tbuckley/cabot-search huggingface dataset:
Abstract 1998: Alternative polyadenylation of eukaryotic initiation factor 5A-2 (eIF5A-2) mRNAs examined by quadruplex single molecule RNA fluorescence <i>in situ</i> hybridization (smRNA-FISH)
Authors: Hans E. Johansson, Raymund H. Yin, Swati Mandal, Myung-Hee Park
Journal: Cancer Research (2016)

Abstract Normal expression of the minor oncogene EIF5A2 in the hypusine pathway is restricted to brain and testis. However aberrant expression has been noted in multiple cancers, including ovarian gastric, colorectal and pancreatic, and artificial overexpression causes tumor growth in naked mice. Unlike cDNAs from the homologous gene EIF5A1, which are readily translated into protein upon transient transfection, EIF5A2-mRNAs only associate with monosomes without production of eIF5A-2 protein. Here we present data from multiple EIF5A2-positive cell lines on the steady state levels of the four different EIF5A2-mRNAs that arise through differential polyadenylation. While considering qPCR and RNA-Seq, we chose to apply Stellaris single molecule RNA fluorescence in situ hybridization with four unique probe sets, each reporting on the dependent A, B, C, or D segments. The probe sets were designed with multiple tiled singly labeled 18-22-mer oligonucleotides with balanced GC content, and hence similar hybridization characteristics, which in turn enabled the simultaneous quadruplex smRNA FISH. Stellaris RNA FISH leaves the cell intact, and also does not require RNA isolation or nucleic acid amplification that may introduce an otherwise hidden experimental bias. The single molecule spots revealed by widefield microscopy and subsequent image analysis co-localized with a high degree of confidence. Taking advantage of the added spatial dimension that RNA FISH affords, we also determined the localization of each mRNA variant and recorded the cell-to-cell variability and the actual range of mRNA copy numbers per cell. Our data is consistent with previous gene expression analysis data, but also provide actual counts of each mRNA variant. The results presented here have direct applications for the expression of the minor oncogene EIF5A2, and the regulated protein synthesis of its mRNAs, as well as of other mRNAs in polyamine and hypusine pathways. Further, the techniques and probes developed here can be directly transferred to the analysis of other mRNA variants that may arise through alternative transcription start site use, alternative splicing or alternative 3’ end processing in normal and aberrant cells. Citation Format: Hans E. Johansson, Raymund H. Yin, Swati Mandal, Myung-Hee Park. Alternative polyadenylation of eukaryotic initiation factor 5A-2 (eIF5A-2) mRNAs examined by quadruplex single molecule RNA fluorescence in situ hybridization (smRNA-FISH). [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1998.
Stereotactic body radiotherapy of spine metastasis.
Authors: S. Lee, C. Min, G. Kim, D. Cho, W. Chung
Journal: Journal of Clinical Oncology (2010)

e19632 Background: We conducted this study to analyze the treatment outcomes and the factors associated with pain relief in patients treated with stereotactic body radiotherapy (SBRT) using Cyberknife for spine metastasis. Methods: We retrospectively reviewed patients who received SBRT for spinal metastasis between April 2007 and June 2009 in Konyang University Hospital, Daejeon, Korea. The treatment response was evaluated by the assessment of pain and neurologic status and the review of radiologic studies. Pain was assessed by verbal/visual analogue scale; from 0 (no pain) to 10 (the worst imaginable pain). Pain relief was defined as a decrease of at least three levels of the pain score without an increase in analgesic consumption. Complete relief was defined as no analgesics or score 0 or 1. Pain progression was defined as an increase in the pain score by three levels and/or increase pain medication. Results: 57 patients with 73 lesions have been reviewed. The follow up period was median 6.8 months (range, 1-31 months). Primary tumor sites were: breast 23%, hepatocellular carcinoma 16%, lung 15%, biliary tract 11%, colorectum 8%, cervix 8%, prostate 5%, stomach 4%, and others 8%. The treated spines were: cervical 18%, thoracic 38%, lumbar 30%, and sacral 14% lesions. The majority of patients (70% of the lesions) experienced moderate to severe pain. Of 59 lesions with pain relief, complete relief was seen in 57% (34 lesions). The time to achieve pain relief was during radiosurgery or within 7 days after radiosurgery. The median duration of pain relief was 3.2 months (range: 1-30). In our results, only performance status (p = 0.002) and the number of treated spine (p = 0.005) affects on the response of palliation for painful bone metastasis in patients treated with stereotactic radiosurgery by the multivariable Cox proportional hazards models. Conclusions: Spine SBRT in patients with spinal metastasis is feasible and safety. SBRT is an effective modality as palliative therapy. No significant financial relationships to disclose.
S87 Differential Inflammatory Responses of Primary Bronchial Epithelial Cells from Subjects with COPD, Healthy Smokers and Never Smokers: Abstract S87 Table 1
Authors: D Comer, M Ennis, JS Elborn
Journal: Thorax (2012)

<h3>Introduction</h3> We investigated the responses of primary bronchial epithelial cells (PBECs) obtained from subjects with COPD, healthy smokers (HS), and non-smokers (NS) to cigarette smoke extract (CSE) treatment. We hypothesised that PBECs from subjects with COPD respond differently to CSE and <i>Pseudomonas aeruginosa</i> lipopolysaccharide (PA LPS) stimulation than PBECs obtained from HS and NS. <h3>Methods</h3> PBECs from 16 COPD subjects, 11 HS and 10 NS were obtained at fibreoptic bronchoscopy and cultured up to air-liquid interface and stimulated with PA LPS, either with or without pre-treatment with CSE for 24 h. COPD patients and HS were similar for smoking history in pack years and all 3 groups were matched for age. Apoptosis was evaluated using Annexin-V staining and the terminal transferase-mediated dUTP nick end-labelling (TUNEL) method. IL-6 and IL-8 were measured by ELISA and Toll-like receptor 4 expression by flow cytometry. CSE was prepared by combusting 1 Marlboro cigarette through 25 ml of media. Activation of NF-κB, mitogen-activated protein kinase (MAPK), and caspase-3 were determined by western blotting. <h3>Results</h3> Constitutive release of IL-8 and IL-6 was greatest from the COPD cultures. 5% CSE pre-treatment followed by PA LPS stimulation reduced cytokine release from COPD PBECs, but increased the release from HS and NS cultures. Constitutive TLR-4 expression, MAPK and NF-κB activation were reduced only in COPD cultures after 5% CSE treatment. After treatment with CSE for 24 h, 44% of the COPD cells were apoptotic and 9% necrotic, whereas only 18% of the healthy smoker’s cells and 6% of the non-smokers cells were apoptotic, with no cells in the latter 2 groups becoming necrotic. COPD cultures had the highest levels of cleaved caspase-3 after CSE treatment. <h3>Conclusions</h3> 5% CSE attenuates inflammatory responses to LPS in cells from people with COPD but not from NS or HS. COPD epithelial cells have an increased susceptibility to apoptosis. Research funded by NI RDO.
Abstract 1264: Targeting nuclear receptors and their coregulators in triple-negative breast cancer
Authors: Ya-Fang Chang, Yuhao Wang, Geoffrey Greene
Journal: Cancer Research (2016)

Abstract Metastasis and chemoresistance remain significant challenges in treating triple-negative breast cancer (TNBC). Nuclear receptors (NRs) are ligand-inducible transcriptional factors that play essential roles in key biological processes from embryonic development to differentiation, regulation of gene expression, and homeostasis, and their dysregulation has been implicated in many different pathologies including cancer. Using MDA-MB-231 cells as a model, we performed a siRNA screening to determine the importance of NRs and their co-regulators in cancer cell proliferation and death of TNBC. A total of 84 siRNA pools, each targeting a different gene, were evaluated. To further validate the candidate genes, we transfected MDA-MB-231 cells with each of the four individual siRNAs comprising each pool. The effect of candidate genes on the invasion and chemoresistance of TNBC cell lines was also assayed in vitro. Among 4 candidate genes, we focused in greater depth on steroid receptor coactivator-3 (NCOA3), which is a member of the p160 steroid receptor coactivators and found to be overexpressed in breast cancer. We found that although NCOA3 knockdown moderately inhibited the tumor growth of TNBC cells (MDA-MB-231, BT549, and HS578), the addition of siNCOA3 and paclitaxel significantly decreased cell proliferation and increased caspase-3/7 activity. In transwell invasion assays, NCOA3 knockdown also significantly decreased the invasion of TNBC cells. These results suggest that targeting NCOA3 is worth investigating for the treatment of TNBCs. Citation Format: Ya-Fang Chang, Yuhao Wang, Geoffrey Greene. Targeting nuclear receptors and their coregulators in triple-negative breast cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1264.
Blood granulocyte patterns as predictors of asthma phenotypes in adults from the EGEA study
Authors: Rachel Nadif, Valérie Siroux, Anne Boudier, Nicole le Moual, Jocelyne Just, Frederic Gormand, Christophe Pison, Regis Matran, Isabelle Pin
Journal: European Respiratory Journal (2016)

To what extent blood granulocyte patterns may predict asthma control remains under-studied. Our aim was to study associations between blood neutrophilia and eosinophilia and asthma control outcomes in adults. Analyses were conducted in 474 asthmatics from the first follow-up of the Epidemiological Study on the Genetics and Environment of Asthma (EGEA2), including 242 asthmatics who were adults a decade earlier (EGEA1). At EGEA2, asthma control was assessed using the Global Initiative for Asthma definition (2015), and asthma exacerbations by use of urgent care or courses of oral corticosteroids in the past year. Blood EOS lo /EOS hi was defined as &lt;/≥250 eosinophils·mm −3 , respectively, and NEU lo /NEU hi as &lt;/≥5000 neutrophils·mm −3 , respectively. Estimates were adjusted for age, sex and smoking. At EGEA2, NEU hi was associated with asthma exacerbations and poor asthma control (OR &gt;2.10). EOS hi was associated with higher bronchial hyperresponsiveness (BHR) (OR (95% CI) 2.21 (1.24–3.97)), poor lung function (p=0.02) and higher total IgE level (p=0.002). Almost 50% of asthmatics had a persistent pattern between surveys. Persistent NEU hi was associated with poor asthma control at EGEA2 (OR (95% CI) 3.09 (1.18–7.05)). EOS hi at EGEA1 and persistent EOS hi were associated with higher BHR (OR (95% CI) 2.36 (1.10–5.07) and 3.85 (1.11–13.34), respectively), poor lung function (p&lt;0.06) and higher immunoglobulin E level (p&lt;10 −4 ) at EGEA2. Granulocyte patterns were differently associated with asthma outcomes, suggesting specific roles for each one, which could be tested as predictive signatures.
Abstract 4081: Stromal autophagy is required for the growth of cutaneous melanoma
Authors: Ran Ellen Zhang, Natalie J. Guo, Nithya Krishnan, David Jelinek, Gizem Karsli Uzunbas, Xiaoqi Xie, Arek Gertych, Janice M. Mehnert, Beatrice Knudsen, Eileen White, Hilary A. Coller
Journal: Cancer Research (2016)

Abstract Through degrading bulk cytoplasmic materials into intermediate building blocks, autophagy refuels metabolism and maintains homeostasis under starvation and stress conditions. The context-dependent role of autophagy in cancer cells during tumorigenesis and tumor progression has been explored over the past decade; however, studies of autophagy in relation to the tumor microenvironment are still lacking. In this study, we investigated the role of autophagy in the cancer-associated fibroblasts (CAFs), a major component of the microenvironment that is important for the growth and development of cutaneous melanoma. Analysis of clinical biopsies revealed high levels of autophagy in fibroblasts that surrounded melanoma cells, but not in the non-tumor adjacent area. Fibroblasts co-cultured with any of multiple melanoma cell lines, but not melanocytes, also showed increased autophagic flux, which requires transforming growth factor beta (TGF-β) signaling. Knocking down autophagy-related (ATG) genes ATG5 or ATG7 in fibroblasts did not impair their proliferation in vitro, but inhibited the growth of co-engrafted melanoma cells in vivo. Further, by introducing intradermal melanoma allografts into mice that harbored fibroblast-specific Atg7 deletion, we observed remarkable tumor growth retardation. In order to mimic anti-autophagy therapy for patients, we generated mice that allowed conditional Atg7 depletion in their entire bodies, and found significant tumor growth suppression. Atg7 knockout mice contained elevated plasma levels of immune cell attractants, including CXCL9, CXCL10 and MCP-1. By inhibiting these cytokines/chemokines with atorvastatin, tumor growth in Atg7 knockout mice was completely rescued; while, there was no effect of atorvastatin on control mice. Taken together, our data show that through modulating the tumor microenvironment, stromal autophagy plays an important role during melanoma growth and development. Our findings indicate that stromal autophagy may represent a valuable therapeutic target that might induce less side effects and systemic toxicity. Citation Format: Ran Ellen Zhang, Natalie J. Guo, Nithya Krishnan, David Jelinek, Gizem Karsli Uzunbas, Xiaoqi Xie, Arek Gertych, Janice M. Mehnert, Beatrice Knudsen, Eileen White, Hilary A. Coller. Stromal autophagy is required for the growth of cutaneous melanoma. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4081.
Arterial Remodeling and Endothelial Shear Stress Exhibit Significant Longitudinal Heterogeneity Along the Length of Coronary Plaques
Authors: Antonios P. Antoniadis, Michail I. Papafaklis, Saeko Takahashi, Koki Shishido, Ioannis Andreou, Yiannis S. Chatzizisis, Masaya Tsuda, Shingo Mizuno, Yasuhiro Makita, Takenori Domei, Tomokazu Ikemoto, Ahmet U. Coskun, Junko Honye, Shigeru Nakamura, Shigeru Saito, Elazer R. Edelman, Charles L. Feldman, Peter H. Stone
Journal: JACC. Cardiovascular imaging (2016)
Abstract 1362: Novel proton coupled folate transporter (PCFT) and reduced folate carrier (RFC) pharmacophore models for development of transporter-selective antifolates
Authors: Sudhir Raghavan, Aleem Gangjee, Larry H. Matherly
Journal: Cancer Research (2016)

Abstract RFC is a ubiquitously expressed folate transporter that is present in normal tissues and tumors. RFC is utilized by reduced folates and by all the clinically used classical antifolates. In contrast, PCFT shows more limited expression in normal tissues and is highly effective in folate transport under low pH conditions associated with hypoxic solid tumors. Antifolates that are selectively transported by PCFT over RFC offer significant promise for development of targeted therapies of tumors (over)expressing PCFT. We previously reported 6-substituted pyrrolo[2,3-d]pyrimidines and thieno[2,3-d]pyrimidines as part of a continued effort to elucidate the SAR for substrate binding and cellular uptake for RFC, PCFT as well as folate receptors (FRs). While the X-ray crystal structure of FRs bound to antifolates has been resolved, the absence of X-ray crystal structures of PCFT and RFC has hindered structure-based medicinal chemistry efforts for development of antifolates selectively transported by PCFT. To address this, pharmacophore models were developed for the first time using Discovery Studio for PCFT and RFC using a series of thirty six 6-substituted bicyclic pyrrolo[2,3-d]pyrimidines and/or thieno[2,3-d]pyrimidines that included highly potent and selective compounds such as AGF94 (PCFT = 0.3 nM; RFC = 101 nM) previously reported by us. Compounds used for model development displayed a 3-log range inhibition of cancer cells overexpressing PCFT or RFC. The best models display a 4-point pharmacophore with excellent regression values (r2 PCFT = 0.96; RFC = 0.92). The models were internally validated by leave-one-out analysis (q2 PCFT = 0.752; RFC = 0.59) and externally validated using a test set of 6-substituted bicyclic analogs not used in model development. Comparison of the pharmacophore models indicates different conformational and structural requirements for compounds for binding to PCFT or RFC. We have used these models to explain the potent PCFT inhibitory activity and selectivity of compounds such as AGF94. These models are being used in the development of selectively transported targeted antifolates that would result in decreased toxicity compared to standard antifolates such as methotrexate (MTX) or pemetrexed (PMX) which utilize all three folate transport systems. Citation Format: Sudhir Raghavan, Aleem Gangjee, Larry H. Matherly. Novel proton coupled folate transporter (PCFT) and reduced folate carrier (RFC) pharmacophore models for development of transporter-selective antifolates. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1362.
Effect on Joint Health of Routine Prophylaxis with Bayer’s Sucrose-Formulated Recombinant Factor VIII (rFVIII-FS) in Adolescents and Adults Previously Treated on Demand: MRI Analyses from the 3-Year Spinart Study
Authors: Bjorn Lundin, Walter Hong, David Raunig, Sylvia Engelen, Charles Peterfy, Michael Werk, Marilyn J. Manco-Johnson
Journal: Blood (2014)
Validation of a second-generation mia (MIA2G) for triage of adnexal masses.
Authors: Judith Wolf, Todd Pappas, Zhen Zhang, Alan Smith, Tina Hudson, Brian Carpenter, Donald Gordon Munroe, Lori J. Sokoll
Journal: Journal of Clinical Oncology (2015)

5556 Background: Many women with ovarian cancer receive non-guideline care. Failure to refer to a gynecologic oncologist is one likely cause. To improve specificity of Multivariate Index Assay (MIA) for ovarian cancer triage, we undertook the re-design and validation of a second-generation test (MIA2G). Methods: A panel of MIA-positive malignant and benign case- controls was used to evaluate candidate biomarkers to improve specificity. These, and the 5 MIA biomarkers were then further ranked and developed into the MIA2G using banked samples from a previously published prospective, multi-site FDA registration trial of MIA (N = 585). Upon verification, the algorithm was encoded into diagnostics-grade software to calculate MIA2G in subsequent validation studies. Clinical validity was established under a double-blinded protocol using banked samples from the OVA500 trial, a second prospective MIA multi-site pivotal trial. Samples were assayed at 3 external sites, results were generated at a commercial laboratory and submitted to an independent statistician for decoding and analysis. MIA2G was compared with physician assessment (PA) or MIA. Results were compared for sensitivity, specificity, positive and negative predictive value (PPV and NPV), positive and negative likelihood ratios, concordance and percent overall accuracy. Results: Three MIA markers (CA125-II, transferrin and Apo A-1) and 2 new biomarkers (FSH and HE4) were selected for inclusion in MIA2G. MIA2G results range from 0-10, with a single cut-off separating hi- and low- malignancy risk of ³5.0. 493 of 519 OVA500 subjects were evaluable (276 pre and 217 post-menopausal). MIA2G specificity (69.1%) and PPV (40.4%) were significantly improved over MIA (53.6% and 31.4%, respectively). Sensitivity and NPV were not significantly different. Overall accuracy was significantly improved from 60.9% (MIA) to 73.2% (MIA2G). When MIA2G was combined with PA sensitivity was 93.5% and specificity was 64.8% Conclusions: The redesigned multivariate index assay, MIA2G, has significantly improved specificity, PPV and accuracy compared with MIA. These changes enable high-sensitivity detection of malignancy while reducing likelihood of over-referral.
Abstract 5152: Inhibition of TLR/IRAK pathway in hepatocellular carcinoma augmented therapeutic responses
Authors: Yik Ling Bowie Cheng, Oi Lin Irene Ng, Kin Wah Terence Lee.
Journal: Cancer Research (2016)

Abstract Hepatocellular carcinoma (HCC) is the second most lethal cancer worldwide. Frequent relapse and drug resistance accounts for the poor prognosis, which could be attributed by the presence of cancer stem cells (CSCs), a subpopulation that harbor the properties of self-renewal, clonal tumor initiation and long-term repopulation capacity. Toll like receptors (TLRs) are widely expressed on immune cells and TLR/Interleukin-1 receptor associated kinase (IRAK) pathway was originally best known for their role in the induction of innate immune responses, but it was recently found to be frequently up-regulated in various cancers, although its role in cancer development remains largely unexplored. By RNA sequencing analysis of 16 pairs of HCC clinical samples, we found IRAK1 to be significantly overexpressed in HCC among all members of IRAK family. By quantitative PCR and western blot analyses, overexpression of IRAK1 at both mRNA and protein level was confirmed, which correlated with advanced tumor stage (p = 0.04). By lentiviral-based over-expression and knockdown approaches, we demonstrated that IRAK1 promoted cell proliferation and invasiveness. Interestingly, IRAK1 regulated CSC properties including tumorigenicity, self-renewal, drug resistance and expression of liver CSC markers including CD24 and CD47. To further examine the therapeutic potentials of targeting IRAK1 in HCC, we treated HCC cells with IRAK1/4 inhibitor. Suppression of IRAK1 at 10μM not only consistently inhibited CSC properties, but also augmented the effect of sorafenib, a molecularly targeted drug for treatment of advanced HCC. The cancer-promoting and drug desensitization effect of IRAK1 could be partly explained by activation of NF-κB signaling pathway as well as down-regulation of apoptotic cascade. Conclusion: Overexpression of IRAK1 in HCC promotes cancer progression by enhancing proliferation and invasiveness; Importantly, IRAK1 may promote cancer stemness and confers resistance to sorafenib. All in all, targeting IRAK1 with specific small molecule inhibitor alone or in combination with other drugs may be a novel therapeutic regimen for treatment of HCC. Citation Format: Yik Ling Bowie Cheng, Oi Lin Irene Ng, Kin Wah Terence Lee. Inhibition of TLR/IRAK pathway in hepatocellular carcinoma augmented therapeutic responses. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 5152.