tbuckley/cabot-search huggingface dataset:
Abstract 2241: Molecular characterization of circulating tumor cells in head and neck squamous cell carcinoma: Direct comparison of a label-independent size-based microfluidic device with EpCAM-based CTC enrichment
Authors: Martha Zavridou, Sophia Mastoraki, Areti D. Strati, George Koutsodontis, Apostolos Klinakis, Amanda Psyrri, Evi S. Lianidou
Journal: Cancer Research (2019)

Abstract Background: Circulating tumor cells (CTCs) heterogeneity is highly affecting the efficiency of their isolation and thus the reliability of downstream analysis. Especially in Head and Neck Squamous Cell Carcinoma (HNSCC) epithelial mesenchymal transition (EMT) is highly affecting CTC isolation and downstream analysis. We directly compared two different approaches used for CTC isolation, a label-independent size-based microfluidic-based system versus an EpCAM-based positive selection for downstream molecular characterization of CTC both at the gene expression and DNA methylation level in HNSCC. Methods: Peripheral blood (PB) in EDTA (20mL) was collected from 50 HNSCC patients and 18 healthy donors (HD). A size-based microfluidic device (Parsortix, ANGLE) and an EpCAM-based positive immune-magnetic isolation procedure were applied in parallel, using 10mL PB in each case. Total RNA was isolated from enriched CTCs and RT-qPCR was used to study the expression levels of CK-19, PD-L1, EGFR, TWIST1, CDH2 and B2M. Real time methylation specific PCR (MSP) was used to study the methylation status of SOX17, RASSF1A and MLL3 genes in DNAs isolated from the same enriched CTCs. Results: In identical blood draws, the label-free size-based CTC-isolation system was superior in terms of sensitivity when compared to the EpCAM-based CTC enrichment, since a significantly higher percentage of identical PB samples was found positive for all genes tested both at the gene expression and DNA methylation level, while the specificity was not affected. Conclusions: In HNSCC CTC molecular characterization at the gene expression and DNA methylation level should be based on a label-free size-based isolation system. Citation Format: Martha Zavridou, Sophia Mastoraki, Areti D. Strati, George Koutsodontis, Apostolos Klinakis, Amanda Psyrri, Evi S. Lianidou. Molecular characterization of circulating tumor cells in head and neck squamous cell carcinoma: Direct comparison of a label-independent size-based microfluidic device with EpCAM-based CTC enrichment [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2241.
Abstract LB-284: miRNAs/Ago2/YY1/PcG protein/DNMT complex mediates epigenetic silencing in bortezomib-induced apoptosis of leukemia
Authors: Ju-Ming Wang
Journal: Cancer Research (2019)

Abstract miRNAs are a class of non-coding RNAs, which bind to the 3'-untranslated regions of their target mRNAs to repress translation. However, the details of miRNA-mediated epigenetic regulation targeting genomic DNA remained largely unknown. Here, we demonstrated that transcription factor CCAAT/enhancer binding protein delta (CEBPD) was responsive to the anticancer drug bortezomib, is a highly selective reversible inhibitor for leukemia treatment, and resulting in caspase activation and apoptosis. Interestingly, following the identification of CEBPD-induced miRNAs, we found that miR-744, miR-3154 and miR-3162 feedback to suppress the transcription of CEBPD itself and genes adjacent to its 5'-flanking region, including protein kinase DNA-activated catalytic polypeptide (PRKDC), minichromosome maintenance-deficient 4 (MCM4) and ubiquitin-conjugating enzyme E2 variant 2 (UBE2V2), upon bortezomib treatment. Additionally, we previously demonstrated that the Yin Yang 1 (YY1)/polycomb group (PcG) protein/DNA methyltransferase (DNMT) complex is important for mediating epigenetic silencing of the CEBPD gene; we further found that Argonaute 2 (Ago2) interacts with YY1 and binds to the CEBPD promoter. Moreover, we revealed that miRNA binding plays a key role for YY1/PcG group protein/DNMT complex-mediated epigenetic gene silencing and is associated with bortezomib-induced methylation on genomic DNA. Altogether, we provided new insights for miRNA-mediated epigenetic regulation in the case of bortezomib-induced cell death in leukemia. Citation Format: Ju-Ming Wang. miRNAs/Ago2/YY1/PcG protein/DNMT complex mediates epigenetic silencing in bortezomib-induced apoptosis of leukemia [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr LB-284.
Abstract 1495: Alternative humanized PD-1 mouse models provide more options for PD-1 antibody efficacy study in vivo
Authors: Qing Lin, Huimin Ma, Xiaoyu Zhang, Hengbin Li, Wenjing Yang, Zhewei Yang, Xingchen Shen, Qunsheng Ji
Journal: Cancer Research (2019)

Abstract The Programmed Death-1 (PD-1) binding to its ligands PD-L1 and PD-L2 plays a critical role in suppression of T cell function and tumor immune evasion. Blocking antibodies against PD-1 have been shown to induce durable antitumor responses in multiple cancers in many clinical trials. So a well-characterized mouse model is essential for preclinical studies of antibodies that target human PD-1. Here we generated several humanized PD-1 knock-in mouse models, one expresses a hybrid PD1 protein by replacing the amino acids that involve in binding to PD-L1 (mostly IgV domain) with the human counterpart in both C57BL/6J and Balb/C genetic background, another one have both the IgV domain and signal peptide replaced by human counterpart. These mouse models were confirmed by PCR and southern blotting. And homozygous mouse models from these different strategies were also successfully generated and both of them could survive and the birth rate were very similar to heterozygous and wild type littermates. Staining for human and mouse PD-1 in stimulated CD8+ and CD4+ T cells indicate the up regulated expression of human PD-1 and absence of mouse PD-1 in these mouse model. Homozygous human PD-1 knock-in mice displayed normal development, and no obvious signs of autoimmunity for at least six months, whereas PD-1 knockout mice developed tissue-specific autoimmunity. With these human PD-1 knock-in mice engrafted with MC38 and treated with anti-human PD-1 antibodies, we confirmed the binding of anti-human antibody to chimeric PD-1 protein, and found anti-human PD-1 antibodies could significantly inhibit tumor growth in these models. Head to head comparison of these mice with current commercial available models for in vivo efficacy studies are undergoing and will reveal how the signal peptide effect the protein refolding or signaling transduction pathway for these ‘human-mouse’ chimeric proteins. In summary, these human PD-1 knock-in mouse models are functional and can be used to evaluate anti-human PD1 antibodies in vivo, we provide more options for antibodies which is targeting PD-1. Citation Format: Qing Lin, Huimin Ma, Xiaoyu Zhang, Hengbin Li, Wenjing Yang, Zhewei Yang, Xingchen Shen, Qunsheng Ji. Alternative humanized PD-1 mouse models provide more options for PD-1 antibody efficacy study in vivo [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1495.
Abstract 2980: The role of USP7 and USP7 inhibitor in HER2+ breast cancer treatment
Authors: Jia Yu, Bo Qin, Judy Boughey, Matthew Goetz, Liewei Wang
Journal: Cancer Research (2019)

Abstract INTRODUCTION: Breast cancer is the most common invasive cancer and the second leading cause of cancer death in women. Approximately 20% of breast cancer tumors overexpress human epidermal growth factor receptor 2 (HER2), which is associated with an aggressive clinical phenotype and with a poorer prognosis. The development of trastuzumab, an immunoglobulin G monoclonal antibody directed against HER2, has changed the treatment paradigm for this disease. However, approximately 15-20% still does not respond to anti-HER2 therapy. Furthermore, despite advances in the management of metastatic HER2-positive breast cancer, response rate varies greatly, with most patients eventually succumbing to their disease. It is crucial to develop additional therapeutic strategies to improve outcomes for HER2 positive patients, especially those with tumors that do not respond to anti-HER2 therapy. METHODS and RESULTS: Using HER2+ breast cancer cell lines, we found that an USP7 inhibitor, P5091, dramatically sensitized cancer cells to HER2 inhibitor, trastuzumab treatment. To confirm it in vivo, we tested the drug combination in BT474 xenografts and found P5091 and trastuzumab synergistically suppressed tumor growth. Furthermore, using trastuzumab resistant HER2+ breast cancer cell line, we found that USP7 inhibitor, P5091, can dramatically re-sensitize trastuzumab-resistant BT474 cell line to trastuzumab treatment both in vitro and in vivo. More importantly, using patient derived xenograft (PDX) HER2+ models, we confirmed the synergistic combination effect of P5091 and trastuzumab. Mechanistically, USP7 inhibitor, P5091 led to significantly increased degradation of all four HER family members (HER1-4). When we knocked down USP7 by RNA interference or small hairpin RNA (shRNA), we observed similar substantial decrease in HER family member proteins. CONCLUSIONS: We have demonstrated the feasibility of using USP7 inhibitor P5091 to sensitize HER2+ breast cancers to trastuzumab treatment. These results provide a rationale for the use of combination therapy of USP7 inhibitors and HER2 inhibitors to treat HER2+ breast cancer. This combination therapy might also be effective in other cancers with upregulated HER signaling, such as GI cancer, lung cancer or ovarian cancer. Citation Format: Jia Yu, Bo Qin, Judy Boughey, Matthew Goetz, Liewei Wang. The role of USP7 and USP7 inhibitor in HER2+ breast cancer treatment [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2980.
Abstract 3528: Novel enzymatic DNA fragmentation integrated into library construction
Authors: Vaishnavi Panchapakesa, Lynne Apone, Karen Duggan, Bradley Langhorst, Chen Song, Pingfang Liu, Timur Shtatland, Christine Rozzi, Christine Sumner, Fiona Stewart, Eileen Dimalanta, Theodore Davis
Journal: Cancer Research (2019)

Abstract Next Generation Sequencing (NGS) is rapidly becoming a powerful tool, by providing a high resolution and global view of the cancer genome mainly through whole genome, whole exome and transcriptome sequencing. This knowledge is important to support drug development targeted towards precision medicine. Obtaining high quality sequencing data begins with optimal sample preparation. DNA fragmentation is one of the critical first steps in the construction of high quality libraries for NGS, but current fragmentation methods create a bottleneck on library preparation throughput. We have developed an efficient, one tube fragmentation system that integrates enzyme-based DNA fragmentation with end-repair and dA-tailing in a single step, followed by adaptor ligation in the same tube. This streamlined method is compatible with a wide range of DNA samples and input amounts, resulting in reproducible and reliable fragment sizes. Genomic DNA (100pg to 500ng) with various GC content, was used in the construction of libraries, that were sequenced on an Illumina platform. For low input samples, PCR amplification was performed prior to sequencing. Libraries constructed using intact genomic DNA and this novel library preparation method produced substantially higher yields than standard methods and mechanically-fragmented DNA. Enzyme-based shearing increases library yield by reducing DNA damage and sample loss. High library yields also enable PCR-free workflows from as little as 50ng starting material. This method can be used for DNA extraction and library preparation from whole blood and dried blood samples.Sequencing quality of libraries generated with inputs ranging from 100pg to 500ng DNA show similar coverage uniformity and fragment size distribution, with minimal GC bias. We have developed an enzymatic DNA fragmentation kit that enables the construction of high quality libraries from a range of sample types and inputs with minimal sequence bias, high yields and low duplication rates. This method eliminates the need for expensive equipment to fragment DNA as well as numerous cleanup and liquid transfer steps thereby reducing the time, cost and errors associated with library construction. These advances in NGS technologies, supported by powerful bioinformatics tools, promises to revolutionize cancer research, diagnosis and therapy. Citation Format: Vaishnavi Panchapakesa, Lynne Apone, Karen Duggan, Bradley Langhorst, Chen Song, Pingfang Liu, Timur Shtatland, Christine Rozzi, Christine Sumner, Fiona Stewart, Eileen Dimalanta, Theodore Davis. Novel enzymatic DNA fragmentation integrated into library construction [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3528.
Immunosuppressant mycophenolic acid biosynthesis employs a new globin-like enzyme for prenyl side chain cleavage
Authors: Xiwei Chen, Lu Wang, Jinmei Zhang, Tao Jiang, Changhua Hu, Dehai Li, Yi Zou
Journal: Acta Pharmaceutica Sinica B (2019)

Mycophenolic acid (MPA, 1) and its derivatives are first-line immunosuppressants used in organ transplantation and for treating autoimmune diseases. Despite chemical synthetic achievements, the biosynthetic formation of a seven-carbon carboxylic acid pharmacophore side chain of 1, especially the processes involving the cleavage of the prenyl side chain between DHMP (4) and DMMPA (5), remains unknown. In this work, we identified a membrane-bound prenyltransferase, PgMpaA, that transfers FPP to 4 to yield FDHMP (6). Compound 6 undergoes the first cleavage step via a new globin-like enzyme PgMpaB to form a cryptic intermediate 12. Heterologous expression of PgMpa genes in Aspergillus nidulans demonstrates that the second cleavage step (from 12 to 5) of 1 is a PgMpa cluster-independent process in vivo. Our results, especially the discovery of the broad tolerance of substrates recognized by PgMpaB, set up a strategy for the formation of "pseudo-isopentenyl" natural products using fungal globin-like enzymes.
Abstract 5193: Conditional knockout of histone chaperone FACT in mice: Consequences for normal tissues
Authors: Masaki A. Ito, Poorva Sandlesh, Imon Goswami, Laura A. Prendergast, Katerina Gurova
Journal: Cancer Research (2019)

Abstract Histone chaperone FAcilitates Chromatin Transcription (FACT) is, a complex of SSRP1 and SPT16, involved in chromatin remodeling during transcription, replication, and DNA repair. FACT is selectively expressed during early stages of development and later exclusively present in the stem cell niches in adult normal tissues. It is expressed in undifferentiated aggressive tumors with poor prognosis.¹ FACT inhibition is not tolerated by most tumor, unlike normal cells. This vulnerability of tumor cells upon FACT inactivation suggests evaluating FACT inhibition as an antitumor therapeutic approach.¹ Since FACT knockout (KO) is embryonically lethal (E3.5),² study of FACT’s function in different non-tumor cells of mammalian organisms was not possible and was mostly studied in single cell organisms and in tumor cell lines. Therefore, to assess the safety of FACT inhibition as an anticancer approach, by understanding its role in normal physiology, we generated a conditional KO of Ssrp1 mouse model using CreERT2-LoxP system.³ We harvested stem cells of different lineages to better understand the role of FACT in normal mouse physiology. Using the hematopoietic stem cells (HSCs) from the bone marrow (BM), we performed BM colony formation assay. We found that FACT inactivation significantly decreased the number of colonies of HSCs. Furthermore, inhibiting FACT significantly increased caspase 3 expression in mouse adipose stem cells (ASCs), resulting in apoptosis and decreased survival. These results prompted us to comprehensively evaluate roles of FACT in stem cell development and survival. To this end, fibroblasts in a conditional knockout mouse were reprogrammed by retroviral vector encoding four pluripotency transcription factors (Oct3/4, Klf4, Sox2 and c-Myc). We have found successful generation of induced pluripotent stem (iPS) cells 14 days after reprogramming. In conclusion, FACT associates with development and/or survival of mouse HSCs and ASCs. Further evaluation using iPS cells is expected to delineate roles of FACT in various stages of stem cell development and thus normal physiology. 1. Garcia H, et al. Cell Rep, 2013 4(1) 2. Cao S, et al. Mol Cel Bio. 2003 23(15) 3. Sandlesh P et al. PLOS ONE. 2018 13(6) Citation Format: Masaki A. Ito, Poorva Sandlesh, Imon Goswami, Laura A. Prendergast, Katerina Gurova. Conditional knockout of histone chaperone FACT in mice: Consequences for normal tissues [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 5193.
Abstract 14049: Outcomes of Post-operative Atrial Fibrillation After Lung Transplantation: A Meta-analysis.
Authors: Marwan Saad, Akram Y Elgendy, Amgad Mentias, Amr F Barakat, Hesham K Abdelaziz, Ahmed Abuzaid, Islam Y Elgendy, Ahmed N Mahmoud
Journal: Circulation (2016)

Background: Post-lung transplantation atrial fibrillation is relatively common. The outcomes of such complication remain uncertain. Objectives: To systematically evaluate the impact of post-lung tr...
Abstract 1048: CD44 promotes epithelial-mesenchymal transition (EMT) by regulating snail, ZEB1, and Caveolin-1 expression and predicts poor survival of ovarian cancer
Authors: Jiayi Zhou, Yan Du, Baoxin Luan, Yinhua Yu, Hongbo Zhao
Journal: Cancer Research (2019)

Abstract CD44 is a stem cell marker which is involved in the generation of a stem cell niche and maintaining stem cell quiescence. Our data first demonstrated that CD44 knockdown by small silencing RNA abrogated both basal Snail expression and TGF-β1 induced Snail expression in HOPM and HOPM-snail cells. In addition, CD44 knockdown caused an decrease in ZEB1 expression. Further, RPPA data indicated that Caveolin-1 may be another regulative target of CD44, and western blotting analysis confirmed that CD44 knockdown caused an increase in Caveolin-1 expression. However, there was no obvious reciprocal regulation among ZEB1, Caveolin-1, and snail. Moreover, CD44 knockdown caused a decrease in cell migration, cell invasion and clone formation of HOPM and HOPM-snail cells. We next observed the role of CD44 expression in the prognosis of ovarian cancer. Over-expression of CD44 was associated with advanced FIGO stage (P&amp;lt;0.05). Univariate analysis result showed that histological subtype, FIGO stage, intravascular tumor thrombus, CA125 and CD44 expression were associated with overall survival and disease-free survival of ovarian cancer patients. Multivariate analysis showed that CD44 expression was an independent prognostic factor to predict both overall survival and disease-free survival of ovarian cancer patients. Taken together, our data showed that CD44 may be crucial for EMT process by regulating Snail, ZEB1, and Caveolin-1 expression. And CD44 is a potential prognostic factor as well as a treatment target for ovarian cancer. Citation Format: Jiayi Zhou, Yan Du, Baoxin Luan, Yinhua Yu, Hongbo Zhao. CD44 promotes epithelial-mesenchymal transition (EMT) by regulating snail, ZEB1, and Caveolin-1 expression and predicts poor survival of ovarian cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1048.
Abstract P151: Primary ASCVD Risk Associated With Undiagnosed Conditions Decreased Over NHANES 1999-2014
Authors: David R Nelson, Jessica A Davis
Journal: Circulation (2018)

Introduction: Atherosclerotic cardiovascular disease (ASCVD) is a general term for a group of diseases characterized by atherosclerosis that affect the heart and blood vessels. ASCVD is the leading cause of death in the United States contributing to at least 200,000 preventable deaths from heart disease and stroke each year. Cardiovascular disease, heart disease, and stroke mortality has declined since the year 2000, due to broader use of evidence-based therapies and changes to risk factors and lifestyle modifications, but the decline began to slow after 2011. Two main risk factors contributing to ASCVD are high blood pressure and high cholesterol. Efforts have been made to increase control of these factors at the population-level, however, only those who are diagnosed can be treated. While awareness has increased over time, there is still a significant contribution to ASCVD events from those who were undiagnosed but have high blood pressure, high cholesterol, and/or diabetes. Hypothesis: To assess how much of the total U.S. population ASCVD risk is undiagnosed from 1999-2014. Methods: The Pooled Cohort Equations assessed 10-year ASCVD risk, based on age, sex, race, total cholesterol, HDL level, systolic blood pressure, use of blood pressure medication, smoking status, and diabetes status. The undiagnosed risk of the primary risk population (age 40-79 years, without missing values for necessary cholesterol, blood pressure, and glucose measures) from 1999-2014 Continuous National Health and Nutrition Examination Survey (NHANES) was calculated based on self-report questions and clinical measures, after age, sex, race, smoking, and diagnosed risks were accounted for. Linear regression for complex survey data tested whether undiagnosed risk was changing over time. Results: Applying the ASCVD risk equation to the NHANES subset (n=8,763; weighted n=104,421,757), undiagnosed conditions were associated with 10% of the projected ASCVD events. That is, per 100,000 Americans in this subset, 7,747 ASCVD events were estimated over 10-years, and 800 were based on risk from undiagnosed diabetes, hypercholesterolemia, or hypertension. However, ASCVD risk associated with undiagnosed conditions over time decreased (p&lt;0.001), from 1,169 per 100,000 in 1999-2000, to 642 per 100,000 in 2013-2014. Conclusions: NHANES creates a unique opportunity to quantify undiagnosed ASCVD risk in a nationally representative sample. Since 1999, a sizeable portion of the US primary ASCVD risk was based on undiagnosed conditions, however, this proportion of undiagnosed risk decreased over time.