checkerboard pattern to a multitude of cell lines from other entities beyond melanoma and colorectal cancer. Based on these results we correlated the observed synergistic and non-synergistic effects with gene expression profiles of these cell lines and analyzed the requirement of a MAPK activating signaling. Our approach revealed that synergistic activity is not confined to melanoma and colon cancer but is observed in tumors from other entities as well. This observation may expand the usefulness of MEK/Raf inhibitor co-treatment to a larger panel of cancer types. Citation Format: Alokta Chakrabarti, Daniel Feger, Sarah Umber, Orysya Stus, Marianne Birkle, Oliver Siedentopf, Jan E. Ehlert. Analysis of the combinatorial antiproliferative effect of pan RAF inhibitor AZ-628 and MEK1-inhibitor AZD-6244 on a large panel of tumor cell lines [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1208. doi:10.1158/1538-7445.AM2017-1208
Abstract 5540: Transcriptional control of signaling pathways in T-cell lymphoblastic leukemia by Ikaros tumor suppressor
Authors: Tommy Hu, Mario Soliman, Malika Kapadia, Elanora Dovat, Jonathan Payne, Chunhua Song, Sinisa Dovat
Journal: Cancer Research (2017)

Abstract Cellular proliferation in T-cell acute lymphoblastic leukemia is regulated by multiple signaling pathways. The Phosphoinositide 3-kinase (PI3K)/AKT pathway is frequently dysregulated in T-ALL. Targeting the PI3K pathway has shown promise as a novel therapeutic approach for T-ALL. However, regulation of the PI3K pathway is still not well understood. Here, we report that PI3K activity in T-ALL can be controlled by transcriptional regulation of key members of this pathway, PIK3CD and PIKFYVE. DNA binding analysis of primary T-ALL using qChIP revealed that the tumor suppressor protein, Ikaros, binds the promoter regions of PIK3CD and PIKFYVE. Since Ikaros acts as a regulator of transcription, we tested whether Ikaros binding to PIK3CD and PIKFYVE affects their expression. Overexpression of Ikaros results in reduced transcription of PIK3CD and PIKFYVE in T-ALL. Targeting Ikaros with a specific shRNA, resulted in increased transcription of PIK3CD and PIKFYVE in T-ALL. Together, these results demonstrate that Ikaros functions as a transcriptional repressor of both PIK3CD and PIKFYVE, and suggest that Ikaros can regulate the PI3K pathway in T-ALL. It has been previously shown that Ikaros function in B-cell acute lymphoblastic leukemia is regulated by oncogenic Casein Kinase II (CK2). We tested whether Ikaros ability to repress transcription of PIK3CD and PIKFYVE is regulated by CK2. Inhibition of CK2 by a specific pharmacological inhibitor, CX-4945, resulted in increased Ikaros binding to the promoters of PIK3CD and PIKFYVE, as well as in transcriptional repression of both of these genes. These results suggest that Ikaros function as a repressor of PIK3CD and PIKFYVE transcription is impaired by CK2 in T-ALL. CK2 inhibition restores Ikaros-mediated transcriptional repression of PIK3CD and PIKFYVE, which results in downregulation of the PI3K pathway. In conclusion, the presented data demonstrate that the PI3K signaling pathway is regulated by transcriptional repression of PIK3CD and PIKFYVE by Ikaros in T-ALL. Results reveal interplay between two signaling pathways in T-ALL, CK2 and PI3K, where CK2 positively regulates the PI3K pathway by inhibiting Ikaros function. These data reveal novel mechanisms that regulate cellular proliferation in T-ALL. Citation Format: Tommy Hu, Mario Soliman, Malika Kapadia, Elanora Dovat, Jonathan Payne, Chunhua Song, Sinisa Dovat. Transcriptional control of signaling pathways in T-cell lymphoblastic leukemia by Ikaros tumor suppressor [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5540. doi:10.1158/1538-7445.AM2017-5540
Abstract 4556: MEDI5395: An armed oncolytic Newcastle disease virus
Authors: Danielle Carroll, James Harper, Travers Jon, Shannon Burke, Ruth Franks, Christel Navarro, Xing Cheng, Robert Wilkinson, Hong Jin
Journal: Cancer Research (2017)

Abstract Oncolytic viruses are live, replication-competent viruses that infect and/or replicate selectively in tumour cells leading to the destruction of the infected cell. Cell lysis occurs as a natural consequence of the viral life cycle and released virions can infect and kill neighbouring tumour cells leading to an amplified therapeutic effect. Oncolysis has the added benefit of releasing multiple tumour antigens that may further induce an immune-mediated therapeutic response. Newcastle Disease Virus (NDV) is an avian paramyxovirus, which has proven safety and demonstrated efficacy against a variety of preclinical cancer models and in PhI clinical studies as an oncolytic agent, oncolysate or whole cell vaccine. Using reverse genetics, we have generated a recombinant strain of NDV that overcomes environmental and regulatory concerns uncoupling oncolytic potency and avian pathogenicity. Furthermore we have enhanced the immune modulatory properties of NDV by engineering the virus to express granulocyte/macrophage colony-stimulating factor (GM-CSF). We have evaluated the biological characteristics of recNDVGM-CSF (MEDI5395) in vivo and in vitro. MEDI5395 selectively replicates in and kills a wide variety of human and mouse tumour cell lines. Additionally infection of cancer cells with MEDI5395 results in the increased production and secretion of pro-inflammatory cytokines and chemokines which are able to recruit mediators of both the innate and adaptive immune responses. MEDI5395 is a potent activator of the type I interferon response. In vivo, using a range of syngeneic and xenograft models we have demonstrated that NDV treatment has robust anti-tumour activity. In a HT1080 fibrosarcoma xenograft model a single administration (intra-tumoural or systemic) was able to cure 80% of tumour bearing mice. In syngeneic mouse tumour models, which support minimal viral replication MEDI5395 treatment causes significant changes in the local immune suppressive microenvironment and results in long-lasting anti-tumour immune responses. These responses are further enhanced in models that permit greater replication and also when combined with immune checkpoint blockade. The inherent properties of NDV (self-propagation, tumour-selective replication, and immunostimulatory properties) coupled with the ability to genetically engineer NDV to express therapeutic transgenes may provide a multi-modal attack on the tumour, delivering greater benefit to patients. Citation Format: Danielle Carroll, James Harper, Travers Jon, Shannon Burke, Ruth Franks, Christel Navarro, Xing Cheng, Robert Wilkinson, Hong Jin. MEDI5395: An armed oncolytic Newcastle disease virus [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4556. doi:10.1158/1538-7445.AM2017-4556
Abstract 1319: Epigenome-wide association study reveals differential DNA methylation consistent with progression of multiple myeloma
Authors: Stephen D. Gragg, Devin Absher, Xiangqin Cui, Christina Pillion, Richard Myers, Shaji Kumar, Luciano Costa, Brian Chiu, Celine Vachon, Elizabeth Brown
Journal: Cancer Research (2017)

Abstract Purpose: Multiple myeloma (MM) is the second most common hematological malignancy in the US. It is characterized by a clonal expansion of plasma cells in the bone marrow and extramedullary sites and is preceded by two precursor conditions including monoclonal gammopathy of undetermined significance (MGUS) and smoldering myeloma (SMM). Strong evidence suggests a germline and environmental etiology. However, efforts to characterize heritable changes in gene activity, such as DNA methylation, have not been widely reported. Methods: We examined epigenome-wide DNA methylation as markers of MGUS, SMM and MM in peripheral blood obtained from treatment-naïve European American cases with heavy-chain IgG or IgA MGUS (n=60), SMM (n=31) and MM (n=54) and age- and sex-matched controls (n=79) included from the University of Alabama at Birmingham, University of Chicago and the Mayo Clinic, Rochester [54.5% males; mean age, 64 years (range, 36 to 86)]. We quantified DNA methylation of over 450,000 CpG and non-CpG loci using the Infinium HumanMethylation450 array (Illumina). Differentially methylated positions were calculated using a general linear model framework adjusted for confounders and cellular heterogeneity. Results: A total of 6 CpGs were differentially methylated in MM cases compared to controls at a level of genome-wide statistical significance. MM was associated with hypomethylation at differentially methylated positions inside SBNO2 (P=3.37x10-10), WIZ (P=1.12x10-8), CA6 (P=4.29x10-8) and ADORA1 (P=3.68x10-8) as well as intergenic positions proximal to TNFRSF8 (Chr 1p36.22; P=2.24x10-9) and ENDOV (Chr 17q25.3; P=2.74x10-8). Each of these loci, with the exception of CA6 and ADORA1, were hypomethylated in each of the 3 plasma cell dyscrasia phenotypes including MGUS and SMM and MM cases compared to controls (P&amp;lt;0.03), albeit not at a level of genome-wide statistical significance. Conclusions: These preliminary findings suggest that differences in DNA methylation may contribute to altered risk of MM, as well as its precursor conditions, and may play a role in plasma cell dyscrasia progression as a consequence of heritable changes in gene activity due to past exposures. Replication in a large yet similarly well-characterized population is warranted. Citation Format: Stephen D. Gragg, Devin Absher, Xiangqin Cui, Christina Pillion, Richard Myers, Shaji Kumar, Luciano Costa, Brian Chiu, Celine Vachon, Elizabeth Brown. Epigenome-wide association study reveals differential DNA methylation consistent with progression of multiple myeloma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1319. doi:10.1158/1538-7445.AM2017-1319
Abstract 420: Preclinical evaluation of the SF3B1 inhibitor E7107 in triple negative breast cancer
Authors: Praveen Sridhar, Stefanie Chan, Ying-Jie Lock, Fabio Petrocca
Journal: Cancer Research (2017)

Abstract Triple-negative breast cancers (TNBC) are the most aggressive subtype of breast cancer and account for roughly 15% of human breast cancers. No effective targeted therapies are currently available against these tumors, at least in part due to their genetic and epigenetic heterogeneity. Yet, TNBCs are commonly enriched for cells arrested in a progenitor-like state. We therefore performed a genome-wide siRNA lethality screen to identify selective TNBC dependencies associated with this particular phenotype in vitro. These studies led to the identification of several spliceosome genes, including the core splicing factor SF3B1, as selectively and recurrently essential for progenitor-like (or basal-A) TNBC cell lines. On this basis, we examined the antitumor effect of E7107, a clinically tested SF3B1 inhibitor, on multiple TNBC cell lines. In vitro, treatment with E7107 for 24-48 hr selectively killed basal-A cell lines relative to differentiated luminal cell lines, decreasing viability by ≈40% or more in 5 of 6 basal-A lines tested. E7107-treated cells appeared to die of apoptosis based on immunoblotting for multiple apoptotic markers. In mice, E7107 (5 mg/kg i.v. for 4 consecutive days) suppressed the growth of preformed tumors by ≈80% and ≈50% in 2 different cell-line-derived xenograft models and was remarkably well-tolerated at this dose. Of note, tumor response in vivo closely mirrored cell sensitivity in vitro, suggesting that in vitro analysis provides a fair estimate of TNBC response to E7107 in mice. Amongst 2 additional patient-derived xenograft (PDX) models tested, E7107 inhibited tumor growth by ≈50% in one model. Thus, E7107 was therapeutically active against 3 of 4 xenograft models tested. Preliminary mechanistic studies in vitro and in vivo pointed to MCL1 inactivation as a major mechanism of action of E7107 in top responders. Together, these data suggest that the spliceosome is a druggable target in TNBC, and that E7107 or similar SF3B1 inhibitors could be effective in a TNBC subset that needs to be further defined. Citation Format: Praveen Sridhar, Stefanie Chan, Ying-Jie Lock, Fabio Petrocca. Preclinical evaluation of the SF3B1 inhibitor E7107 in triple negative breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 420. doi:10.1158/1538-7445.AM2017-420