tbuckley/cabot-search huggingface dataset:
Abstract 1445: Understanding the 8q24 colorectal cancer risk locus via CRISPR/Cas9 scarless genome editing
Authors: Nicole Coggins, Jacob Stultz, David Segal, Luis Carvajal-Carmona
Journal: Cancer Research (2017)

Abstract Colorectal Cancer (CRC) is one of the leading causes of mortality in the US, being the third most common cancer among both men and women. While an exact cause of CRC has not yet been elucidated, the existence of a clear heritable genetic component has been established. With the recent surge of data from Genome-Wide Association Studies, a handful of CRC-associated loci have been identified, each containing numerous Single Nucleotide Polymorphisms (SNPs). We hypothesize that among the ~25 loci associated with increased risk for CRC, there are driver SNPs functioning to contribute to initiation or progression of CRC development. It is crucial, in order to enhance our understanding CRC tumorigenesis, to extract these functional variants from the pool of associated SNPs and validate their causative significance within the cell. To model these functional SNPs, we have developed a novel “scarless” isolation pipeline for selecting isogenic clones with the desired single-base edit without selection markers following CRISPR-Cas9 mediated HDR. With this pipeline, we have successfully modeled our first selected SNP, rs6983267, from the 8q24 risk locus in HCT-116 cells, producing the heterozygous genotype (G/T) from the parental homozygous risk (G/G) genotype. Rs6983267 is located within a known c-Myc enhancer and has been shown to exert risk-allele specific increase in enhancer activity. Oncogenic c-Myc is known to play a significant role in CRC pathogenesis. In line with previous studies, we observe a slight decrease in c-Myc expression in our heterozygous clones compared to wildtype homozygous risk. Moreover, we observe a preferential binding of the transcription factor in control of c-Myc transcriptional regulation, TCF7L2, to the risk allele over the reference allele while binding of proximal factors such as CTCF show no allelic preference. Interestingly, we also see significant changes in expression of target genes of the WNT signaling pathway. Dysregulation of WNT is a hallmark characteristic of CRC. These changes indicate there is indeed an effect of the risk allele of rs6983267 on overall WNT activity in CRC cells due to increased binding of transcription factor TCF7L2. This novel SNP editing pipeline provides a method to study precise effects of single base changes located anywhere in the genome. Utilizing it to model other risk SNPs will enable the enhancement of our current understanding of GWAS-identified risk loci in CRC pathogenesis at the molecular level. Citation Format: Nicole Coggins, Jacob Stultz, David Segal, Luis Carvajal-Carmona. Understanding the 8q24 colorectal cancer risk locus via CRISPR/Cas9 scarless genome editing [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 1445. doi:10.1158/1538-7445.AM2017-1445
Abstract 1365: Sensitivity of oncogenic KRAS to adenosine triphosphate suppression
Authors: Matthew Holderfield, Kanika Sharma
Journal: Cancer Research (2017)

Abstract KRAS proteins regulate many cellular processes including initiation of cell division in response to mitogens. Gain of function KRAS mutations appear in approximately 30% of all human cancers and activate effector signal transduction pathways independent of mitogenic stimuli. KRAS driven cancers also frequently have high metabolic rates and may have increased sensitivity to metabolic inhibitors but the underlying mechanism is not fully understood. In this study, we characterized the cellular mechanism of a small molecule inhibitor identified using a transgenic Drosophila melanogaster model that expresses human KRAS-G12V in the fly wing. The compound partially restored wing development in the KRAS-G12V flies and inhibited growth and signal transduction in multiple KRAS driven cancer cells and KRAS-G12V dependent MEF cells but not in MEF cells expressing BRAF-V600E. The compound also had a profound impact on mitochondrial function by inhibiting electron transport (ETC) complex I. Multiple other ETC or ATP synthase inhibitors similarly impaired oncogenic KRAS signal transduction. ATP production through glucose metabolism was sufficient to rescue KRAS function and cellular growth after ETC inhibition, suggesting that inhibition of MAPK signaling is due to low ATP levels rather than a direct consequence of ETC or complex I inhibition. These data indicate that oncogenic KRAS signal transduction requires high cellular ATP levels and suggests a synthetic lethal interaction between KRAS and multiple metabolic targets that could be exploited to target KRAS driven cancers. Citation Format: Matthew Holderfield, Kanika Sharma. Sensitivity of oncogenic KRAS to adenosine triphosphate suppression [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 1365. doi:10.1158/1538-7445.AM2017-1365
Abstract 4767: Identifying CDCA7 as a novel regulator of tumor-initiating cells in triple-negative breast cancer
Authors: Chang-Ching Lin, Miao-Chia Lo, Rebecca Moody, Nicholas Stevers, Samantha Tinsley, Max Wicha, Duxin Sun
Journal: Cancer Research (2017)

Abstract Tumor-initiating cells (TICs) are a small fraction of cancer cells that stands at the apex of the tumor hierarchy. Given their tumor-initiating ability and resistance to conventional chemotherapies, TICs are considered potential therapeutic targets for preventing the relapse and metastasis of malignancies. Our group has identified a novel gene, Cell division cycle associated 7 (CDCA7), as an important regulator of TICs in triple-negative breast cancer (TNBC). CDCA7 is a target gene of MYC and NOTCH. Ectopic expression of CDCA7 has been demonstrated to induce neoplastic transformation in vitro and tumorigenesis in vivo. Despite its potential tumor-initiating ability, CDCA7 has not yet been well-studied in breast cancer. We found that CDCA7 was highly expressed in TNBC compared to other subtypes of breast cancer according to the RNA-sequencing data from The Cancer Genome Atlas. Furthermore, our Kaplan-Meier analysis of multiple datasets demonstrated that higher expression of CDCA7 was associated with poor prognosis in breast cancer. When we knocked down CDCA7 by siRNA in TNBC cell lines including SUM149, HCC1937, MDA-MB-231, and MDA-MB-436, CD44+/CD24- stem-like cell population and primary and secondary mammosphere formation were significantly decreased. In addition to suppressing the stem-like properties, knockdown of CDCA7 also inhibited the invasion and migration of breast cancer cells. These phenotypes indicated the inhibition of epithelial-to-mesenchymal transition (EMT), which was in accordance with the up-regulation of E-Cadherin and down-regulation of Vimentin after CDCA7 knockdown in TNBC cell lines. In conclusion, our results have demonstrated that CDCA7 is an important regulator of TICs in TNBC. Loss-of-function of CDCA7 leads to the inhibition of EMT and stemness in TNBC cells. Citation Format: Chang-Ching Lin, Miao-Chia Lo, Rebecca Moody, Nicholas Stevers, Samantha Tinsley, Max Wicha, Duxin Sun. Identifying CDCA7 as a novel regulator of tumor-initiating cells 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 4767. doi:10.1158/1538-7445.AM2017-4767
Abstract 2895: Octamer-4/microRNA-1246 signaling axis drives Wnt/β-catenin activation in liver cancer stem cells
Authors: Stella Chai, Kai-Yu Ng, Man Tong, Eunice Y. Lau, Terence K. Lee, Kwok Wah Chan, Yun Fei Yuan, Tan To Cheung, Siu Tim Cheung, Xiao Qi Wang, Nathalie Wong, Chung Mau Lo, Kwan Man, Xin Yuan Guan, Stephanie K. Ma
Journal: Cancer Research (2017)

Abstract Hepatocellular carcinoma (HCC), the main type of liver cancer in human, is one of the most prevalent and deadly malignancies in the world. Despite advances in therapy, prognosis remains dismal, largely attributed by our limited understanding on information related to the progressive development of the disease, particularly in their cancer-initiating and stem cell-like properties. Wnt/β-catenin signaling is activated in CD133 liver cancer stem cells (CSC), a subset of cells known to be a root of tumor recurrence and therapy resistance in HCC. However, the regulatory mechanism of this pathway in CSCs remains unclear. Here, we show that human miRNA, miR-1246, promotes cancer stemness including self-renewal, drug resistance, tumorigencity and metastasis by activation of Wnt/β-catenin pathway via suppressing the expression of AXIN2 and GSK3β, two key members of the β-catenin destruction complex. This observation was validated by both in vitro and in vivo functional / cell biological studies on HCC cell lines with or without miR-1246 expression modulated by lentiviral based knockdown and overexpression strategies as well as in miR-1246 repressed HCC cells with concomitant expression of wild-type or constitutively active β-catenin. Clinically, high endogenous and circulating miR-1246 was identified in HCC clinical samples and correlated with a worse prognosis. Further functional analysis identified Oct4 to be the direct upstream regulator of miR-1246, which cooperatively drive β-catenin activation in liver CSCs. In conclusion, our findings not only uncover the non-canonical regulation of Wnt/β-catenin in liver CSCs by Oct4/miR-1246 signaling axis, but also provide a novel diagnostic marker as well as therapeutic intervention for HCC. Citation Format: Stella Chai, Kai-Yu Ng, Man Tong, Eunice Y. Lau, Terence K. Lee, Kwok Wah Chan, Yun Fei Yuan, Tan To Cheung, Siu Tim Cheung, Xiao Qi Wang, Nathalie Wong, Chung Mau Lo, Kwan Man, Xin Yuan Guan, Stephanie K. Ma. Octamer-4/microRNA-1246 signaling axis drives Wnt/β-catenin activation in liver cancer stem cells [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 2895. doi:10.1158/1538-7445.AM2017-2895
Abstract 4612: Development and validation of a screening platform for the identification of novel immuno-oncology targets
Authors: Ariane Scoumanne, Virginie Rabolli, Lea Legrand, Murielle Martini, marie-claire Letellier, Stefano Crosignani, Christophe Quéva, Michel Detheux, Sandra Cauwenberghs, Jakub Swiercz
Journal: Cancer Research (2017)

Abstract Although immune therapy of cancer, including immune-checkpoint blockade have demonstrated therapeutic benefit in patients with various advanced cancers, further understanding of human immune pathology triggered by the tumor microenvironment, is essential to improve these therapeutic approaches. In order to shed light on novel immune suppressive mechanisms in tumor, iTeos Therapeutics developed a target discovery and drug repurposing platform based on phenotypic screening assays. We established a co-culture assay combining tumor immune suppressive cells and T-cells. This assay is flexible to allow the screening of chemicogenomics, shRNA and cDNA libraries. Multi-parameter readouts are combined to assess both T cell activation and proliferation, through high content imaging of T cell clusters formation, complemented with detection of IFNγ secretion and tumor cell death, as assessed using a cytotoxicity assay. The 96-well format of the assay allows medium-throughput testing of up to 3000 samples/screen. From the technical point of view we were able to adapt the assay to low level of automation, making it affordable to the biotech start-ups and academic laboratories. As a proof-of-concept we evaluated the assay for its ability to detect metabolic immune-oncology targets in A549 cells, a lung cancer immune suppressive cell line. A549 express indoleamine-2,3-dioxygenase 1 (IDO1), an enzyme expressed in many cancers that mediates local T-cell suppression through depleting the essential amino acid tryptophan. The assay conditions were validated with an IDO1 inhibitor as positive control and subsequently scaled up for automation. A commercially available small molecule library of 1900 compounds, with a high percentage of clinically tested drugs was screened. The library was tested at two different concentrations (0.3μM and 3μM), with two independent T-cell donors and spiked with IDO1 inhibitor as control. Combined analysis of T-cell activity and tumor killing led to the identification of 42 compounds with activity on multiple, potential immune suppressive pathways, including metabolism, epigenetics, autophagy, TGFβ, Wnt/β-catenin and TNFα/NF-κB signaling. Citation Format: Ariane Scoumanne, Virginie Rabolli, Lea Legrand, Murielle Martini, marie-claire Letellier, Stefano Crosignani, Christophe Quéva, Michel Detheux, Sandra Cauwenberghs, Jakub Swiercz. Development and validation of a screening platform for the identification of novel immuno-oncology targets [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 4612. doi:10.1158/1538-7445.AM2017-4612
Nectin-3 suppresses the invasive nature of human prostate cancer cells
Authors: Tracey A. Martin, Gareth Watkins, Wen G. Jiang, Malcom D. Mason
Journal: Cancer Research (2005)

950  Background: Nectin-3 is a member of the Nectin family of integral molecules belonging to the Ig superfamily. They are involved in the formation of functioning Adherens and Tight Junctions. Aberrant expression of Nectins’ is associated with cancer. This study aimed to ascertain the distribution of Nectin-3 in human prostate cancer, and the effect of introducing the Nectin-3 gene into human prostate cancer cells. Methods: 42 human cancer cell lines were screened for expression of Nectin-3. An invasive prostate cell line, PC-3 (PC-3WT) which exhibited aberrant Nectin-3 expression was chosen for introduction of the Nectin-3 gene (PC-3N3). The gene, after amplification from normal bladder cDNA was cloned into a pEF6/V5-His TOPO plasmid before electroporation. Expression of the protein was confirmed by RT-PCR, Western blotting and fluorescent microscopy. Functional testing was carried out using cell invasion and cell adhesion assays. Immunohistochemistry was also performed on all 42 cell lines together with 5 paired prostate tumour/normal tissues, to determine the distribution of Nectin-3 in prostate cancer. Results: 41 of the cancer cell lines screened showed aberrant expression for Nectin-3. Following transformation of the prostate cancer cells with the Nectin-3 gene the presence of the gene was demonstrated by the presence of mRNA expression and by the protein signal clearly observable at the cell-cell membrane. Nectin-3 transformed cells (PC-3N3) showed retarded invasion, even when treated with HGF (25 ng/ml) compared to PC-3WT cells (PC-3N3untreated 0.05±0.003 RFU, HGF treated 0.04.33±0.008; PC-3WT untreated 0.06±0.006, HGF treated 0.08±0.002). Invasion was significantly different between PC-3N3 and PC-3WT cells; HGF induced a significantly higher invasive pattern for both (p
Abstract 3467: A DAXX-KIFC3 fusion potentiates alternative lengthening of telomeres in osteosarcoma
Authors: Sarah F. Clatterbuck Soper, Soyeon A. Showman, Kathryn E. Driest, Joshua J. Waterfall, Robert L. Walker, Marbin A. Pineda, Yuelin J. Zhu, Yonghong Wang, Corbin D. Ester, Sven Bilke, Paul S. Meltzer
Journal: Cancer Research (2017)

Abstract Proliferating cells must enact a program of telomere lengthening to counteract the chromosome end replication problem. In most types of cancer cells, telomeres are maintained through the action of the ribonucleoprotein telomerase, but some cancer cells, particularly those of mesenchymal origin, utilize an alternative method of telomere repair and lengthening termed the alternative lengthening of telomeres (ALT) pathway. Since telomere maintenance is essential for tumor cell immortality, better understanding of the ALT mechanism could potentially reveal drug targets that could be used to develop novel therapies for tumors that use ALT. It has been previously observed that ALT tumors frequently carry mutations in ATRX, which partners with the protein DAXX in a chromatin remodeling complex, but how these mutations facilitate the ALT pathway is not well understood. Work in our lab identified an ALT-positive osteosarcoma cell line, identified here as OS1, in which DAXX has undergone a fusion event with the non-canonical kinesin KIFC3. We find that knockdown of the DAXX-KIFC3 fusion neither impairs ALT nor cell proliferation, suggesting that the fusion represents a loss of function. Furthermore, inducible restoration of wild-type DAXX, reversibly abrogates ALT function in this cell line. One of the hallmarks of ALT is localization of telomeres and DNA recombination machinery to nuclear PML bodies, resulting in formation of ALT- associated PML Bodies, or APBs. Thus it may be considered that changes in PML body composition represent a key aspect of the ALT mechanism. We observe that in OS1 both DAXX and ATRX fail to localize to PML bodies. This finding is consistent with the fact that the DAXX-KIFC3 fusion results in loss of a C-terminal SUMO interaction motif that normally mediates PML body interaction. Leveraging our inducible system, using biochemical and imaging approaches, we are working to define the role of DAXX in maintaining PML body composition. Citation Format: Sarah F. Clatterbuck Soper, Soyeon A. Showman, Kathryn E. Driest, Joshua J. Waterfall, Robert L. Walker, Marbin A. Pineda, Yuelin J. Zhu, Yonghong Wang, Corbin D. Ester, Sven Bilke, Paul S. Meltzer. A DAXX-KIFC3 fusion potentiates alternative lengthening of telomeres in osteosarcoma [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 3467. doi:10.1158/1538-7445.AM2017-3467
Abstract 1738: Platelet activation and heterotypic platelet leukocyte conjugate formation in the blood of glioblastoma patients
Authors: Sascha Marx, Maximilian Splittstöhser, Heiko Paland, Carolin Seifert, Madlen Juettner, Andreas Boehm, Christoph A. Ritter, Sandra Bien-Moeller, Henry W. Schroeder, Bernhard Rauch
Journal: Cancer Research (2017)

Abstract Objective Glioblastoma patients (GBM) suffer from an increased incidence of cardiovascular events. Platelets are well known as main player of the primary hemostasis, but have a broad range of additional functions. The formation of heterotypic conjugates between platelets and leukocytes (PLC) represents a pro-inflammatory surrogate marker and is usually increased after platelet activation. The aim of the present study was to evaluate the platelet activation status and the rate of circulating PLC in GBM. Methods Blood samples were drawn of consecutive patients before surgery for a suspected glioblastoma. The formation of PLC and several parameters of platelet activation were determined by flow cytometry before and after stimulation with either ADP or the thrombin receptor-activating peptide (TRAP) in vitro: expression of P-Selectin, CD63, CD40L and fibrinogen-binding to the activated GPIIb/ IIIa. Blood samples from age and gender matched healthy volunteers were used as controls. Statistical analysis was done with the Mann-Whitney-Test. Results Final analysis included 22 patients with histopathological proven virgin glioblastoma (9f, 13m, mean age 67.5 years, range from 55 to 86 years) and their respective controls. Basal platelet activation and in vitro platelet reactivity was increased in GBM. The difference got significant in the basal expression of CD63 (2.8% versus 1.9%, p=0.008), the Fibrinogen-binding after ADP-stimulation (110.3 MFI versus 63.1 MFI, p=0.04) and the CD63 expression after TRAP-stimulation (38.4% versus 33.3%, p=0.04). Furthermore, a reduced number of circulating PLC and in vitro PLC formation was seen in GBM without getting statistically significant. Conclusions In this preliminary report, we show for the first time an increased level of platelet activation and agonist-induced platelet reactivity in GBM. Both could be a reflection of the pro-thrombotic status in these patients. Interestingly, the formation of PLC was not increased, but in tendency decreased. Whether this observation potentially mirrors the intratumoral, anti-inflammatory microenviroment in GBM remains unclear. Citation Format: Sascha Marx, Maximilian Splittstöhser, Heiko Paland, Carolin Seifert, Madlen Juettner, Andreas Boehm, Christoph A. Ritter, Sandra Bien-Moeller, Henry W. Schroeder, Bernhard Rauch. Platelet activation and heterotypic platelet leukocyte conjugate formation in the blood of glioblastoma patients [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 1738. doi:10.1158/1538-7445.AM2017-1738
Abstract 2784: Identifying biomarkers to predict cardiotoxicity of doxorubicin in individual patients
Authors: Liqun Zhao, Baolin Zhang
Journal: Cancer Research (2017)

Abstract Doxorubicin is a highly effective anticancer agent but causes cardiotoxicity in many patients. This study aims to identify biomarkers to predict potential cardiotoxicity before the onset of cardiac tissue damage and dysfunction in individual cancer patients. First, we established a human cellular system to model the cardiac toxicity of oncology drugs using human induced pluripotent stem cells-derived cardiomyocytes (iPS-CMs). We tested a panel of clinically used drugs including anthracyclines (doxorubicin, daunorubicin, epirubicin and idarubicin), 5-FU, Taxol, Trastuzumab, and tyrosine kinase inhibitors (sunitinb, imatinib, and sorafinib). These drugs displayed varying degrees of cytotoxicity in iPS-CMs which are generally consistent with their known cardiotoxicity patterns. Second, we found that doxorubicin selectively upregulated the expression of death receptors in iPS-CMs. As a result, the treated iPS-CMs underwent spontaneous apoptosis that was further enhanced in the presence of specific cytokines. Based on these findings, we hypothesize that the baseline levels of the predefined cytokines in blood could be predictive of cardiotoxicity associated with doxorubicin treatment in individual patients. We are currently investigating the relationships between the levels of the predefined cytokine signature in blood and cardiac events in patients who received doxorubicin or related anthracycline therapy. Citation Format: Liqun Zhao, Baolin Zhang. Identifying biomarkers to predict cardiotoxicity of doxorubicin in individual patients [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 2784. doi:10.1158/1538-7445.AM2017-2784