tbuckley/cabot-search huggingface dataset:
33. Advancing a State of the Art Gene Therapy Called OXB-202 That Resists Corneal Rejection in High Risk Patients
Authors: Naghmeh Fouladi, Katie Binley, Laura McCloskey, Julie Loader, Michelle Kelleher, Kyriacos Mitrophanous, Scott Ellis
Journal: Molecular Therapy (2016)

Due to both the avascularity of the cornea and the relatively immune-privileged status of the eye corneal transplantation is one of the most successful clinical transplant procedures. However in high risk patients, which account for >20% of the 100,000 transplants carried out worldwide each year, the rejection rate is high due to vascularization of the recipient corneal bed. In some of these patients the prognosis is extremely poor, with grafts failing at an accelerating rate to the point where patients are no longer considered suitable for further transplants and are left blind, despite an otherwise normally functioning visual system. The main reason for graft failure is irreversible immunological rejection and it is therefore unsurprising that neovascularization (both pre-and post-grafting) is a significant risk factor for subsequent graft failure. Neovascularization is thus an attractive target to prevent corneal graft rejection. OXB-202 (previously known as EncorStat®) is a human donor cornea modified prior to transplant by ex vivo genetic modification with genes encoding secretable forms of the angiostatic human proteins, endostatin and angiostatin. This is achieved using a lentiviral vector derived from the Equine Infectious Anaemia Virus (EIAV) called pONYK1EiA, which subsequently prevents rejection by suppressing neovascularization. Previously we have shown that rabbit corneas treated with pONYK1EiA substantially suppress corneal neovascularization, opacity and subsequent rejection in rabbit models of cornea graft rejection (Parker et al, 2014). We will present data from a 3-month GLP toxicology and biodistribution safety study of pONYK1EiA modified rabbit corneas in a rabbit corneal transplant model. In particular, the GLP study has been designed to include a number of high content in-life assessments that include regular slitlamp ophthalmic examinations, evaluation of corneal thickness and endothelial cell density using pachymetry and specular microscopy respectively and intraocular pressure measurements. We will present a summary of these data to show that there are no safety issues with pONYK1EiA modified corneas. The GLP safety study data to be presented supports the evaluation of OXB-202 corneas in a First-in-Man trial. The toxicology study, GMP manufactures and clinical development of OXB-202 has been supported by the UK Technology Strategy Board (Innovate UK).
Abstract 3896: Recurrent TERT promoter mutations in primary central nervous system lymphoma
Authors: Aurélie Bruno, Mailys Daniau, Karima Mokhtari, Amithys Rahimian, Marc Polivka, Anne Jouvet, Clovis Adam, Dominique Figarella-Branger, Catherine Miquel, Sandrine Eimer, Caroline Houillier, Carole Soussain, Agusti Alentorn, Khê Hoang-Xuan
Journal: Cancer Research (2015)

Abstract Primary central nervous system lymphoma (PCNSL) is a rare extranodal diffuse large B-cell lymphoma (DLBCL) restricted to the CNS and associated with a poor prognosis. Despite a notable effort contributing to better characterize the genomic basis of these tumors, few molecular abnormalities were proposed as predictive or prognostic biomarkers. Recently, two hotspot mutations, C228T and C250T, and the polymorphism rs2853669, located within TERT core promoter region have known a growing interest due to their prognostic value in a wide range of tumors, including melanoma, hepatocellular carcinoma or glioblastoma. Forty-one PCNSL tumor samples of newly diagnosed PCNSL were sequenced for C228T and C250T TERT somatic mutations. TERT promoter mutations status was correlated with clinical outcome and rs2853669 genotype. We identified C228T and C250T mutations and rs2853669 genotype in 20%, 9.4% and 50%, respectively. No case with co-occurrence of C228T and C250T mutations was identified. C228T mutations, but not C250T, were significantly associated with shorter overall survival (OS) (median OS = 4.5 months vs 33 months for non-mutated, p = 0.0048) and progression free survival (PFS) (median PFS = 3 months vs 11.5 months for non-mutated, p = 0.0260). We found no association between TERT promoter mutations and the rs2853669 genotype. To our knowledge, we showed the presence of TERT promoter mutations in PCNSL for the first time. In addition, C228T promoter mutation was associated with a poor outcome. Considering that these mutations are known to confer enhanced TERT promoter activity, we speculate that an increased telomerase activity could play a role in PCNSL aggressiveness. This work was granted by the LOC study group network (réseau national de centres experts des lymphomes primitifs du SNC, INCa), the Ligue contre le Cancer (Comité du Val d’Oise), the Fondation pour la Recherche Médicale (FDT20140930968), the APHP-CRIC 2013 (assistance publique - hôpitaux de Paris), and the Association pour la Recherche sur les Tumeurs Cérébrales. Citation Format: Aurélie Bruno, Mailys Daniau, Karima Mokhtari, Amithys Rahimian, Marc Polivka, Anne Jouvet, Clovis Adam, Dominique Figarella-Branger, Catherine Miquel, Sandrine Eimer, Caroline Houillier, Carole Soussain, Agusti Alentorn, Khê Hoang-Xuan. Recurrent TERT promoter mutations in primary central nervous system lymphoma. [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 3896. doi:10.1158/1538-7445.AM2015-3896
Identification of New Multiple Myeloma-Specific Cell Surface Antigens As Immunotherapeutic Targets
Authors: Naoki Hosen, Kana Hasegawa, Yasutaka Aoyama, Hiroyoshi Ichihara, Atsuko Mugitani, Takafumi Nakao, Masahiro Manabe, Yusuke Oji, Haruo Sugiyama
Journal: Blood (2016)
Enzyme Tunnels and Gates As Relevant Targets in Drug Design
Authors: Sergio M. Marques, Lukas Daniel, Tomas Buryska, Zbynek Prokop, Jan Brezovsky, Jiri Damborsky
Journal: Medicinal Research Reviews (2016)

Abstract Many enzymes contain tunnels and gates that are essential to their function. Gates reversibly switch between open and closed conformations and thereby control the traffic of small molecules—substrates, products, ions, and solvent molecules—into and out of the enzyme's structure via molecular tunnels. Many transient tunnels and gates undoubtedly remain to be identified, and their functional roles and utility as potential drug targets have received comparatively little attention. Here, we describe a set of general concepts relating to the structural properties, function, and classification of these interesting structural features. In addition, we highlight the potential of enzyme tunnels and gates as targets for the binding of small molecules. The different types of binding that are possible and the potential pharmacological benefits of such targeting are discussed. Twelve examples of ligands bound to the tunnels and/or gates of clinically relevant enzymes are used to illustrate the different binding modes and to explain some new strategies for drug design. Such strategies could potentially help to overcome some of the problems facing medicinal chemists and lead to the discovery of more effective drugs.
Imatinib Mesylate Discontinuation in Patients with Chronic Myelogenous Leukaemia in Complete Molecular Remission for More Than Two Years.
Authors: Philippe Rousselot, Françoise Huguet, Jean Michel Cayuela, Odile Maarek, Gérald Marit, Eliane Gluckman, Josy Reiffers, François X. Mahon
Journal: Blood (2005)
Absence of Cytomegalovirus in Glioblastoma and Other High-grade Gliomas by Real-time PCR, Immunohistochemistry, and <i>In Situ</i> Hybridization
Authors: Matthias Holdhoff, Gunes Guner, Fausto J. Rodriguez, Jessica L. Hicks, Qizhi Zheng, Michael S. Forman, Xiaobu Ye, Stuart A. Grossman, Alan K. Meeker, Christopher M. Heaphy, Charles G. Eberhart, Angelo M. De Marzo, Ravit Arav-Boger
Journal: Clinical Cancer Research (2016)

Purpose: Reports of cytomegalovirus (CMV) detection in high-grade gliomas (HGG)/glioblastoma have been conflicting. We undertook a comprehensive approach to determine the presence or absence of CMV in tissue, plasma, and serum of HGG patients.Experimental Design: In a retrospective arm, 25 fresh frozen tissues from glioblastoma patients were tested for CMV by real-time PCR. Tissue microarrays from 70 HGG patients were tested by IHC and 20 formalin-fixed paraffin-embedded (FFPE) glioblastoma tissues by IHC and chromogenic in situ hybridization (CISH), targeting CMV-encoded IE1/2 and pp65. In a prospective arm, 18 patients with newly diagnosed HGG provided tissue and blood samples.Results: All retrospectively collected tissues were negative for CMV by all methods. In the prospective cohort, 18 patients with newly diagnosed HGG provided blood samples at the time of diagnosis and during follow-up. Of 38 plasma specimens, CMV DNA was detected in 3 of 18 samples at baseline and 1 of 20 follow-up samples. Serum CMV IgG was positive in 8 of 15 (53%) of patients. Among the FFPE samples tested in the prospective arm, all were negative for CMV by IHC, CISH, and PCR.Conclusions: Utilizing 6 highly sensitive assays with three orthogonal technologies on multiple specimens and specimen types, no evidence for CMV in glioblastoma tissues was found. Our findings call for multicenter blinded analyses of samples collected from different geographical areas with agreed upon study designs and determination of causality or lack thereof of CMV in HGG/glioblastoma for future guidance on the necessary antiviral and/or CMV-based therapies. Clin Cancer Res; 23(12); 3150-7. ©2016 AACR.
Phase I trial assessing safety and pharmacokinetics of afatinib (BIBW 2992) with intravenous weekly vinorelbine in advanced solid tumors.
Authors: R. Bahleda, J. Soria, Y. Berge, C. Massard, S. Wind, M. M. Uttenreuther-Fischer, F. Fleischer, H. De-Montserrat, F. Solca, I. Tschoepe, J. Delord
Journal: Journal of Clinical Oncology (2011)

2585 Background: Afatinib (BIBW 2992) is an oral irreversible ErbB family blocker with activity in a wide range of tumor cell lines dependent on erbB signaling. Vinorelbine, a semi-synthetic vinca alkaloid, interferes with tubulin polymerization and spindle formation during metaphase. Additive or supraadditive activity of afatinib or EGFR TKI with vinorelbine has been demonstrated in preclinical models in vitro and in vivo. Methods: This is a dose-escalation study to define the MTD and characterize the pharmacokinetics (PK), pharmacodynamics and safety profile of afatinib with i.v. weekly vinorelbine. Eligible patients (pts) were ≥18 years of age with advanced or metastatic tumors, refractory to standard therapies, ECOG 0-1, and adequate organ and bone marrow function. In each 28-day treatment course, a fixed dose of vinorelbine (25 mg/m2) was administered weekly on days 1, 8, 15 and 22 with escalating afatinib daily doses of 20 mg, 40 mg and 50 mg given orally. Results: The study treated 15 patients (7 M/ 8 F), median age 59 years (range 42-70) to establish the MTD. Most patients had either NSCLC (n = 4), head and neck cancer (n = 3) or cervical cancer (n = 3). Three pts were treated at 20 mg of afatinib without DLT. Four of six pts experienced DLTs when treated at 50 mg afatinib (NCI CTCAE v 3.0 grade 3 mucositis, febrile neutropenia and diarrhea ). At 40 mg one pt with DLT was observed (febrile neutropenia, and grade 3 hyperlipasemia and asthenia).The MTD of afatinib given continuously with vinorelbine i.v. (25 mg/m2) weekly was determined at 40 mg daily. At or below the MTD of 40 mg, the majority of AEs were mild-moderate and included diarrhea, asthenia, nausea, vomiting, neutropenia, constipation, abdominal pain, mucositis. Preliminary PK and efficacy analyses demonstrate no drug-drug interaction (DDI) between both compounds, and a rate of patients who received > 2 and > 4 cycles of 67% and 40%, respectively. Conclusions: Afatinib in combination with weekly i.v. vinorelbine has been well tolerated, with reversible, target-related AEs and promising efficacy in heavily pretreated patients. The MTD for afatinib is 40 mg daily.
300. Changing the Route of Administration to Improve Liver Transduction by Recombinant AAV-Based Vectors
Authors: Nerea Zabaleta, David Salas, Anna Majowicz, Rubén Hemandez-Alcoceba, Valerie Sier-Ferreira, Jesús Prieto, Ignacio Bilbao, Gloria González-Aseguinolaza
Journal: Molecular Therapy (2016)

The liver is a central organ in metabolism and there are numerous inherited metabolic disorders that have their origin in this organ. Gene therapy represents a promising therapeutic approach for this type of diseases. Although in preclinical studies using AAV-based vectors high and long-term hepatic expression has been achieved, there are still some concerns about the expression levels and the percentage of hepatocytes that can be transduced. This is of particular importance for diseases in which the deficiency of an enzymatic activity is associated with the generation of toxic products that require the transduction of a high percentage of hepatocytes. Therefore, the main goal of our study was to improve liver transduction efficacy by an AAV serotype. For this purpose, the vector was administered directly to the liver via suprahepatic veins (SHV) using a catheter and balloon occlusion or via the hepatic artery (HA) with balloon occlusion of the suprahepatic vein. The experiment was performed in Macaca fascicularis, with 8 animals being infected with a dose of 3×1013 gc/kg of an AAV5 expressing the reporter gene hSEAP (human secreted embryonic alkaline phosphatase) under the control of a liver specific promoter (AAV5-AAT-hSEAP). The first group (2 animal) received the virus systemically in the saphenous vein, the second group (3 animals) received the virus via the SHV with 10 minutes of balloon occlusion and the third group (3 animals) via the HA with 10 minutes of balloon occlusion of the SHV. The procedure could only be performed on the right branch of SHV and HA due to the small size of the left SHV and HA branches, reaching only 40% of the liver. hSEAP-specific activity in serum samples of the groups that received the virus directly in the hepatic blood flow was higher compared to the animals receiving the vector by peripheral intravenous injection. This was correlated with the presence of a higher number of viral genomes in the liver of the animals. Moreover, when their distribution was analyzed we found that the animals that had received the virus through the SHV or HA displayed higher infection rates in the right side of the liver, where the administration had been performed. In conclusion, direct administration of the vector AAV5-AAT-hSEAP through the hepatic blood flow with balloon occlusion was associated with higher transgene expression and an increase in vector genomes in the injected area. Studies in bigger animals in order to reach both sides of the liver should be performed in order to explore the potential use of alternative routes of administration in the clinic.
Clathrin Assembly Protein CALM Is Necessary for Leukemia Cell Proliferation and Erythroid Development Via Regulating Transferrin Receptor Endocytosis
Authors: Yuichi Ishikawa, Manami Maeda, Min Li, Sung-Uk Lee, Julie Teruya Feldstein, Hitoshi Kiyoi, Tomoki Naoe, Mitchell J. Weiss, John E Heuser, Takahiro Maeda
Journal: Blood (2011)
687. Therapeutic Correction of an LCA-Causing Splice Defect in the CEP290 Gene by CRISPR/Cas-Mediated Genome Editing
Authors: Morgan L. Maeder, Shen Shen, Erin R. Burnight, Sebastian Gloskowski, Rina Mepani, Ari E. Friedland, Hari Jayaram, Greg Gotta, Budd A. Tucker, David Bumcrot
Journal: Molecular Therapy (2015)

Leber congenital amaurosis (LCA) comprises a genetically heterogeneous group of early-onset retinal disorders characterized by severe loss of vision in the first years of life. Approximately 30% of LCA patients harbor mutations in the CEP290 gene, which codes for a centrosomal protein involved in ciliogenesis and ciliary trafficking in the photoreceptors. While AAV-mediated gene therapy is showing promise in clinical trials for RPE65-associated LCA, the size of CEP290 exceeds the limit for efficient packaging in AAV. Thus, alternative approaches to treat CEP290 associated LCA are needed. Here, we report a gene editing approach in which the CRISPR/Cas9 system is used to modify the endogenous CEP290 locus and restore normal function of the gene. The most common mutation in CEP290 is the IVS26 c. 2991+1655 A>G mutation. This point mutation in intron 26 of the gene generates a novel splice donor, resulting in aberrant splicing and the inclusion of an extra 128bp cryptic exon into the coding sequence of the transcript. Using the S. aureus CRISPR/Cas9 system, we employed a dual-cut approach in which two gRNAs are used to induce a pair of double strand breaks and excise the region of DNA containing the mutation. We screened gRNA pairs in primary fibroblasts derived from LCA patients harboring homozygous IVS26 mutations and identified pairs capable of generating targeted deletions with high efficiency. Using qRT-PCR, we showed that deletion of the mutation results in increased expression of wildtype CEP290 and concomitant decrease in expression of the aberrantly spliced mutant RNA species. Genome-wide specificity profiling allows for assessment of potential off-target modifications induced by the gRNAs and informs selection of optimal gRNA pairs for further study. Assays to assess ciliogenesis, as well as molecular characterization of gene editing in patient-derived photoreceptor precursor cells, demonstrate phenotypic correction in the relevant cell population. The use of the S. aureus CRISPR/Cas9 system enables efficient packaging of the Cas9 gene, as well as two gRNA genes, into a single AAV vector and provides a method for delivery of this system into patient photoreceptors.
339. GENIS: A Bioinformatics Tool for Reliable and Automated Genome Insertion Site Analysis
Authors: Saira Afzal, Raffaele Fronza, Stefan Wilkening, Cynthia Bartholomä, Christof von Kalle, Manfred Schmidt
Journal: Molecular Therapy (2015)

Over the last two decades, gene therapy has shown rapid advancements as a promising approach to treat genetic diseases by introducing corrected genes into patient cells. Viruses are the most common carriers in the vector-mediated gene therapy. However, integration of viral vectors at undesirable genomic locations can lead to deleterious effects, e.g. insertional mutagenesis. Therefore, an efficient, stable and safe vector system is the major prerequisite for a successful gene therapy. Long term monitoring of the distribution pattern of vector integration sites (IS) is the most feasible strategy to address vector safety and stability concerns. Recent advancements in next generation sequencing technologies have dramatically increased the possibility to generate substantial amount of vector-genome sequencing data for comprehensive IS analysis. An efficient downstream analysis of this data requires automated and fast computational methods. Here, we present Genome Insertion Site (GENIS) pipeline, a suite for time-efficient and reliable analysis of vector-genome junctions. GENIS has been designed to analyze the sequencing data generated from traditional linear amplification mediated PCR (LAM-PCR) based methods and also from new targeted DNA single and paired end sequencing technologies (e.g., Agilent SureSelect). Our suite consists of six basic modules including barcode sorting, quality filtering and adapter trimming, mapping of sequence reads to the reference genome, extraction of soft-clip reads and clustering of IS for subsequent annotation. GENIS is implemented on Linux platform with minimum external software dependencies. Users can adjust the required parameters in the provided configuration file. It takes about 30 minutes for complete processing, starting from raw reads till annotation, of 10 million paired end reads generated by targeted sequencing. In case of LAM-PCR data, 30 million reads are sorted in about 30 minutes (50 different PCR) and time required for rest of processing to obtain annotated IS is also approximately 30 minutes for 15 million reads. Three final files present the conclusion of the analysis process and contain: 1) the information about read ID, chromosome position (genomic IS), vector position (vector IS), sequence, genomic and vector orientation and sequence span; 2) all the clustered IS with their respective sequence count and 3) the annotated IS with respect to nearby genomic features, including gene identifier and gene name, transcription start site, coding region start and end sites etc. Our tool is highly appropriate for in-depth quantitative analysis of biosafety and transduction efficiency of viral vectors.
Abstract 4045: MRAS and SHOC2 interact with SCRIB and coordinate ERK pathway activation with polarity and tumorigenic growth
Authors: Lucy C. Young, Nicole Hartig, Marta Munoz-Alegre, Juan A. Oses-Prieto, Sevi Durdu, Sabine Bender, Vineetha Vijakumar, Matteo Vietri Rudan, Christina Gewinner, Amit P. Jathoul, Rupinder Ghatrora, Mark L. Lythgoe, Alma L. Burlingame, Pablo Rodriguez-Viciana
Journal: Cancer Research (2015)

Abstract SHOC2 is mutated in Noonan syndrome and plays a key role in the activation of the ERK-MAPK pathway, which is upregulated in the majority of human cancers. SHOC2 functions as a PP1-regulatory protein and as an effector of MRAS. Here we show that SHOC2 and MRAS form a complex with SCRIB, a polarity protein with tumor suppressor properties. SCRIB functions as a PP1-regulatory protein and antagonizes SHOC2-mediated RAF dephosphorylation through a mechanism involving competition for PP1 molecules within the same macromolecular complex. SHOC2 function is selectively required for the malignant properties of tumor cells with mutant RAS, and both MRAS and SHOC2 play a key role in polarized migration. We propose that MRAS, through its ability to recruit a complex with paradoxical components, coordinates ERK pathway spatiotemporal dynamics with polarity and that this complex plays a key role during tumorigenic growth. Citation Format: Lucy C. Young, Nicole Hartig, Marta Munoz-Alegre, Juan A. Oses-Prieto, Sevi Durdu, Sabine Bender, Vineetha Vijakumar, Matteo Vietri Rudan, Christina Gewinner, Amit P. Jathoul, Rupinder Ghatrora, Mark L. Lythgoe, Alma L. Burlingame, Pablo Rodriguez-Viciana. MRAS and SHOC2 interact with SCRIB and coordinate ERK pathway activation with polarity and tumorigenic growth. [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 4045. doi:10.1158/1538-7445.AM2015-4045