tbuckley/cabot-search huggingface dataset:
Aryl Hydrocarbon Receptor (AhR) Antagonist Stemregenin 1 (SR1) Enhances in Vitro- and in Vivo-Derived Platelets (PLTs) From Human Megakaryocytes (MKs)
Authors: Yuhuan Wang, Vincent M. Hayes, Lin Lu, Xiaoji Chen, Rudy Fuentes, Qiang Jeremy Wen, Stella T Chou, John Crispino, Patrick Paddison, Deborah L. French, Beverly Torok-Storb, Mortimer Poncz
Journal: Blood (2012)
235. Improved Ex Vivo Gene Therapy Using Highly Purified Hematopoietic Stem and Progenitor Cells
Authors: Erika Zonari, Oriana Meo, Samantha Scaramuzza, Eugenio Montini, Giuliana Ferrari, Luigi Naldini, Bernhard Gentner
Journal: Molecular Therapy (2016)

Ex vivo gene addition into CD34+ hematopoietic stem and progenitor cells (HSPC) followed by autologous transplantation has proven a safe and efficacious therapy for immunodeficiencies, storage diseases and hemoglobinopathies. According to xenograft models and population size estimates of vector-marked cells in gene therapy-treated patients, less than 0.01% of infused CD34+ cells drive long-term (LT) repopulation. Advances in clinical-grade cell sorting technology may make HSC-enriched CD34+ subpopulations accessible for gene therapy, with advantages in terms of lentiviral vector (LV) cost, safety (lowering of integration load) and, potentially, efficacy. By differentially marking mobilized peripheral blood (mPB) CD34 subpopulations distinguished by increasing levels of CD38 expression in order to quantitatively assess their hematopoietic output in an NSG xenograft model over 6 months, we previously mapped most (>90%) LT repopulating capacity to CD34+CD38- cells (lowest 10% CD38 staining), while CD34+CD38int cells drove short-term (ST) reconstitution during the first 2 months after transplantation. We now characterize these subpopulations in terms of CD90 expression, a marker, which has been used in conjunction with CD34 for HSC purification in past clinical trials. CD34+ mPB cells were sorted into CD38-90+ (5% of CD34+), CD38-90- (5%), CD38+90+ (30%) and CD38+90- (60%) fractions and exhaustively transduced with GFP-, OFP-, BFP- and mCherry-expressing LVs, respectively. Differentially marked subfractions were pooled maintaining their original proportions and transplanted into NSG mice. ST engraftment mainly came from CD38+ cells, with equal contribution from the CD90+ and CD90- compartment. LT engraftment was almost exclusively derived from CD34+CD38- cells, of which 70% came from CD90+ and 30% from CD90- cells. Hence, CD34+CD38- is a more sensitive and specific marker combination than CD34+CD90+ to purify LT-HSC. CD34+CD38- cells can be purified by a sequential bead-based selection (CD34 selection of CD38-depleted cells) potentially applicable to clinical practice. We show that CD34+CD38- cells can be efficiently transduced with clinical grade LVs using shortened ex vivo manipulation protocols, reaching similar gene marking levels as with the standard protocol currently used in clinical trials that comprises a double dose of LV. Transduction was stable for at least 5 months when serially measured in xenotransplanted mice, and mice showed multi-lineage hematopoiesis indistinguishable from CD34+ grafts. Based on these results, we are aiming towards clinical development of a new gene therapy protocol based on CD34+CD38-HSPC efficiently transduced with minimum ex vivo culture time (<36h). Our platform will substantially improve the efficacy, safety and feasibility of future ex vivo gene therapy studies.
In Vitro Evaluation of Apixaban, a Novel, Potent, Selective and Orally Bioavailable Factor Xa Inhibitor.
Authors: Joseph M. Luettgen, Tracy A. Bozarth, Jeffrey M. Bozarth, Frank A. Barbera, Patrick Y. Lam, Mimi L. Quan, Donald J. Pinto, Ruth R. Wexler, Alan R. Rendina, Robert M. Knabb
Journal: Blood (2006)
Soft tissue sarcoma after haematological malignancies in childhood/adolescence: a hospital series
Authors: R. Bracci, E. Maccaroni, M. Del Prete, F. Bianchi, L. Belvederesi, C. Brugiati, S. Pagliaretta, M. Pistelli, A. Pagliacci, N. Battelli, Z. Ballatore, M.G. De Lisa, A. Della Mora, S. Cascinu
Journal: Annals of Oncology (2015)
Abstract 1209: Dissecting by 13C tracers the utilization of glucose and glutamine for the synthesis of fatty acids in triple negative breast cancer cells
Authors: Alexander Strigun, Regina Reszka, Hans-Joerg Schiewe, Jean-Philippe Laine, Ulrike Rennefahrt
Journal: Cancer Research (2015)

Abstract Triple negative breast cancer (TNBC) is an aggressive cancer, which is resistant to the majority of available chemotherapies. We have recently identified significant differences in the levels of membrane lipids and fatty acids between two distinct TNCB metabolic subtypes (MST2 and MST3) (Beatty et al., 2014, manuscript submitted). Fatty acid synthesis has recently been discussed as potential pharmaceutical target. In order to evaluate whether glucose or glutamine is the preferred carbon source for palmitic acid synthesis, TNBC cell lines (BT549 and HCC1806) were fed with fully labelled glucose and fully labelled glutamine ([U-13C6]glucose and [U-13C5]glutamine) in independent experiments. Fully labelled glutamine allows conclusions on total usage of glutamine via the reductive and the oxidative part of the TCA-cycle. In order to assess the contribution of glutamine to palmitic acid synthesis via the reductive pathway we fed the subtypes with single labelled glutamine [5-13C1]glutamine. Enrichment of 13C in palmitic acid from all labelling experiments was measured via GC-MS (gas chromatography coupled mass spectrometry). Feeding the TNBC subtypes with [U-13C6]glucose and [U-13C5]glutamine resulted in a higher enrichment of 13C in palmitic acid derived from glucose as compared to glutamine in both subtypes, indicating that glucose is the main carbon source at the tested conditions. Feeding the cells with [5-13C1]glutamine also resulted in an enrichment of 13C in palmitic acid in both subtypes, which indicates that reductive glutamine metabolism contributes to palmitic acid synthesis in both subtypes. Based on the 13C-palmitic acid data from both glutamine isotopes we found that palmitic acid synthesis preferably occurs via the reductive path in MST3 (61% of total glutamine use) while the oxidative path seems the preferred route (34% of total glutamine use) in MST2. The presented data indicate that glucose is the main carbon source for fatty acid synthesis in both MSTs, suggesting a higher sensitivity towards pharmacological targeting of glucose metabolism. Despite of the lower dependency on glutamine, TNCBs of the MST3 subtype seem more sensitive towards targeting the reductive glutamine metabolism. Citation Format: Alexander Strigun, Regina Reszka, Hans-Joerg Schiewe, Jean-Philippe Laine, Ulrike Rennefahrt. Dissecting by 13C tracers the utilization of glucose and glutamine for the synthesis of fatty acids in triple negative breast cancer cells. [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 1209. doi:10.1158/1538-7445.AM2015-1209
A Randomised Dose De-Escalation Safety Study of Oral Fludarabine, ±Oral Cyclophosphamide and Intravenous Rituximab (OFOCIR) As First-Line Therapy of Fit Patients with Chronic Lymphocytic Leukaemia (CLL) Aged ≥65 Years – End of Recruitment Analysis of Response and Toxicity of the Australasian Leukaemia and Lymphoma Group (ALLG) and CLL Australian Research Consortium (CLLARC) CLL5 Study
Authors: Stephen P Mulligan, Devinder S Gill, Paul Turner, William E. P. Renwick, Rosemary Harrup, Maya Latimer, Naomi Mackinlay, Leanne Berkahn, David Simpson, Philip Campbell, Campbell Tiley, Gavin Cull, Marnie Collins, Paul Cortissos, Melanie Sulda, Giles Best, Bryone J Kuss
Journal: Blood (2012)
397. Allogenic CAR T-Cells Targeting CD123 Effectively Eliminate Myeloid Leukemia Cells
Authors: Roman Galetto, Céline Lebuhotel, Agnès Gouble, Alexander Bank, Gail J. Roboz, Monica L. Guzman, Julianne Smith
Journal: Molecular Therapy (2016)

Chimeric antigen receptor (CAR)-redirected T-cells have given rise to long-term durable remissions and remarkable objective response rates in patients with refractory leukemia. At present, CAR technology is administered through the custom-made manufacturing of therapeutic products from each patient's own T-cells. However, this patient-specific autologous paradigm is a significant limiting factor in the large-scale deployment of CAR technology. We have developed a platform for the production of "off-the-shelf" CAR T-cells from unrelated third-party donor T-cells. This platform utilizes Transcription Activator-Like Effector Nuclease (TALEN) gene editing technology to inactivate the TCRα constant (TRAC) gene, eliminating the potential for T-cells bearing alloreactive TCR's to mediate Graft versus Host Disease (GvHD). We have previously demonstrated that editing of the TRAC gene can be achieved at high frequencies, obtaining up to 80% of TCRα negative cells. This allows us to efficiently produce TCR-deficient T-cells that have been shown to no longer mediate alloreactivity in a xeno-GvHD mouse model. Acute myeloid leukemia (AML) is incurable in the majority of patients. While allogeneic stem cell transplantation remains the most effective therapy for AML to date, other types of cellular therapy have not yet been successful in this disease. We have adapted this allogeneic platform to the production of T cells targeting CD123, the alpha chain of the interleukin-3 receptor, which is expressed in tumor cells of patients with AML. We will present both in vitro and in vivo data demonstrating specific anti-tumor activity of engineered CAR T cells against AML cells. The ability to carry out large scale manufacturing of allogeneic, non alloreactive CD123 specific T cells from a single healthy donor will offer the possibility of an off-the-shelf treatment that would be immediately available for administration to a large number of AML patients.
Improving the Accuracy of Mesothelioma Diagnosis in China
Authors: Zhenying Guo, Michele Carbone, Xing Zhang, Dan Su, Wenyong Sun, Jianlin Lou, Zhibin Gao, Dichu Shao, Junqiang Chen, Gu Zhang, Jinlin Hu, Kaiyan Chen, Fang Wang, Harvey I. Pass, Herbert Yu, Andrea Napolitano, Haining Yang, Weimin Mao
Journal: Journal of Thoracic Oncology (2016)

IntroductionIn the Western world, malignant mesothelioma (MM) is most prevalent in the pleura of older males who have been professionally exposed to asbestos. Information about MM from rapidly industrializing countries such as China is minimal. There is concern that a proportion of MM diagnoses in China may be incorrect because most Chinese physicians do not have experience diagnosing this rare cancer. We recently reported an unusually high incidence of peritoneal MM among eastern Chinese female patients. Here, we review the accuracy of MM diagnoses in China and provide suggestions to improve the accuracy of diagnosis.MethodsWe reviewed 92 pathological diagnosis of MM in 2002–2015 from two reference centers in the province of Zhejiang in eastern China. We performed a large set of immunohistochemistry analyses to increase the reliability of the diagnosis.ResultsWe confirmed the MM diagnosis in 12 of 34 of the pleural tumors (35.3%), in 38 of 56 of the peritoneal tumors (67.9%), and in two of two of the MMs of the tunica vaginalis (100%). MMs were characterized by tumor cells showing nuclear Wilms tumor 1 and calretinin staining and by strong membranous staining for cytokeratin CAM5.2. The results of staining for the epithelial markers carcinoembryonic antigen, thyroid transcription factor-1, MOC31, BerEP4, p63, p40, paired box 8, ER and PR were negative. BRCA1 associated protein 1 nuclear staining was lost in percentages similar to what has been reported for samples from Western countries.ConclusionsOur findings suggest that MM—especially in its pleural localization—is often misdiagnosed in eastern China. Identifying pitfalls and possible solutions in the pathological diagnosis of MM will affect both the standard of care and research in China.
Mechanisms of ACL injury in professional rugby union: a systematic video analysis of 36 cases
Authors: Connor Montgomery, Jeff Blackburn, Daniel Withers, Gregory Tierney, Cathal Moran, Ciaran Simms
Journal: British Journal of Sports Medicine (2016)

The mechanisms of ACL injury in rugby are not well defined.To describe the mechanisms of ACL injury in male professional rugby players using systematic video analysis.36 cases from games played in top professional leagues and international matches were analysed. 5 analysts independently assessed all videos to record the estimated frame/time of initial ground contact, frame/time of ACL tear and a range of play specific variables. This included contact versus non-contact ACL injuries, injury timing, joint flexion angles and foot contact with the ground. 37 side-stepping manoeuvres from a control game were analysed to allow comparison of non-injury versus injury situations.57% of ACL injuries occurred in a contact manner. 2 main scenarios were identified: (1) offensive running and (2) being tackled, indicating that the ball carrier might be at higher risk of ACL injury. The majority of non-contact ACL injuries resulted from a side-stepping manoeuvre. In most non-contact cases, initial ground contact was through heel strike. Statistical assessment of heel strike at initial ground contact versus non-heel strike cases showed a significant difference in injury versus non-injury outcomes, with heel strike associated with higher injury risk. Non-contact ACL injuries had lower median knee flexion angles and a more dorsiflexed ankle when compared with a control group (10° vs 20°, p≤0.001 and 10° vs 0°, p=0.033 respectively).Over half of ACL injuries in rugby in our analysis resulted from a contact mechanism. For non-contact injuries, lower knee flexion angles and heel-first ground contact in a side-stepping manoeuvre were associated with ACL injury.
T3 Human rhinovirus impairs the innate immune response to bacteria in monocyte derived macrophages from patients with chronic obstructive pulmonary disease
Authors: LJ Finney, KBR Belchamber, P Mallia, SL Johnston, LE Donnelly, JA Wedzicha
Journal: Thorax (2016)

<h3>Introduction</h3> Exacerbations of Chronic Obstructive Pulmonary Disease (COPD) are associated with accelerated disease progression, hospitalisation and death. Respiratory viruses are identified in approximately half of all exacerbations. We have previously found that human rhinovirus infection leads to a secondary outgrowth of bacteria which is associated increased exacerbation severity. The mechanisms of how HRV increases risk of secondary bacterial outgrowth are unknown. <h3>Hypothesis</h3> We hypothesised that HRV infection impairs phagocytosis of bacteria by monocyte derived macrophages (MDM) which may lead to an increased risk of secondary bacterial outgrowth during COPD exacerbations. <h3>Methods</h3> Participants were recruited from the London COPD Cohort. MDM were generated by culture in GM-CSF or M-CSF for 12 days. MDM were incubated with HRV 16 for 24 hours at increasing multiplicity of infection (MOI) 0.5–10 for 24 hours or poly-IC at increasing concentrations 0–300 µg/ml. Phagocytic capacity was then assessed by incubating MDMs with fluorescently labelled heat killed <i>Haemophilus influenzae</i> or <i>Streptococcus pneumoniae</i> for 4 hours and uptake measured by fluorimetry. The pro-inflammatory cytokine CXCL-8 and anti-inflammatory cytokine IL-10 were measured by ELISA according to the manufacturer’s instructions. <h3>Results</h3> HRV16 impaired phagocytosis of <i>H. influenzae</i> (HRV (MOI of 5) 2.84 ± 0.92 <i>vs</i> media control 4.36 ± 1.06 RFU × 10³ n = 8, p = 0.01) and <i>S. pneumoniae </i>(p &lt; 0.01) by MDM in a virus-dose- dependent manner without impairing cell viability. HRV16 alone induced CXCL-8 and IL-10 release from MDM compared to media alone. HRV16 (MOI 5) significantly impaired IL-10 response to <i>H. influenzae</i> compared to media alone (0.59 (0.33–0.96) ng/ml <i>vs </i>1.83 (1.11–3.00) ng/ml respectively, n = 6, p = 0.03) and impaired CXCL-8 response to <i>H influenzae</i> compared to media alone 4.41 (3.45–5.85) ng/ml <i>vs</i> 24.65 (11.63–29.77) ng/ml respectively, n = 5, p = 0.01). Poly-IC impaired phagocytosis of <i>H. influenzae</i> in a concentration-dependent manner without significantly impairing cell viability. Poly IC alone also induced IL-8 release from MDM. <h3>Conclusions</h3> HRV impairs phagocytosis of bacteria by MDM in COPD and impairs cytokine response to bacteria which may inhibit neutrophil influx and prevent resolution of inflammation. This may lead to an outgrowth of bacteria and prolonged exacerbations in COPD.
572. Successful Generation of CAR+PD-1-Primary T Cells Using Cas9-Mediated Genome Editing
Authors: Grant Welstead, Justin Fang, Chris Nye, Frank Buquicchio, McKensie Collins, Will Selleck, Hari Jayaram, Ruth Salmon, Alex Baturevych, Sherri Mudri, Jon Jones, David Bumcrot, Blythe D. Sather
Journal: Molecular Therapy (2016)

Cancer immunotherapy is an exciting area of cancer treatment bolstered by recent success of anti-immune checkpoint antibodies in the clinic. Engineered T cells that are programmed to attack tumors via chimeric antigen receptors (CARs) have also shown promise in early clinical trials. It is speculated, however, that the PD-1/PD-L1 axis dampens the effectiveness of CAR T therapy in certain cancer types. In order to improve the function of transplanted CAR T cells in these contexts, we have deleted PDCD1 using the genome editing system, CRISPR/Cas9. Delivery of the Cas9 protein and a PDCD1 specific gRNA to primary T cells resulted in the deletion of PD1 expression in over 90% of cells. Additionally, we were able to achieve similar editing efficiencies in the context of a lentivirus CAR infection and successfully generated CAR+/PD-1 knockout primary T cells with a very high level (>60%) of duel CAR expression and PD-1 editing. Utilizing a variety of assays, we have determined that the CAR+/PD-1− primary T cells are viable, proliferate normally and can kill target expressing cells both in the presence and absence of PD-L1 on the target cells. In conclusion, we have successfully generated CAR+/PD-1− primary T cells using Cas9-mediated editing that can be directed to kill PD-L1 expressing target cells.
Abstract 4863: Streamlining NGS workflows using cancer samples by the application of the DNA Integrity Number (DIN) from the Genomic DNA ScreenTape assay
Authors: Eva Schmidt, Isabell Pechtl, Barry McHoull, Melissa Liu
Journal: Cancer Research (2015)

Abstract The results of numerous molecular screening and assay methods often rely on the overall quality of the genomic DNA (gDNA) input material. However extraction of genetic material can be challenging and often results in low amounts or variable quality of gDNA samples, which are further subjected to time and cost intensive downstream applications. For example, array comparative genome hybridization (aCGH) and Next Generation Sequencing (NGS) can require intact, high quality gDNA to ensure high quality, unambiguous results. It is therefore widely recommended to perform an initial quality control (QC) of the input material. Especially as only the final step of these workflows reveals if meaningful results have been achieved. In order to provide an objective and automated measure to standardize the gDNA integrity assessment, a software algorithm has been developed. This functionality of the 2200 TapeStation system provides a numerical determination of the gDNA integrity and is referred to as the DNA Integrity Number (DIN). This study demonstrates how DIN obtained by the upfront QC of gDNA on the Agilent Genomic DNA ScreenTape assay has allowed for significant saving of sequencing and sample preparation overhead using cancer samples in NGS workflows. Citation Format: Eva Schmidt, Isabell Pechtl, Barry McHoull, Melissa Liu. Streamlining NGS workflows using cancer samples by the application of the DNA Integrity Number (DIN) from the Genomic DNA ScreenTape assay. [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 4863. doi:10.1158/1538-7445.AM2015-4863
Angiogenic Activity in IgVH Mutated and Unmutated Chronic Lymphocytic Leukemia (CLL): Indications for the Therapeutic Use of VEGF-Signaling Inhibitors.
Authors: Roberta Maggio, Nadia Peragine, Monica Messina, Sabina Chiaretti, Stefania M. De Propris, Simona Tavolaro, Marilisa Marinelli, Elisabetta Calabrese, Ilaria Del Giudice, Francesca R. Mauro, Anna Guarini, Robert Foa
Journal: Blood (2006)
Abstract LB-214: DNAJB1-PRKACA chimera increases Aurora kinase A expression in fibrolamellar hepatocellular carcinoma
Authors: Irene Isabel P. Lim, Emily A. Greene-Colozzi, Jennifer M. Murphy, Todd E. Heaton, Sanford M. Simon, Michael P. LaQuaglia
Journal: Cancer Research (2015)

Abstract Purpose: Treatment of fibrolamellar hepatocellular carcinoma (FL-HCC), a rare liver cancer affecting the pediatric and adolescent population, is limited to surgical resection with no agents or therapeutic modalities available for unresectable disease. There has been recent interest in using Aurora kinase A (AURKA) inhibitors, with a clinical trial evaluating its efficacy in FL-HCC pending. Previously, we described a consistent single deletion of approximately 400 kB in chromosome 19 that results in a chimera between the heat shock protein DNAJB1 and the catalytic subunit of protein kinase A, PRKACA, in all FL-HCC tumor tissue studied. Furthermore, comparative ribonucleic acid sequence analysis has demonstrated that expression of AURKA, a regulator of cytokinesis and mitosis, is increased in FL-HCC tumor tissue compared with adjacent normal tissue. We hypothesize that the DNAJB1-PRKACA chimera is responsible for changes in AURKA expression in FL-HCC. Methods: The DNAJB1-PRKACA chimera was cloned into a lentiviral vector with a fluorescent reporter. Two stable cell lines (HeLa and a hepatocyte cell line, Huh-7) were transduced with a lentivirus containing either an empty multicloning site (control) or the DNAJB1-PRKACA chimera. Transduction was confirmed by the presence of a positive epifluorescent signal and immunoblots showing expression of the chimeric protein. Microarray data were evaluated for changes in AURKA expression while immunoblots were analyzed for the presence of AURKA in all transduced cells. Results: Microarray analysis showed an increase in AURKA transcripts in cells stably expressing the DNAJB1-PRKACA chimera. Compared to cells transduced with the control lentivirus, HeLa and Huh-7 cells transduced with the DNAJB1-PRKACA chimera demonstrated an increase in AURKA on immunoblots. Levels of a loading control, actin, were equivalent, indicating equal levels of protein examined between samples. Conclusion: Expression of the DNAJB1-PRKACA chimera results in an increase in AURKA. Upregulation of AURKA, in turn, may be responsible for subsequent tumor formation in FL-HCC. This finding further supports the DNAJB1-PRKACA chimera's role in the pathogenesis of FL-HCC and provides a potential therapeutic target for a disease that has no effective treatment besides surgery. Citation Format: Irene Isabel P. Lim, Emily A. Greene-Colozzi, Jennifer M. Murphy, Todd E. Heaton, Sanford M. Simon, Michael P. LaQuaglia. DNAJB1-PRKACA chimera increases Aurora kinase A expression in fibrolamellar hepatocellular carcinoma. [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 LB-214. doi:10.1158/1538-7445.AM2015-LB-214