tbuckley/cabot-search huggingface dataset:
Abstract 1403: PCNA-dependent cleavage and degradation of SDE2 regulates response to replication stress
Authors: Ukhyun Jo, Winson Cai, Jingming Wang, Yoojin Kwon, Alan D. D’Andrea, Hyungjin Kim
Journal: Cancer Research (2017)

Abstract Maintaining genomic integrity during DNA replication is essential for cellular survival and for preventing tumorigenesis. Proliferating cell nuclear antigen (PCNA) functions as a processivity factor for DNA replication, and posttranslational modification of PCNA plays a key role in coordinating DNA repair against replication-blocking lesions by providing a platform to recruit factors required for DNA repair and cell cycle control. Here, we identify human SDE2 as a new genome surveillance factor regulated by PCNA interaction. SDE2 contains an N-terminal ubiquitin-like (UBL) fold, which is cleaved at a diglycine motif via a PCNA-interacting peptide (PIP) box and deubiquitinating enzyme activity. The cleaved SDE2 is required for negatively regulating ultraviolet damage-inducible PCNA monoubiquitination and counteracting replication stress. The cleaved SDE2 products need to be degraded by the CRL4CDT2 ubiquitin E3 ligase in a cell cycle- and DNA damage-dependent manner, and failure to degrade SDE2 impairs S phase progression and cellular survival. Collectively, this study uncovers a new role for CRL4CDT2 in protecting genomic integrity against replication stress via regulated proteolysis of PCNA-associated SDE2 and provides insights into how an integrated UBL domain within linear polypeptide sequence controls protein stability and function. Knowledge on such mechanism will be useful to identify novel cancer therapeutic interventions exploiting deregulated ubiquitin signaling and SDE2 activities in cancer. Citation Format: Ukhyun Jo, Winson Cai, Jingming Wang, Yoojin Kwon, Alan D. D’Andrea, Hyungjin Kim. PCNA-dependent cleavage and degradation of SDE2 regulates response to replication stress [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 1403. doi:10.1158/1538-7445.AM2017-1403
Abstract 1844: Investigating the role of amphiregulin in breast cancer
Authors: Serena P. Chiang, George S. Karagiannis, John S. Condeelis, Jeffrey E. Segall
Journal: Cancer Research (2017)

Abstract Breast cancer is the most prevalent cancer in women worldwide and afflicts more than 3.1 million women in the US alone. The epidermal growth factor receptor (EGFR) is frequently overexpressed in breast cancer and is associated with poor clinical outcome. Several therapies involving anti-EGFR agents have been developed to target breast cancer. However, clinical trials have shown mixed outcomes with these therapies. Amphiregulin (AREG) is a ligand for EGFR that mediates estrogen-induced mammary ductal morphogenesis during development. Expression of AREG is enriched in invasive breast carcinomas, particularly ERα-positive breast tumors. Studies have shown that AREG increases the in vitro invasiveness of breast cancer cells. Furthermore, suppression of AREG expression in transformed human breast epithelial cells reduces tumor formation when injected in nude mice. These observations suggest that AREG plays an important role in breast cancer development and progression. To investigate the role of AREG in breast cancer development and progression, we utilized a spontaneous mammary tumor mouse model where oncogenesis is driven by expression of the polyoma middle T oncoprotein (PyMT) through the mouse mammary tumor virus (MMTV) promoter. We have crossed AREG knockout mice with the MMTV-PyMT mice to generate AREG KO mice that spontaneously form mammary tumors. Tumors in AREG KO PyMT mice initially grow more quickly but eventually reach 2 cm in diameter at a relatively time as compared to tumors formed in AREG WT PyMT mice. Histologically, AREG KO tumors appear more differentiated and display a greater proportion of tumor stroma. This prompted us to further hypothesize that AREG may have diverse effects in the tumoral or stromal compartment of developing tumors. To individually assess the effects of AREG knockout in the tumor cells and the stroma, we utilized a transplantation model in which we prepared tumor chunks from AREG WT and KO PyMT tumors and transplanted them into AREG WT and KO mice. Through this model, we have found that AREG expression in the tumor has a greater impact on tumor growth and progression than the tumor stroma. Regardless of the AREG status of the recipient mice, AREG KO tumors display a significant growth impairment and reduced transplant efficiency. In summary, these results demonstrate that AREG is important for mammary tumor progression. Citation Format: Serena P. Chiang, George S. Karagiannis, John S. Condeelis, Jeffrey E. Segall. Investigating the role of amphiregulin in 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 1844. doi:10.1158/1538-7445.AM2017-1844
Participation of BTK in MYD88 signaling in malignant cells expressing the L265P mutation in Waldenstrom’s macroglobulinemia, and effect on tumor cells with BTK-inhibitor PCI-32765 in combination with MYD88 pathway inhibitors.
Authors: Guang Yang, Lian Xu, Yangsheng Zhou, Xia Liu, Yang Cao, Christina Tripsas, Christopher J Patterson, Zachary R Hunter, Yu-Zu Tai, Kenneth Carl Anderson, Steven P. Treon
Journal: Journal of Clinical Oncology (2012)

8106 Background: Bruton’s tyrosine kinase (BTK) promotes B-cell receptor signaling along with B-cell expansion and survival through NF-κB and MAPK. MYD88 L265P is a widely expressed somatic mutation in tumor cells from WM patients. MYD88 L265P promotes enhanced tumor cell survival through IRAK 1/4 mediated NF-κB and MAPK signaling. We therefore sought to clarify the role of BTK signaling in MYD88 L265P expressing WM cells, and the impact of BTK and MYD88/IRAK inhibition on WM cell signaling and survival. Methods: Western blot analysis was performed using total and phospho-specific BTK antibodies in MYD88 L265P expressing primary WM patient cells, BCWM.1 and MCWL-1 WM cell lines following MYD88 knockdown by lentiviral transduction, and/or use of MYD88 or IRAK signal inhibitors. Cells were also treated with the BTK inhibitor PCI-32765, in the presence or absence of MYD88 homodimerization or IRAK1/4 inhibitors. Annexin V / PI staining was used to assess cell survival, and synergism assessed with CalcuSyn software. Results: BTK was phosphorylated in MYD88 L265P expressing WM cells. Knockdown of MYD88 by lentiviral transduction, and/or use of MYD88 or IRAK 1/4 kinase inhibitors led to decreased BTK phosphorylation. Phosphorylation of BTK, TIRAP, a major TLR adapter protein for MYD88 signaling, IRAK1, IKBα, ERK1/2 and STAT3 were significantly reduced following treatment with PCI-32765. Treatment with PCI-32765 also induced apoptosis of MYD88 L265P expressing WM cells, and showed synergistic tumor cell killing in the presence of either MYD88 homodimerization or IRAK 1/4 kinase inhibitors. Conclusions: BTK activation is facilitated by MYD88 pathway signaling in L265P expressing WM cells, and participates in MYD88 downstream signaling. Inhibition of BTK by PCI-327625 led to robust tumor cell killing of MYD88 L265P expressing WM,cells, which was potentiated by MYD88 pathway inhibitors. These studies provide the framework for the investigation of BTK inhibitors in WM, as single agents and in combination with MYD88 pathway inhibitors.
Abstract 1631: Sequencing the circulating and infiltrating T-cell repertoire on the Ion S5TM
Authors: Geoffrey Lowman, Elizabeth Linch, Lauren Miller, Denise Topacio-Hall, Timothy Looney, Alex Pankov, Yongming Sun, Xinzhan Peng, Mark Andersen, Fiona Hyland, Ann Mongan
Journal: Cancer Research (2017)

Abstract T-cell repertoire (TCR) sequencing by next-generation sequencing (NGS) is a valuable tool for building a deeper understanding of the adaptive immune system. As immunotherapies, particularly T-cell dependent therapies, show increasing potential in treating cancer, the ability to gain a detailed, unbiased view of the TCR becomes imperative for biomarker discovery, immune response to treatment, and study of tumor microenvironments. A key question the field seeks to understand is the relationship between circulating T-cells and infiltrating T-cells at the tumor site. Here, we present a novel approach for TCR sequencing using the Ion S5 ™ sequencer which leverages simplified library construction workflows and offers a more complete characterization of the entire V(D)J region of TCRB. This method can leverage mRNA as input, minimizing requirements in starting materials and focusing sequencing to productive TCRB arrangements. This approach targets the constant (C) and the FR1 regions, minimizing the potential for primer bias and greatly increasing the phylogenetic information content compared to techniques that exclusively characterize the CDR3 domain. Our results show that the observed circulating T-cell repertoire size is approximately 2 orders of magnitude higher than the infiltrating T-cell repertoire. Accordingly, while it is difficult to fully capture the complete repertoire of circulating T-cells due to its vast diversity, we show that it is possible to reliably capture the complete infiltrating T-cell repertoire with as high as 10 samples on the Ion 530 ™ chip. Replicate sequencing runs of infiltrating T-cells offers correlation of ~0.9, indicating that the results were reproducible, and the samples were sequenced to appropriate depth. In summary, we believe that this workflow will allow researchers to more routinely characterize the infiltrating T-cell repertoire and offers the field a better understanding of the impact of repertoire diversity on tumor elimination. Citation Format: Geoffrey Lowman, Elizabeth Linch, Lauren Miller, Denise Topacio-Hall, Timothy Looney, Alex Pankov, Yongming Sun, Xinzhan Peng, Mark Andersen, Fiona Hyland, Ann Mongan. Sequencing the circulating and infiltrating T-cell repertoire on the Ion S5TM [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 1631. doi:10.1158/1538-7445.AM2017-1631
Abstract 5: The effects of SIRT1 inhibitors nicotinamide and Ex-527 on lymphoma cells
Authors: Manuela Guardi, Mariaelena Pistoni, Raffaele Frazzi
Journal: Cancer Research (2017)

Abstract SIRT1 is a well-known lysine-deacetylase, having both histone and non-histone proteins as molecular targets. SIRT1 may function as a tumor promoter as well as a tumor suppressor in a context-dependent manner. We previously demonstrated that the treatment with resveratrol at concentrations able to induce apoptosis leads to SIRT1 down-regulation in lymphoma cells. Here we look for SIRT1 inhibition in order to investigate the effects on proliferation potential, apoptosis induction and targets modulation at a molecular level. The aim is to study whether SIRT1 inhibition affects cell cycle and proliferation capability of lymphoma cells. Experimental procedures. Diffuse large-B cell lymphoma derived cell line Toledo; human lymphoblastoid cell line GGB #7; SIRT1 inhibitors: nicotinamide (NAM) and Ex-527; cell cycle analysis; caspase-3 activity fluorimetric assay; genotoxicity assay gamma-H2AX; fluorescence-activated cell sorting intracellular staining for acetylated-H4K16 histone. New data. We found that the calculated IC50s for SIRT1 inhibition is 50mM for NAM and 343μM for Ex-527. The treatment with either NAM or Ex-527 leads to cell cycle arrest in both Toledo and GGB#7 cells, although in a different fashion. Namely, NAM causes an S-phase accumulation of Toledo while it leads GGB #7 to G0/G1 phase arrest with a concomitant decrease in S-phase already after 10mM. In both cell lines NAM 50mM induces apoptosis as demonstrated by caspase-3 activation and sub-G1 peak appearance in the cell cycle profiles. Ex-527 causes an accumulation in the S phase of Toledo cells and a decrease of G2/M in GGB#7 cells. No induction of apoptosis at the IC50 concentration was observed in both cell lines. Genotoxicity of the above mentioned treatments was investigated through the quantitation of gamma-H2AX histone released by treated cells. No genotoxic effects have been observed upon the treatments with these two inhibitors even at the concentration where NAM induces apoptosis. In order to correlate the observed changes with SIRT1 inhibition, we studied the acetylated H4K16 histone, a direct target of SIRT1 deacetylation. Our preliminary data indicate that NAM treatment increases the percentage of acetylated H4K16. Conclusions. Lymphoma and lymphoblastoid cells are affected by SIRT1 inhibition. NAM and Ex-527 cause cell cycle arrest and growth inhibition. Only NAM 50mM induces apoptosis without genotoxic effects. Overall, our data suggest the direct involvement of SIRT1 during the observed cell cycle arrest and growth inhibition mediated by these inhibitors. Citation Format: Manuela Guardi, Mariaelena Pistoni, Raffaele Frazzi. The effects of SIRT1 inhibitors nicotinamide and Ex-527 on lymphoma 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 5. doi:10.1158/1538-7445.AM2017-5
Abstract 1222: Developing kinase inhibitors with polypharmacological profiles for the treatment of resistant cancers
Authors: Suman Rao, Tan Li, Robert Everley, Guangyan Du, Peter Sorger, Nathanael Gray
Journal: Cancer Research (2017)

Abstract Small molecule kinase inhibitors targeting a specific oncoprotein driving cancer cells have shown great clinical success in the past (e.g. imatinib against leukemia). However, resistance to targeted therapies quickly arises due to plasticity associated with cancer cell signaling and tumor heterogeneity. One way to overcome this problem is to rationally design drugs with polypharmacology that can target multiple signaling pathways engaging in cancer cell proliferation and survival. To this end, we have developed a strategy based on combining phenotypic screens of small molecule inhibitors and affinity-based mass spectrometry to identify drugs with multi-targeted properties and piloted this approach using the highly resistant KRAS mutant non-small cell lung cancer cell lines. We began this study by screening kinase inhibitors targeting MEK, ERK, PI3K, Akt and mTOR and found that the lung cancer cells were largely resistant to single drugs but showed enhanced sensitivity towards triple inhibition of MEK, ERK and PI3K. These cell lines were then screened with a library of covalent and non-covalent kinase inhibitors in an attempt to identify a small molecule inhibitor that could mimic the activity of the triple drug combination. This led to the discovery of SM1-71 that not only recapitulated the growth inhibitory activity of MEK+ERK+PI3K inhibition, but also blocked phosphorylation of ERK, Akt, mTOR and S6K in cells. Target profiling of the drug was carried out using chemoproteomics, which revealed that SM1-71 inhibited 55 kinases at a 1μM concentration. Dose-dependent evaluation further determined the IC50 of inhibition across the 55 kinases and rank ordered them based on binding affinity. Top hits including MEK1, MEK2, ERK1, ERK2, AURKA, SRC and RPS6KA3 were confirmed using alternate kinase screens and cellular assays. Growth factor receptors such as IGF1R, MET and EGFR were also identified and further validated using cell-based assays. Taken together, these results elucidated the polypharmacology associated with SM1-71 and uncovered key targets responsible for inducing strong cytotoxicity in KRAS mutant lung cancer cells. Through the combination of phenotypic screens and mass spectrometry-based target identification, we have demonstrated the proof of principle for developing kinase inhibitors with polypharmacology targeting resistant cancers. Citation Format: Suman Rao, Tan Li, Robert Everley, Guangyan Du, Peter Sorger, Nathanael Gray. Developing kinase inhibitors with polypharmacological profiles for the treatment of resistant cancers [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 1222. doi:10.1158/1538-7445.AM2017-1222
Abstract 1069: Inhibition of the nuclear import receptor, KpnB1 synergizes with cisplatin toxicity in cervical cancer cells
Authors: Ru-pin Chi, Wei Wei, Michael Birrer, Virna D. Leaner
Journal: Cancer Research (2017)

Abstract Elevated expression of members of the nuclear transport protein family has been reported in multiple cancers and presents as novel anticancer therapeutic targets. Using a cervical cancer model system, we have previously shown that inhibition of the nuclear import receptor, KpnB1 by siRNA and a novel small molecule, Inhibitor of Nuclear Import (INI-43) resulted in cancer cell death via apoptosis. In this study, we investigated the cancer cell killing effects of KpnB1 inhibition in combination with Cisplatin (CDDP), a first-line chemotherapeutic agent used in the treatment of many cancers. KpnB1 siRNA and INI-43 treatment at sub-lethal concentrations enhanced cancer cells' sensitivity to CDDP. Our data shows that the combination treatment of INI-43 and CDDP significantly decreases CDDP IC50 compared to CDDP treatment alone. Increased PARP-cleavage was observed in combination treated cells and this correlated with increased γH2A.X, indicating increased apoptosis and DNA damage. Furthermore, INI-43 treatment reduced the nuclear import of NFκB, a stress-regulated response transcription factor known to be a KpnB1 cargo protein that promotes cancer cell survival. Decreased levels of downstream pro-survival and DNA-repair targets of NFκB were observed, including cyclinD1, c-Myc and XIAP, which correlated with increased DNA damage and apoptosis. Taken together, results suggest increased Cisplatin sensitivity of cervical cancer cells when nuclear import via KpnB1 is inhibited. Citation Format: Ru-pin Chi, Wei Wei, Michael Birrer, Virna D. Leaner. Inhibition of the nuclear import receptor, KpnB1 synergizes with cisplatin toxicity in cervical cancer 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 1069. doi:10.1158/1538-7445.AM2017-1069
Abstract 3046: Identification of lncRNAs involved in regulation of androgen receptor splice variants in prostate cancer through CRISPR-Cas9-based screen
Authors: Tsui-Ting Ho, Pratirodh Koirala, Nanjiang Zhou, Yin-Yuan Mo
Journal: Cancer Research (2017)

Abstract Prostate cancer is the second leading cause of death in men in the USA. Despite the high initial response rates to androgen deprivation therapy (ADT), these tumors ultimately develop the resistance, i.e., castration-resistant prostate cancer (CRPC). One of the contributing factors is constitutive expression of androgen receptor (AR) splice variants such as AR3, a major splice variant identified in clinical specimens. However, little is known about long non-coding RNAs (lncRNAs) on regulation of AR splicing. In this study, we generate CRISPR/Cas9-based libraries against a focus group of lncRNAs and an AR3 mini-gene reporter to identify lncRNAs involved in regulation of AR splicing. The principles of this screening system is that only sgRNAs capable of promoting AR3 expression will be enriched in SAM (Synergistic Activation Mediator) library, whereas these clones are lost from the knockout gRNA library after selection. This screen identifies several candidate lncRNA sgRNAs and dual gRNAs (targeting Lnc-DC/ Har1B/ LINC00568/ DHRS4-AS1/ SNHG5). Further characterization confirms the regulation of their corresponding endogenous genes and AR3 expression. Importantly, overexpression of Lnc-DC increases AR3 level and enhances tumor cell growth in response to androgen deprivation. Moreover, while ectopic expression of DHRS4-AS1 increases, DHRS4-AS1 knockout suppresses AR3. Finally, rescue experiments restore the ability of DHRS4-AS1 to induce AR3, further supporting a role for Lnc-DC and DHRS4-AS1 in AR3 regulation. Together, we demonstrate that the CRISPR/Cas9-based screening system provides a powerful tool for lncRNA research. As a result, these lncRNAs may serve as biomarkers to predict the response to ADT or therapeutic targets for treatment of CRPC. Citation Format: Tsui-Ting Ho, Pratirodh Koirala, Nanjiang Zhou, Yin-Yuan Mo. Identification of lncRNAs involved in regulation of androgen receptor splice variants in prostate cancer through CRISPR-Cas9-based screen [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 3046. doi:10.1158/1538-7445.AM2017-3046
Abstract 1040: LIN28B-mediated <i>let-7</i> independent activation of AKT promotes neuroblastoma pathogenesis
Authors: Ting Tao, John T. Powers, Hui Shi, Pavlos Missios, Antonio R. Perez-Atayde, Shizhen Zhu, George Q. Daley, Thomas A. Look
Journal: Cancer Research (2017)

Abstract LIN28 is well known as a RNA-binding protein and a suppressor of microRNA biogenesis, by selectively blocking the processing of let-7 precursors. It plays diverse functions in cellular reprogramming, development, metabolism and tumorigenesis. Many of these functions are executed through its ability to inhibit let-7 maturation. However, little is known about its function independent of let-7. Here we made zebrafish transgenic lines expressing high levels of either wild-type or mutant LIN28B (does not block the maturation of let-7) in the peripheral sympathetic nervous system driven by the dopamine beta-hydroxylase promoter. We bred these lines with a transgenic zebrafish line overexpressing the MYCN oncogene in these cells. Either wild-type or mutant LIN28B overexpression accelerated the onset and increased the penetrance of MYCN-induced neuroblastoma, despite the fact that only wild-type LIN28B blocked let-7 maturation compared to MYCN-only tumors. Mechanistically, both wild-type and mutant LIN28B overexpression enhanced MYCN-induced hyperplasia by increasing cell proliferation in the sympathoadrenal lineage. Further studies revealed that overexpression of either wild-type or mutant LIN28B resulted in hyperphosphorylation of AKT on both Ser473 and Thr308 in zebrafish tumors and also serum-deprived human neuroblastoma cell lines. Both wild-type and mutant LIN28B interacted with IGF2BP1, a known interactor that increases stability and translation of a subset of RNAs. We found IGF2 RNA levels to be increased in response to either form of LIN28B. Coincident with IGF2 overexpression, IGF1R was phosphorylated, providing an explanation for PI3K-AKT activation in LIN28B overexpressing cells. Finally, overexpression of a constitutively active, myristoylated murine Akt2 (myr-mAkt2) alone in zebrafish induced ganglioneuroma in the interregnal gland (the zebrafish equivalent of the human adrenal medulla), without a requirement for MCYN overexpression. Thus, our studies indicate that overexpression of LIN28B leads to AKT activation mediated through its interaction with IGF2BP1 and subsequent upregulation of IGF2. This pathway provides a mechanism underlying enhanced transformation in LIN28B overexpressing neuroblastomas, which is independent of the inhibitory activity of LIN28B on let-7 maturation. Citation Format: Ting Tao, John T. Powers, Hui Shi, Pavlos Missios, Antonio R. Perez-Atayde, Shizhen Zhu, George Q. Daley, Thomas A. Look. LIN28B-mediated let-7 independent activation of AKT promotes neuroblastoma pathogenesis [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 1040. doi:10.1158/1538-7445.AM2017-1040