tbuckley/cabot-search huggingface dataset:
Abstract A40: Specific mutations in the D1-D2 linker region of VCP/p97 enhance ATPase activity and confer resistance to VCP inhibitors
Authors: Prabhakar Bastola, Bret Freudenthal, Matthew Schaich, Tsui-Fen Chou, Taiping Gan, Feng Wang, Jeremy Chien
Journal: Clinical Cancer Research (2018)

Abstract Valosin-containing protein (VCP) has been shown to be involved in various protein quality control pathways including ubiquitin proteasome system, endoplasmic reticulum-associated degradation, chromatin-associated degradation, protein aggregate processing, and autophagy. Recent studies also identified VCP as a lineage-specific essential gene in ovarian cancer. An orally bioavailable VCP inhibitor, CB-5083, is currently in phase I clinical trials because it shows therapeutic effects in multiple tumor xenograft models. However, the mechanism of resistance to CB-5083 is unknown. Here, we characterized molecular mechanism of resistance to CB-5083. Using incremental exposure to CB-5083, we established CB-5083-resistant ovarian cancer cells that showed 5-6 fold resistance in vitro compared to parental cells. Genomic and complementary DNA sequencing of the VCP coding region reveal a pattern of coselected mutations: (1) missense mutations at codon 470 in one copy resulting in increased ATPase activity and (2) nonsense or frameshift mutations at codon 606 or codon 616 in another copy causing the loss of allele-specific expression. Unbiased molecular docking studies show codon 470 as a putative binding site for CB-5083. Analysis of somatic mutations in cancer genomes from The Cancer Genome Atlas indicates that codon 616 contains hotspot mutations in VCP. Thus, identification of these mutations associated with in vitro resistance to VCP inhibitors may be useful as potential theranostic markers while screening for patients to enroll in clinical trials. VCP has emerged as a viable therapeutic target for several cancer types, and therefore targeting such hyperactive VCP mutants should aid in improving the therapeutic outcome in cancer patients. Citation Format: Prabhakar Bastola, Bret Freudenthal, Matthew Schaich, Tsui-Fen Chou, Taiping Gan, Feng Wang, Jeremy Chien. Specific mutations in the D1-D2 linker region of VCP/p97 enhance ATPase activity and confer resistance to VCP inhibitors. [abstract]. In: Proceedings of the AACR Conference: Addressing Critical Questions in Ovarian Cancer Research and Treatment; Oct 1-4, 2017; Pittsburgh, PA. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(15_Suppl):Abstract nr A40.
Abstract 282: Inferring transcriptional regulatory programs in gynecological cancers
Authors: Hatice U. Osmanbeyoglu, Petar Jelinic, Douglas Douglas, Christina Leslie
Journal: Cancer Research (2018)

Abstract Cancer cells acquire genetic and epigenetic alterations that often lead to dysregulation of oncogenic signal transduction pathways, which in turn alter downstream transcriptional programs. Transcription factors (TFs) are the main link between signaling pathways and the transcriptional regulatory programs. The Cancer Genome Atlas (TCGA) has studied several of the most common and aggressive gynecologic tumors including high-grade serous ovarian carcinomas (HGSOC), uterine carcinosarcoma (UCS), and the serous-like subset of endometrial cancer (UCEC), together with basal breast cancer, which shares many genomic features with serous ovarian tumors. TFs impacts on gene regulation have not been well characterized in gynecological and basal breast cancers. The majority of these tumors lack accurate predictors of response and resistance and share an unmet need for adequate treatment of recurrent disease. We developed a multitask learning framework for integrating regulatory sequence from ATAC-mapped promoters and enhancers from cell line models with RNA-seq data from patient tumors in order to infer transcription factor (TF) regulatory activities and explore similarities and differences between uterine, ovarian, and basal breast tumors. We showed that our multitask learning framework enables us to selectively share the information across tumors and strongly improves the accuracy of gene expression prediction models for gynecological and basal breast tumors. Our analysis identified histologic type specific and common TF regulators of gene expression as well as predicted distinct dysregulated transcriptional regulators downstream of somatic alterations in these different cancers. Moreover, many of the identified TF regulators were significantly associated with survival outcome within the histological subtype. Computationally dissecting the role of TFs in these cancers may ultimately lead to new therapeutics tailored to groups of subtypes or individuals. Citation Format: Hatice U. Osmanbeyoglu, Petar Jelinic, Douglas Douglas, Christina Leslie. Inferring transcriptional regulatory programs in gynecological cancers [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 282.
Abstract 4675: B-cell and T-cell repertoire sequencing enables somatic hypermutation and minimal residual disease assessment
Authors: Chen Song, Pingfang Liu, Andrew Barry, Eileen T. Dimalanta, Fiona J. Stewart, Salvatore Russello, Theodore B. Davis
Journal: Cancer Research (2018)

Abstract The study of complex immunological diseases has progressed through recent developments that enable the sequencing of the immune repertoire. Using this approach, the interrogation of disease progression is facilitated through analysis of millions of V(D)J combinations from both B-cell antibodies and T-cell Receptors (TCR). One major challenge of immune repertoire sequencing is to capture the structural and sequence complexities of antibody and TCR genes. We have developed and optimized a method for accurate sequencing of full-length immune gene repertoires of B-cells and T-cells. RNA extracted from PBMCs were used to generate immune sequencing libraries in duplicate from a single patient. Using a unique barcoding scheme specifically designed to discretely barcode each mRNA molecule with a unique molecule index (UMI), PCR copies of each mRNA fragment can be collapsed into a single consensus sequence, improving accuracy through the resolution of PCR bias and sequencing errors. Utilization of the UMIs enabled absolute quantification of input RNA molecules and accurate ranking of the antibody/TCR clone abundance. This approach was also applied to the analysis of tumor samples for abundance of expanded clones through clustering based on V gene, J gene and CDR3 similarity and ranking by mRNA abundance. The use of isotype-specific primers (IgM, IgD, IgG, IgA and IgE) enabled measurement of the heavy chain isotype proportions within the samples. Full-length heavy chain antibody sequences generated using this method were aligned to germline genes from reference databases, enabling quantitation of the mutation level of each antibody sequence, providing information on the overall maturity and mutational profile of the sample repertoire. Additionally, this approach was capable of detecting minimal residual diseases by sensitive quantification of TCR rearrangement. This novel method allows for exhaustive somatic mutation profiling across complete V, D and J segments and full isotype information analysis. The information obtained enables the possibility for synthesis and expression of complete antibody chains and T-cell receptor chains for downstream immunological assays. Citation Format: Chen Song, Pingfang Liu, Andrew Barry, Eileen T. Dimalanta, Fiona J. Stewart, Salvatore Russello, Theodore B. Davis. B-cell and T-cell repertoire sequencing enables somatic hypermutation and minimal residual disease assessment [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 4675.
Abstract IA09: Targeting the CRL4CRBN E3 ligases for treatment of hematologic cancers
Authors: Rajesh Chopra
Journal: Clinical Cancer Research (2017)

Abstract Manipulation of the ubiquitin-proteasome system to achieve targeted degradation of proteins within cells using chemical tools and drugs has the potential to transform pharmacologic and therapeutic approaches in cancer and other diseases. Thalidomide and its analogues lenalidomide and pomalidomide exert their mechanism of action through the modulation of the CRL4CRBN E3 ligase family. Binding of the thalidomide to analogues Cereblon (CRBN) results in the degradation of neomorphic protein such as Aiolos and iKaros in multiple myeloma. This degradation explains the antitumor activity as well as the immunomodulatory effects of these drugs. The degradation of multiple context-specific proteins by the thalidomide analogues provides a means to uncover new cell biology as well as generate future drug molecules against currently undruggable targets. In parallel, the development of larger bifunctional molecules that bring together highly specific protein targets in complexes with Cereblon, von Hippel-Lindau or other E3 ligases to promote ubiquitin-dependent degradation has progressed to generate selective chemical compounds with potent effects in cells and in vivo models, providing valuable tools for biological target validation and with future potential for therapeutic use. This presentation will survey recent breakthroughs achieved in these two complementary methods, with a greater focus of CRL4CRBN modulation. Citation Format: Rajesh Chopra. Targeting the CRL4CRBN E3 ligases for treatment of hematologic cancers [abstract]. In: Proceedings of the Second AACR Conference on Hematologic Malignancies: Translating Discoveries to Novel Therapies; May 6-9, 2017; Boston, MA. Philadelphia (PA): AACR; Clin Cancer Res 2017;23(24_Suppl):Abstract nr IA09.
Abstract 5822: Secretory acetylated APE1/Ref-1 requirement for suppression of tumor growth in triple-negative breast cancer in vivo: Extracellular apoptotic initiator
Authors: Yu Ran Lee, Myoung Soo Park, Hee Kyoung Joo, Ki Mo Kim, Jeryong Kim, Byeong Hwa Jeon, Sung Choi
Journal: Cancer Research (2018)

Abstract Triple-negative breast cancer (TNBC) represents a relatively small proportion of all BCs but a relatively large proportion of BC-related death. Thus more effective therapeutic strategies are needed for the management of TNBC. We previously demonstrated that the stimulation of apoptosis by the binding of secreted acetylated-apurinic apyrimidinic endonuclease 1/redox factor-1 (Ac-APE1/Ref-1) to the receptor for advanced glycation end products (RAGE) was essential for the TNBC cell death in response to hyperacetylation. The aim of the present study was to assess the potential therapeutic efficacy of secretory Ac-APE1/Ref-1 in orthotopic TNBC xenografts in vivo. We found that hyperacetylation in xenografts caused secretion of Ac-APE1/Ref-1 into the blood, where the factor bound directly to RAGE in hyperacetylated tumor tissues. Hyperacetylation in the TNBC xenografts induced strong inhibition of tumor growth and development. Hyperacetylation also caused cell death in tumors, accompanied by increased RAGE expression and generation of reactive oxygen species, which induced apoptosis. Tissues exhibited markedly higher counts of apoptotic bodies, a reduced proliferation index, and reduced neovascularization compared with control tumors. Ac-APE1/Ref-1-stimulated apoptosis was markedly reduced in RAGE-knockdown tumors compared with RAGE-overexpressing tumors, even in the presence of hyperacetylation. The function of secreted Ac-APE1/Ref-1 was confirmed in other hyperacetylated TNBCs xenografts using BT-459 and MDA-MB-468 cells, demonstrating its relevance as an anticancer molecule. Our findings suggest that the Ac-APE1/Ref-1 possesses potent chemotherapeutic efficacy against hyperacetylated TNBCs based on stimulation of cell death by RAGE-dependent triggering of Ac-APE1/Ref-1. Citation Format: Yu Ran Lee, Myoung Soo Park, Hee Kyoung Joo, Ki Mo Kim, Jeryong Kim, Byeong Hwa Jeon, Sung Choi. Secretory acetylated APE1/Ref-1 requirement for suppression of tumor growth in triple-negative breast cancer in vivo: Extracellular apoptotic initiator [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 5822.
JAK/STAT3-Regulated Fatty Acid β-Oxidation Is Critical for Breast Cancer Stem Cell Self-Renewal and Chemoresistance
Authors: Tianyi Wang, Johannes Francois Fahrmann, Heehyoung Lee, Yi-Jia Li, Satyendra C. Tripathi, Chanyu Yue, Chunyan Zhang, Veronica Lifshitz, Jieun Song, Yuan Yuan, George Somlo, Rahul Jandial, David Ann, Samir Hanash, Richard Jove, Hua Yu
Journal: Cell Metabolism (2018)
Abstract 2378: Histone H4 tyr88-phosphorylation mediated by ACK1 promotes castration-resistant prostate cancer by epigenetic reprogramming of androgen receptor
Authors: Nupam P. Mahajan, Kiran Mahajan, Nicholas Lawrence, Harshani Lawrence
Journal: Cancer Research (2018)

Abstract Androgen receptor (AR) plays a paramount role in the onset and progression of prostate cancer (PC). This very facet underlies androgen deprivation therapy (ADT), a preferred treatment to negate AR transcriptional activity. While ADT provides immediate palliative benefits, it is ineffective long term, as the recalcitrant disease recurs within 2-3 years and progresses to a lethal stage, referred to as the metastatic castration-resistant prostate cancer (mCRPC). The AR gene (AR) is amplified or mutated in &amp;gt;50% of mCRPCs, suggesting that PC cells may have reinvigorated AR transcription as a response to the loss of existing AR activity by ADT. Consequently, resistance to ADT has become one of the most vexing problems in PC therapy. AR antagonists are often ineffective due to their inability to repress the expression of AR or its splice variant, AR-V7. Here, we report that the tyrosine kinase ACK1 (TNK2) phosphorylates histone H4 at tyrosine 88 upstream of the AR transcription start site. The WDR5/MLL2 complex reads the H4-Y88-phosphorylation marks and deposits the transcriptionally activating H3K4-trimethyl marks promoting AR transcription. We developed a new class of ACK1 kinase-specific small molecule inhibitor (R)-9bMS that suppresses ACK1 kinase activity at IC50= 48 nM. Reversal of the pY88-H4 epigenetic marks by the ACK1 inhibitor (R)-9bMS-sensitized naive and enzalutamide-resistant prostate cancer cells and reduced AR and AR-V7 levels to mitigate CRPC tumor growth. Thus, a feedforward ACK1/pY88-H4/WDR5/MLL2/AR epigenetic circuit drives CRPC and is necessary for maintenance of the malignant state. Citation Format: Nupam P. Mahajan, Kiran Mahajan, Nicholas Lawrence, Harshani Lawrence. Histone H4 tyr88-phosphorylation mediated by ACK1 promotes castration-resistant prostate cancer by epigenetic reprogramming of androgen receptor [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 2378.
Impaired Modulation of Sympathetic Excitability by Nitric Oxide After Long-term Administration of Organic Nitrates in Pigs
Authors: JohannesZanzinger, JürgenCzachurski, HorstSeller
Journal: Circulation (1998)

Background—Endogenous nitric oxide (NO) reduces sympathetic vasoconstriction by attenuating neuronal excitability in the brain stem and inhibition of postganglionic neurotransmission. We studied whether this modulation of sympathetic circulatory control by NO may be altered during chronic administration of NO donor drugs in pigs. Methods and Results—Nitrate tolerance was induced by oral administration of isosorbide dinitrate (ISDN, 4 mg/kg per day for 4 weeks) in eight pigs. Four of them were chronically instrumented for the measurement of mean arterial blood pressure and cardiac output in the conscious state. ISDN treatment caused hemodynamic tolerance to NO donors and significantly increased the hypotensive responses to pharmacologic ganglionic blockade in conscious pigs. In general anesthesia, ISDN-treated animals and age-matched controls (n=5) had similar baseline renal sympathetic nerve activity and in both groups neither inhibition of NO synthases (NOS) nor administration of NO donors to the brain s...
Abstract 5628: Measurement of Fc-mediated ADCC and CDC activity of anti-TNFA and anti-VEGF therapeutic antibodies using reporter-based bioassays and engineered TNFA+ and VEGF+ target cells
Authors: Denise Garvin, Jamison Grailer, Rich Moravec, Jim Hartnett, Vanessa Ott, Frank Fan, Mei Cong, Zhi-jie Jey Cheng
Journal: Cancer Research (2018)

Abstract Fc-mediated effector functions are critical to the efficacy and safety of therapeutic antibodies. Measurement of Fc-mediated antibody-mediated cellular cytotoxicity (ADCC) and complement-dependent cytotoxicity (CDC) during antibody drug discovery and development is not only important for antibodies that harness ADCC and/or CDC as their primary mechanism of action (e.g. rituximab, trastuzumab), but also for antibodies designed to target and block soluble ligands such as TNFA and VEGF. We previously reported the development of a cell-based reporter bioassay platform which has been used to measure ADCC and ADCP mediated through FcΓRI, FcΓRIIa and FcΓRIIIa. These reporter bioassays exhibit the specificity, accuracy, precision, and robustness necessary for qualification according to ICH guidelines and have been used extensively to characterize and measure the potency of antibody-based biologics drugs that target cell surface immune receptors. In the current study, we sought to evaluate Fc-mediated ADCC and CDC activities of therapeutic antibodies designed to target and block soluble ligands including TNFA and VEGF. To measure ADCC activity of anti-TNFA and anti-VEGF blocking antibodies, we developed engineered target cells that express either membrane-bound TNFA or VEGF. When used as target cells with reporter-based effector cells expressing a relevant FcΓR, ADCC activity of adalimumab (anti-TNFA) and bevacizumab (anti-VEGF) was detected in a specific and dose-dependent manner. Similarly, when used in a luminescence-based CDC assay, the engineered target cells elicited an appropriate FcΓR-mediated response. The assay signals demonstrated IgG isotype specificity as IgG4 variants showed minimal activity in both ADCC and CDC assays. Our results demonstrate that the combined use of cell-based reporter bioassays with target cells engineered to express membrane-bound soluble ligands can provide a simple, specific, and quantitative platform to measure Fc-mediated effector functions of therapeutic antibodies targeting soluble ligands. Citation Format: Denise Garvin, Jamison Grailer, Rich Moravec, Jim Hartnett, Vanessa Ott, Frank Fan, Mei Cong, Zhi-jie Jey Cheng. Measurement of Fc-mediated ADCC and CDC activity of anti-TNFA and anti-VEGF therapeutic antibodies using reporter-based bioassays and engineered TNFA+ and VEGF+ target 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 5628.
Restoration of Cardiac Progenitor Cells After Myocardial Infarction by Self-Proliferation and Selective Homing of Bone Marrow–Derived Stem Cells
Authors: FrédéricMouquet, OtmarPfister, MohitJain, AngelosOikonomopoulos, SoeunNgoy, RossSummer, AlanFine, RonglihLiao
Journal: Circulation Research (2005)

Tissue-specific progenitor cells contribute to local cellular regeneration and maintain organ function. Recently, we have determined that cardiac side-population (CSP) cells represent a distinct cardiac progenitor cell population, capable of in vitro differentiation into functional cardiomyocytes. The response of endogenous CSP to myocardial injury, however, and the cellular mechanisms that maintain this cardiac progenitor cell pool in vivo remain unknown. In this report we demonstrate that local progenitor cell proliferation maintains CSP under physiologic conditions, with little contribution from extracardiac stem cell sources. Following myocardial infarction in adult mice, however, CSP cells are acutely depleted, both within the infarct and noninfarct areas. CSP pools are subsequently reconstituted to baseline levels within 7 days after myocardial infarction, through both proliferation of resident CSP cells, as well as through homing of bone marrow–derived stem cells (BMC) to specific areas of myocardi...
Abstract 2312: Phospho-proteomics analysis to determine the signaling pathways affected by a novel CDC7-selective inhibitor TAK-931
Authors: Kenichi Iwai, Masamitsu Gotou, Kazunori Yamanaka, Akihiro Ohashi
Journal: Cancer Research (2018)

Abstract Background: Cell division cycle 7 (CDC7) is a serine/threonine kinase, which plays important roles in initiation of DNA replication by phosphorylating MCM2. We developed the CDC7-selective small molecule inhibitor TAK-931. Treatment with TAK-931 results in delayed S phase progression, DNA replication stress (RS), centrosome disorganization, mitotic aberrations, and potent growth suppression in cancer cells. In this study, we conducted the time-dependent phospho-proteomics analysis to determine the signaling pathways affected by TAK-931. Materials and Methods: TAK-931 was synthesized by Takeda Pharmaceutical Company, Ltd. The SILAC-labeled COLO205 cells were treated with TAK-931 at 100 nM for 0, 4, 24 hours, applying for the phospho-proteomics analysis in the PhosphoScout® Service at Evotec AG (Munich, Germany). Results: The SILAC-labeled COLO205 cells with TAK-931 treatment were subjected to quantitative mass spectrometry, detecting 15,128 phosphorylation sites of the 4,426 phosphoproteins. At 4 h of treatment, only 2 phosphorylation sites were detected as significantly downregulated: MAX gene-associated protein (MGA) and alpha-enolase (ENO1). At 24 h of treatment, however, 51 phosphorylation sites were identified as being significantly altered, including 44 upregulation and 7 downregulation sites. The gene ontology (GO) enrichment analysis in the categories of biological process (BP) and cellular component (CC) revealed that 10 GO terms from BP and 2 GO terms from CC were significantly enriched in the treated cells after 24 h: cell cycle, cell cycle phase, cell cycle process, mitosis, nuclear division, organelle fusion, organelle organization, mitotic cell cycle, M phase of mitotic cell cycle, M phase, chromosomal part, and spindles. Network analysis on the changed phosphorylation prolife also revealed that significant network modules existed at 24 h of treatment, which included DNA replication/damage, mitotic progression/spindle assembly, nucleus assembly, GTPase activity, cell migration, cell adhesion, TP53, and protein translation. Conclusion: The time-dependent phospho-proteomics analysis revealed the dynamics of phospho-signal transduction affected by TAK-931 in the cancer cell, which may help to provide a deeper understanding of the molecular mechanisms of TAK-931. Citation Format: Kenichi Iwai, Masamitsu Gotou, Kazunori Yamanaka, Akihiro Ohashi. Phospho-proteomics analysis to determine the signaling pathways affected by a novel CDC7-selective inhibitor TAK-931 [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 2312.