tbuckley/cabot-search huggingface dataset:
Abstract A77: Screening of conditionally reprogrammed patient-derived carcinoma cells identifies ERCC3-MYC interactions as a target in pancreatic cancer
Authors: Igor Astsaturov, Sandra A. Jablonski, Yan Zhou, Ilya Serebriiskii, Paz Keren, Louis M. Weiner, Erica Golemis, Vladimir Khazak
Journal: Cancer Research (2016)

Abstract Methods: Pancreatic ductal adenocarcinoma (PDAC) is a devastating malignancy that affects 44,000 individuals yearly in the US. The list of agents active against PDAC is limited. We explored in an unbiased fashion the clinically available drugs to identify novel cytotoxics using new physiological models for PDAC including cells rapidly expanded in vitro from surgical or xenografted tumors (PDX). Results: Not unexpectedly, only a small minority of agents showed activity against pancreatic carcinoma cells in vitro. Among these, transcriptional repressors and drugs interfering with protein folding and biosynthesis ranked as most cytotoxic. Triptolide, a covalent inhibitor of the ERCC3, a bifunctional regulator of transcription and DNA repair, was most consistently effective in vitro and highly effective in vivo, causing prolonged complete regression in multiple PDX models. Importantly, triptolide showed superior activity in MYC-amplified PDX models, suggesting a critical role for ERCC3 in this subset. Triptolide elicited rapid and profound depletion of MYC oncoprotein, a transcriptional co-factor for ERCC3. Expression of ERCC3 was MYC-dependent, while resistance to triptolide was associated with elevated ERCC3 and MYC expression. Furthermore, high ERCC3 mRNA level was associated with decreased survival of PDAC patients. Conclusions: These findings provide preclinical evidences for transcriptional vulnerability in PDAC via ERCC3 targeting and a new mechanistic approach for disruption of MYC-dependent pancreatic cancers. Citation Format: Igor Astsaturov, Sandra A. Jablonski, Yan Zhou, Ilya Serebriiskii, Paz Keren, Louis M. Weiner, Erica Golemis, Vladimir Khazak.{Authors}. Screening of conditionally reprogrammed patient-derived carcinoma cells identifies ERCC3-MYC interactions as a target in pancreatic cancer. [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer: Advances in Science and Clinical Care; 2016 May 12-15; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2016;76(24 Suppl):Abstract nr A77.
Abstract 3288: The KCNA5 promoter is hypermethylated in Ewing sarcoma and silencing contributes to cell proliferation
Authors: Katherine Ryland, Allegra Hawkins, Daniel J. Weisenberger, Scott Borinstein, Peter W. Laird, Jeffrey R. Martens, Elizabeth R. Lawlor
Journal: Cancer Research (2015)

Abstract Potassium channels regulate a variety of biological processes and dysfunction of these channels contributes to cancer initiation and progression. We recently showed that the KCNA5-encoded channel, Kv1.5, is a target of polycomb-group (PcG)-dependent repression in aggressive pediatric solid tumors and that this epigenetic silencing of the Kv1.5 channel contributes to cell survival under hypoxic stress. In human cancer, the promoters of PcG target genes are often subject to aberrant DNA hypermethylation. Therefore, in the current study we investigated whether the KCNA5 locus is hypermethylated in Ewing sarcoma. The methylation status of KCNA5 was determined in tumor samples, non-transformed cells and a panel of cancer cell lines using a custom Illumina GoldenGate® methylation array and by MethyLight. Promoter methylation and expression of KCNA5 were measured by MethyLight and qRT-PCR, respectively, before and after exposure to decitabine. Proliferation was assessed in untreated and decitabine treated cells in the presence or absence of the Kv1.5 channel blocker diphenyl phosphine oxide-1 (DPO-1). Methylation array studies of normal tissues and Ewing sarcoma tumors and cell lines showed that the KCNA5 promoter is hypermethylated in Ewing sarcoma compared to normal tissues. This hypermethylation was confirmed by MethyLight analysis in an independent set of primary tumors and cell lines. These studies also showed that methylation was relatively higher in cell lines than primary tumors. Exposure of Ewing sarcoma cells to decitabine led to demethylation of the KCNA5 promoter and directly correlated with increased expression of the KCNA5 transcript. Decitabine treatment did not affect the viability of Ewing sarcoma cell lines; however it led to a decreased proliferation. Significantly, pharmacologic inhibition of the Kv1.5 channel by DPO-1 partially reversed the decitabine-induced reduction in cell proliferation in three different cell lines (TC-71, A673 and A4573). Together these studies show that the KCNA5 promoter is hypermethylated in Ewing sarcoma and that inactivation of the Kv1.5 channel promotes cell proliferation. This work identifies DNA methylation as another epigenetic mechanism that regulates KCNA5 expression in cancer and further implicates epigenetic repression of the Kv1.5 potassium ion channel in tumor pathogenesis. Citation Format: Katherine Ryland, Allegra Hawkins, Daniel J. Weisenberger, Scott Borinstein, Peter W. Laird, Jeffrey R. Martens, Elizabeth R. Lawlor. The KCNA5 promoter is hypermethylated in Ewing sarcoma and silencing contributes to cell proliferation. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 3288. doi:10.1158/1538-7445.AM2015-3288
Specimen Source (BM or PB) Does Not Affect Proteomic Signaling In Patients with AML and Circulating Blasts
Authors: Alessandra Cesano, David B. Rosen, Santosh Putta, Urte Gayko, Larry Cripe, Zhuoxin Sun, Hajime Uno, Mark R. Litzow, Martin S. Tallman, Elisabeth Paietta
Journal: Blood (2010)
The complexity of interpreting genomic data in patients with acute myeloid leukemia
Authors: A Nazha, A Zarzour, K Al-Issa, T Radivoyevitch, H E Carraway, C M Hirsch, B Przychodzen, B J Patel, M Clemente, S R Sanikommu, M Kalaycio, J P Maciejewski, M A Sekeres
Journal: Blood Cancer Journal (2016)

Acute myeloid leukemia (AML) is a heterogeneous neoplasm characterized by the accumulation of complex genetic alterations responsible for the initiation and progression of the disease. Translating genomic information into clinical practice remained challenging with conflicting results regarding the impact of certain mutations on disease phenotype and overall survival (OS) especially when clinical variables are controlled for when interpreting the result. We sequenced the coding region for 62 genes in 468 patients with secondary AML (sAML) and primary AML (pAML). Overall, mutations in FLT3, DNMT3A, NPM1 and IDH2 were more specific for pAML whereas UTAF1, STAG2, BCORL1, BCOR, EZH2, JAK2, CBL, PRPF8, SF3B1, ASXL1 and DHX29 were more specific for sAML. However, in multivariate analysis that included clinical variables, only FLT3 and DNMT3A remained specific for pAML and EZH2, BCOR, SF3B1 and ASXL1 for sAML. When the impact of mutations on OS was evaluated in the entire cohort, mutations in DNMT3A, PRPF8, ASXL1, CBL EZH2 and TP53 had a negative impact on OS; no mutation impacted OS favorably; however, in a cox multivariate analysis that included clinical data, mutations in DNMT3A, ASXL1, CBL, EZH2 and TP53 became significant. Thus, controlling for clinical variables is important when interpreting genomic data in AML.
Skeletal muscle inflammation and insulin resistance in obesity
Authors: Huaizhu Wu, Christie M. Ballantyne
Journal: Journal of Clinical Investigation (2017)

Obesity is associated with chronic inflammation, which contributes to insulin resistance and type 2 diabetes mellitus. Under normal conditions, skeletal muscle is responsible for the majority of insulin-stimulated whole-body glucose disposal; thus, dysregulation of skeletal muscle metabolism can strongly influence whole-body glucose homeostasis and insulin sensitivity. Increasing evidence suggests that inflammation occurs in skeletal muscle in obesity and is mainly manifested by increased immune cell infiltration and proinflammatory activation in intermyocellular and perimuscular adipose tissue. By secreting proinflammatory molecules, immune cells may induce myocyte inflammation, adversely regulate myocyte metabolism, and contribute to insulin resistance via paracrine effects. Increased influx of fatty acids and inflammatory molecules from other tissues, particularly visceral adipose tissue, can also induce muscle inflammation and negatively regulate myocyte metabolism, leading to insulin resistance.
Current Pharmacological Approaches to Reduce Chorea in Huntington’s Disease
Authors: Emma M. Coppen, Raymund A. C. Roos
Journal: Drugs (2016)

There are currently no effective pharmacological agents available to stop or prevent the progression of Huntington's disease (HD), a rare hereditary neurodegenerative disorder. In addition to psychiatric symptoms and cognitive impairments, HD causes progressive motor disturbances, in particular choreiform movements, which are characterized by unwanted contractions of the facial muscles, trunk and extremities. Management of choreiform movements is usually advised if chorea interferes with daily functioning, causes social isolation, gait instability, falls, or physical injury. Although drugs to reduce chorea are available, only few randomized controlled studies have assessed the efficacy of these drugs, resulting in a high variety of prescribed drugs in clinical practice. The current pharmacological treatment options to reduce chorea in HD are outlined in this review, including the latest results on deutetrabenazine, a newly developed pharmacological agent similar to tetrabenazine, but with suggested less peak dose side effects. A review of the existing literature was conducted using the PubMed, Cochrane and Medline databases. In conclusion, mainly tetrabenazine, tiapride (in European countries), olanzapine, and risperidone are the preferred first choice drugs to reduce chorea among HD experts. In the existing literature, these drugs also show a beneficial effect on motor symptom severity and improvement of psychiatric symptoms. Generally, it is recommended to start with a low dose and increase the dose with close monitoring of any adverse effects. New interesting agents, such as deutetrabenazine and pridopidine, are currently under development and more randomized controlled trials are warranted to assess the efficacy on chorea severity in HD.
Whole-Transcriptome Sequencing of a Chronic Myeloid Leukemia (CML) Patient at Diagnosis and at the Time of Progression to Blast Crisis (BC).
Authors: Simona Soverini, Enrico Giacomelli, Alberto Ferrarini, Luciano Xumerle, Sabrina Colarossi, Alessandra Gnani, Fausto Castagnetti, Carolina Terragna, Sandra Durante, Annalisa Astolfi, Serena Formica, Giulia Marzocchi, Nicoletta Testoni, Ilaria Iacobucci, Angela Poerio, Francesca Palandri, Gabriele Gugliotta, Marilina Amabile, Gianantonio Rosti, Michele Baccarani, Massimo Delledonne, Giovanni Martinelli
Journal: Blood (2009)
CD20 Antigen Expression Is Increased in Trisomy 12 CLL as Compared to Other Cytogenetic Subtypes.
Authors: Constantine S. Tam, Joselle Otero-Palacios, Susan Lerner, Lynne V. Abruzzo, Jeffrey L. Jorgensen, Alessandra Ferrajoli, William G. Wierda, Susan O’Brien, Michael J. Keating
Journal: Blood (2006)
Effects of Early Integrated Palliative Care in Patients With Lung and GI Cancer: A Randomized Clinical Trial
Authors: Jennifer S. Temel, Joseph A. Greer, Areej El-Jawahri, William F. Pirl, Elyse R. Park, Vicki A. Jackson, Anthony L. Back, Mihir Kamdar, Juliet Jacobsen, Eva H. Chittenden, Simone P. Rinaldi, Emily R. Gallagher, Justin R. Eusebio, Zhigang Li, Alona Muzikansky, David P. Ryan
Journal: Journal of Clinical Oncology (2017)

Purpose We evaluated the impact of early integrated palliative care (PC) in patients with newly diagnosed lung and GI cancer. Patients and Methods We randomly assigned patients with newly diagnosed incurable lung or noncolorectal GI cancer to receive either early integrated PC and oncology care (n = 175) or usual care (n = 175) between May 2011 and July 2015. Patients who were assigned to the intervention met with a PC clinician at least once per month until death, whereas those who received usual care consulted a PC clinician upon request. The primary end point was change in quality of life (QOL) from baseline to week 12, per scoring by the Functional Assessment of Cancer Therapy-General scale. Secondary end points included change in QOL from baseline to week 24, change in depression per the Patient Health Questionnaire-9, and differences in end-of-life communication. Results Intervention patients ( v usual care) reported greater improvement in QOL from baseline to week 24 (1.59 v -3.40; P = .010) but not week 12 (0.39 v -1.13; P = .339). Intervention patients also reported lower depression at week 24, controlling for baseline scores (adjusted mean difference, -1.17; 95% CI, -2.33 to -0.01; P = .048). Intervention effects varied by cancer type, such that intervention patients with lung cancer reported improvements in QOL and depression at 12 and 24 weeks, whereas usual care patients with lung cancer reported deterioration. Patients with GI cancers in both study groups reported improvements in QOL and mood by week 12. Intervention patients versus usual care patients were more likely to discuss their wishes with their oncologist if they were dying (30.2% v 14.5%; P = .004). Conclusion For patients with newly diagnosed incurable cancers, early integrated PC improved QOL and other salient outcomes, with differential effects by cancer type. Early integrated PC may be most effective if targeted to the specific needs of each patient population.
'First-in-human' phase I dose escalation trial of IL-15N72D/IL-15Rα-Fc superagonist complex (ALT-803) demonstrates immune activation with anti-tumor activity in patients with relapsed hematological malignancy
Authors: Jeffrey S. Miller, Sarah Cooley, Shernan Holtan, Mukta Arora, Celalettin Ustun, Emily Jeng, Hing C. Wong, Michael R. Verneris, John E. Wagner, Daniel J. Weisdorf, Bruce R. Blazar, Todd A Fehniger, Rizwan Romee
Journal: Blood (2015)
Abstract IA23: Immune landscape of human pancreatic cancer
Authors: David Balli, Andrew J. Rech, Ben Z. Stanger, Robert H. Vonderheide
Journal: Cancer Research (2016)

Abstract Survival rates for pancreatic ductal adenocarcinoma (PDA) remain dismal. Immunotherapy has the potential to improve outcomes, but clinical trial results – particularly those employing single-agent CTLA4 or PD1/PD-L1 inhibition – have thus far been disappointing. We stratified human PDA based on a signature of cytolytic T-cell activity. Differences in cytolytic index correlated with defined PDA subtypes and distinct mutational events. Specifically, PDA tumors with low cytolytic activity exhibited increased genomic structural variation, including reproducible copy number alterations in MYC, FGFR1, NOTCH2, and CDKN2. In contrast to other tumors such as kidney cancer or melanoma, PDA tumors with a high cytolytic index lacked an increased mutation or neo-epitope load. Tumors with high cytolytic activity exhibited increased expression of several immune checkpoint genes, but PD-L1 expression was uniformly low. These data establish a link between genomic alterations and immune activation in PDA and suggest that immune checkpoints other than PD-L1/PD-1 may be attractive therapeutic targets in this lethal disease. Citation Format: David Balli, Andrew J. Rech, Ben Z. Stanger, Robert H. Vonderheide.{Authors}. Immune landscape of human pancreatic cancer. [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer: Advances in Science and Clinical Care; 2016 May 12-15; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2016;76(24 Suppl):Abstract nr IA23.
Comparative Effectiveness of Nonsteroidal Anti-inflammatory Drug Treatment vs No Treatment for Patent Ductus Arteriosus in Preterm Infants
Authors: Jonathan L. Slaughter, Patricia B. Reagan, Thomas B. Newman, Mark A. Klebanoff
Journal: JAMA Pediatrics (2017)

Patent ductus arteriosus (PDA) is associated with increased mortality and worsened respiratory outcomes, including bronchopulmonary dysplasia (BPD), in preterm infants. Nonsteroidal anti-inflammatory drugs (NSAIDs) are efficacious in closing PDA, but the effectiveness of NSAID-mediated PDA closure in improving mortality and preventing BPD is unclear.To determine the effectiveness of NSAID treatment for PDA in reducing mortality and moderate/severe BPD at 36 weeks postmenstrual age.This cohort study included 12 018 infants born at 28 gestational weeks or younger discharged between January 2006 and December 2013 from neonatal intensive care units in 25 US children's hospitals included in the Pediatric Health Information System. We performed an instrumental variable analysis that incorporated clinician preference-based, institutional variation in NSAID treatment frequency to determine the effect of NSAID treatment for PDA on mortality and BPD.Proportion of NSAID-treated infants born at each infant's institution within ±6 months of that infant's birth.The primary composite outcome was death, moderate, or severe BPD at 36 weeks postmenstrual age.Of the 6370 male and 5648 female infants in this study, 4995 (42%) were white, 3176 (26%) were African American, 1823 (15%) were Hispanic, and 1555 (13%) were other races/ethnicities. The proportion of NSAID-treated infants at each infant's hospital within ±6 months of that infant's birth was associated with NSAID treatment and not associated with gestation, race/ethnicity, or sex. An infant's chances of receiving NSAID treatment increased by 0.84% (95% CI, 0.8-0.9; P < .001) for every 1% increase in the annual NSAID treatment percentage at a given hospital. An instrumental variable analysis demonstrated no association between NSAID treatment and the odds of mortality or BPD (odds ratio, 0.94; 95% CI, 0.70-1.25; P = .69), mortality (odds ratio, 0.73; 95% CI, 0.43-1.13; P = .18), or BPD (odds ratio, 1.01; 95% CI, 0.73-1.45; P = .94) in survivors.When we incorporated clinician preference-based practice variation as an instrument to minimize the effect of unmeasured confounding, we detected no changes in the odds of mortality or moderate/severe BPD among similar preterm infants born at 28 weeks or younger following NSAID treatment for PDA initiated 2 to 28 days postnatally. Our findings agree with available randomized clinical trial evidence and support a conservative approach to PDA management.
Abstract 1780: Targeted inactivation of CRL4-CDT2 E3 ubiquitin ligase as a novel therapeutic strategy for malignant melanoma
Authors: Mouadh Benamar, Fadila Guessous, Patrick Corbett, Craig L. Slingluff, Tarek Abbas
Journal: Cancer Research (2015)

Abstract The CRL4CDT2 E3 ubiquitin ligase is emerging as a critical regulator cell cycle progression, primarily through the targeted ubiquitylation and degradation of critical cell cycle regulators including CDT1, p21 and SET8 via the 26S proteasome. CDT2, the substrate receptor of the CRL4CDT2 E3 ligase is overexpressed or amplified in several human malignancies, but its role in the development or progression of these cancers remains elusive. We show that CDT2 is overexpressed in primary and metastatic melanoma. Targeted depletion of CDT2 by si-RNA or its pharmacological inhibition by MLN4924, a selective NEDD8-activating enzyme (NAE) inhibitor, suppressed the proliferation of melanoma cancer cells in vitro and inhibited tumor growth of human melanoma xenografts in mice, irrespective of the BRAF mutation status. Inhibition of CRL4CDT2 in melanoma cells with various genetic backgrounds, but not in immortalized human melanocytes, resulted in robust p21- and SET8-dependent rereplication. These results identify the CRL4CDT2 E3 ubiquitin ligase as a promising new therapeutic target for cutaneous melanoma, and demonstrate the efficacy of MLN4924 as a promising anti-melanoma agent. Citation Format: Mouadh Benamar, Fadila Guessous, Patrick Corbett, Craig L. Slingluff, Tarek Abbas. Targeted inactivation of CRL4-CDT2 E3 ubiquitin ligase as a novel therapeutic strategy for malignant melanoma. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 1780. doi:10.1158/1538-7445.AM2015-1780
Abstract 3518: Growth inhibition of SCLC cell lines by treatment with LSD1 inhibitors is associated with modulation of neuroendocrine pathways
Authors: Thomas A. Paul, Shikhar Sharma, Jill Hallin, Tao Xie, Timothy Nichols, Mike Greig, James Hardwick, Martin Wythes, Dominique Verhelle
Journal: Cancer Research (2015)

Abstract Small cell lung cancer (SCLC) is an aggressive malignancy with a high propensity for early metastasis. Response rates to first-line chemotherapy are typically high, but short lived. We describe an epigenetic-based mechanism for targeting SCLC using inhibitors for the LSD1 histone lysine demethylase. Mechanistically reversible and irreversible LSD1 inhibitors (GSK690 and OG-86) demonstrate induction of either cell cycle arrest or apoptosis in 54% of SCLC cell lines (12/22) that becomes apparent upon continuous treatment for 7-to-10 days. Maximal rates of growth inhibition in sensitive cell lines vary from 50-to-95% and plateaus between 18-to-21 days of LSD1 inhibitor treatment. Thus, heterogeneous sensitivity to LSD1 inhibitors exists between cell line models as well as within subpopulations of cells in the same cell line. To understand the mechanisms underlying LSD1 inhibitor activity in SCLC we have performed RNA-seq and ChIP-seq experiments coupled with bioinformatic analysis of expression signatures in sensitive and resistant models. Our data indicate that although LSD1 is over-expressed in SCLC cell lines and patient samples relative to non-small cell lung cancers, high LSD1 expression does not predict sensitivity to LSD1 inhibitors. Pathway analysis demonstrates that LSD1 inhibition modulates the expression of genes involved in cell adhesion and axon guidance including members of the Ephrin and Semaphorins families. At LSD1 target genes, we demonstrate site-specific H3K4me2 histone methylation changes overlapping LSD1 binding sites, however no global changes in H3K4me2 were observed. Interestingly we find morphological and cell adhesion changes in sensitive cell lines that coincide with expression changes in markers of neuroendocrine differentiation of SCLC such as GRP, NCAM, and NEUROD1. Based on these data, we propose a model that LSD1 inhibition modulates the neuroendocrine differentiation program of SCLC cells promoting tumor inhibition in sensitive SCLC models. Citation Format: Thomas A. Paul, Shikhar Sharma, Jill Hallin, Tao Xie, Timothy Nichols, Mike Greig, James Hardwick, Martin Wythes, Dominique Verhelle. Growth inhibition of SCLC cell lines by treatment with LSD1 inhibitors is associated with modulation of neuroendocrine pathways. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 3518. doi:10.1158/1538-7445.AM2015-3518