tbuckley/cabot-search huggingface dataset:
404. Development of Combinational Cellular Immunotherapy to Treat Pediatric Acute Myeloid Leukemia Patients
Authors: Niek P. vanTil, Lea Knežević, Maud Plantinga, Colin de Haar, Rob C. Hoeben, Manuel A. Gonçalves, Stefan Nierkens, Jaap Jan Boelens
Journal: Molecular Therapy (2016)

Hematopoietic stem cell transplantation is the standard of care for pediatric acute myeloid leukemia (AML) patients, but relapse still occurs in approximately 40% of AML patients. Hence there is an unmet need to improve disease control with fewer adverse acute and late effects. We therefore aim to develop 'HLA-matched' modified cellular therapies based on a platform of cord blood transplantation (CBT) to treat pediatric AML patients. In the majority of AML patients the tumor oncogene Wilms tumor 1 (WT1) is overexpressed and can serve as a target for tumor specific therapy. In addition to our previously developed cord blood-derived dendritic cell vaccine (CB-DC) we are currently developing gene modified T lymphocytes from the same CB-unit to specifically target WT1 expressing AML to support and increase the anti-leukemic effects of CBT. Lentiviral vectors were developed to express recombinant T-cell receptors (TCR) specifically recognizing HLA-A2+ restricted WT1 peptide. TCR expression was improved by codon-optimization of the cDNA sequence including cysteines in the alpha and beta chain constant domains. These WT1-specific TCR α/β-chains were incorporated in a single lentiviral vector linked by a 'self-cleaving' T2A peptide to improve efficiency. The order of the alpha and beta TCR chains, and inclusion of a furin cleavage site in the expression cassette did not enhance TCR expression in Jurkat and primary T cells derived from either peripheral blood or cord blood. Primary T cells were stimulated with T2 cells and CB-DCs pulsed with the specific peptide, which resulted in T cell activation as measured by CD69 and CD137 upregulation, as well as IFNgamma production. To reduce the risk of off-target antigen recognition of gene-modified T cells, and to further improve efficacy, CRISPR/Cas9 can be used to eliminate endogenous TCR expression. Cas9 protein and guide RNA (gRNA) were delivered to GFP positive reporter Jurkat cells using plasmid and mRNA electroporation (EP), integrating and non-integrating lentiviral vectors and adenoviral vectors with the highest efficiency of knockout being achieved by EP. Two gRNAs targeting the constant domains of the alpha chain and three targeting those of the beta chain resulted in similar knockout efficiencies in Jurkat cells (approximately 25%). Of note, combining the gRNAs did not result in higher knockout efficiencies. Gene-editing at the molecular level was confirmed by next generation sequencing. We envision that addition of TCR-engineered T cells (introduction of tumor-specific TCR and knockdown of endogenous TCR), derived from the same cord blood as used for the transplantation, will more efficiently and with improved safety prevent early relapse after CBT by targeting WT1 AML.
Serum Interleukin-18 Levels Are Associated with Response to Treatment and Survival in Patients with Aggressive Non-Hodgkin’s Lymphoma.
Authors: Naoe Goto, Hisashi Tsurumi, Masao Takemura, Takeshi Hara, Michio Sawada, Toshiki Yamada, Senji Kasahara, Nobuhiro Kanemura, Takeshi Takahashi, Mitsuru Seishima, Tsuyoshi Takami, Koshiro Saito, Hisataka Moriwaki
Journal: Blood (2004)
484. Preclinical Proof of Concept of Transcriptional Silencing and Replacement Strategy for Treatment of Retinitis Pigmentosa Due To RHODOPSIN Mutations
Authors: Salvatore Botta, Elena Marrocco, Nicola de Prisco, Fabiola Curion, Martina Sofia, Mariangela Lupo, Mario Renda, Maria Laura Bacci, Settimio Rossi, Francesca Simonelli, Enrico Maria Surace
Journal: Molecular Therapy (2015)

Silencing and replacement strategy is a promising approach to overcome mutational heterogeneity of genetic defects. In autosomal dominant retinitis pigmentosa (adRP) due to rhodopsin gene (RHO) approximately 200 different mutations have been described, posing a challenge for the design of effective therapeutics. We designed a silencing and replacement strategy based on transcriptional silencing through an artificial zinc finger DNA-binding protein lacking effector domains (ZF6DBD), and tested both efficacy and safety in two animal models. In a murine model of adRP, we show that AAV-mediate retinal delivery (AAV2/8-CMV-ZF6-DBD) is associated with selective transcriptional silencing of the human mutated allele resulting in morphological and functional (Electroretinography, ERG a-wave and b-wave responses) rescue. We then tested the effect of transcriptional silencing in the porcine large pre-clinical model. Delivery of a low dose (AAV2/8-CMV-ZF6-DBD, 1×10e10 vector genomes, vg) of the ZF6 transcriptional silencer to the porcine retina resulted in robust transcriptional silencing of the endogenous porcine RHO transcript. Cell sorting of transduced photoreceptors showed an almost complete RHO transcriptional silencing effect (90% RHO transcriptional repression), underscoring the potency of the system. To determine the safety of the zinc-finger silencer we performed extensive RNA-seq analysis on treated and control retinae. The data sets generated demonstrate selective RHO gene transcriptional repression and a remarkably low number of differential expressed genes (DEGs), supporting specificity and thus, safety. The co-administration to the porcine retina of the AAV-ZF6 silencer (AAV2/8-CMV-ZF6-DBD) and the AAV-RHO replacement (5×10e11 vg, AAV2/8-GNAT1-HumanRHO) constructs resulted in a balanced silencing and replacement effect. This data support the use of zinc-finger based RHO transcriptional silencing for the development of a clinical trial for adRP patients.
130. Purification of Large Scale mRNA Encoding ZFN Nucleases by dHPLC Technology
Authors: Erica Giuliani, Claudia Piovan, Sergio Bossi, Stefano Corna, Cinzia Scavullo, Monika Pema, Tiziano Di Tomaso, Pietro Genovese, Angelo Lombardo, Luigi Naldini, Claudio Bordignon, Gian Paolo Rizzardi, Chiara Bovolenta
Journal: Molecular Therapy (2016)

A novel strategy of targeted gene correction of the interleukin-2 receptor common gamma chain (IL2RG) gene for the treatment of X-linked Severe Combined Immunodeficiency (SCID-X1) is achieved by the combination of a pair of IL2RG-specific Zinc Finger Nucleases (ZFN) and the correct-gene template DNA delivered by integration-defective lentiviral vector (IDLV).The transient expression of the ZFN pair targeting the disease-causing gene is obtained by the electroporation of the two corresponding mRNAs, produced by in vitro transcription starting from plasmid DNA template. A major limitation of the mRNA transcribed in vitro is the presence of residual contaminants such as short RNAs and double stranded (ds)RNAs that may affect the function and spectrophotometric quantification of the product hampering therefore the delivery of high quality and precise amount of mRNA to target cells. Moreover, dsRNA contaminants represent a possible risk in terms of immunogenicity of the product, leading to activation of unwanted innate immune response with consequent reduction/abrogation of mRNA translation as well as potential alteration of the properties of the transfected cells. To improve nuclease expression while decreasing cellular innate response to mRNA transfection we combined different strategies: (i) inclusion of UTRs and polyA tails in the DNA template used for mRNA production; (ii) use of modified nucleotides during mRNA production and (iii) purification of the mRNAs by dHPLC with a reverse phase column made of non-porous matrix consisting of polystyrene-divinylbenzene copolymer beads alkylated with C-18 chains (Transgenomic, LTD.). In particular, the purification of in vitro transcribed mRNAs by means of dHPLC has been shown to strongly improve the translation of mRNA and significantly reduce the contaminant presence thus preventing innate immunity and eventually increasing modified cells persistence in vivo. We have developed feasible and reproducible, small and large scale mRNA production and downstream purification processes of the ZFN pairs obtaining accurate RNA quantification and reduced risk of immunogenicity. The full process achieved a 60% yield, loading with a 500µg RNA for each run with a single clean chromatographic peak. Furthermore, the level of residual organic solvent (i.e. Acetonitrile) used in the purification process is compatible with that applicable into clinic. The highly translatable non-immunogenic dHPLC-purified mRNA can be delivered without toxicity and represents a powerful and safe tool for the application of gene therapy protocols.
Hepatitis B (HBV) Screening in Patients Receiving Rituximab: A Comprehensive Analysis Including Comparison of Adherence By Oncologists and Non-Oncologists
Authors: Aditi Puri, Ryan L. Stevenson, Jack Khouri, Raymond L. Comenzo, Grace Shih-Hui Kao, Andreas K. Klein, Kenneth B. Miller, Aaron Rosenberg, Hedy Smith, Kellie A. Sprague, Valerie Relias, Andrew M. Evens
Journal: Blood (2014)
High Dose Melphalan with Autologous Stem Cell Transplantation Overcomes Poor Prognosis of Primary Amyloidosis
Authors: Simrit Parmar, Mubeen Khan, Gabriela Rondon, Nina Shah, Qaiser Bashir, Shawndeep Tung, Jatin J Shah, Donna Weber, Robert Z. Orlowski, Sergio Giralt, Richard E. Champlin, Muzaffar H. Qazilbash
Journal: Blood (2010)
Towards a behavioural ecology of obesity
Authors: Andrew D. Higginson, John M. McNamara, Sasha R. X. Dall
Journal: Behavioral and Brain Sciences (2017)

Abstract Addressing the obesity epidemic depends on a holistic understanding of the reasons that people become and maintain excessive fat. Theories about the causes of obesity usually focus proximately or evoke evolutionary mismatches, with minimal clinical value. There is potential for substantial progress by adapting strategic body mass regulation models from evolutionary ecology to human obesity by assessing the role of information.
Mitogenomic phylogeny, diversification, and biogeography of South American spiny rats
Authors: Pierre-Henri Fabre, Nathan S. Upham, Louise H. Emmons, Fabienne Justy, Yuri L. R. Leite, Ana Carolina Loss, Ludovic Orlando, Marie-Ka Tilak, Bruce D. Patterson, Emmanuel J. P. Douzery
Journal: Molecular Biology and Evolution (2016)

Echimyidae is one of the most speciose and ecologically diverse rodent families in the world, occupying a wide range of habitats in the Neotropics. However, a resolved phylogeny at the genus-level is still lacking for these 22 genera of South American spiny rats, including the coypu (Myocastorinae), and 5 genera of West Indian hutias (Capromyidae) relatives. Here, we used Illumina shotgun sequencing to assemble 38 new complete mitogenomes, establishing Echimyidae, and Capromyidae as the first major rodent families to be completely sequenced at the genus-level for their mitochondrial DNA. Combining mitogenomes and nuclear exons, we inferred a robust phylogenetic framework that reveals several newly supported nodes as well as the tempo of the higher level diversification of these rodents. Incorporating the full generic diversity of extant echimyids leads us to propose a new higher level classification of two subfamilies: Euryzygomatomyinae and Echimyinae. Of note, the enigmatic Carterodon displays fast-evolving mitochondrial and nuclear sequences, with a long branch that destabilizes the deepest divergences of the echimyid tree, thereby challenging the sister-group relationship between Capromyidae and Euryzygomatomyinae. Biogeographical analyses involving higher level taxa show that several vicariant and dispersal events impacted the evolutionary history of echimyids. The diversification history of Echimyidae seems to have been influenced by two major historical factors, namely (1) recurrent connections between Atlantic and Amazonian Forests and (2) the Northern uplift of the Andes.
CBM-13CHARACTERIZATION OF CELL-FREE CIRCULATING TUMOR DNA IN LOW GRADE AND MALIGNANT GLIOMAS
Authors: Nadia Faiq, Michelle Lee, Kimberly Banks, Richard Lanman, Sandeep Pingle, Santosh Kesari, David Piccioni
Journal: Neuro-Oncology (2015)

BACKGROUND: Glioblastoma is the most common primary malignant brain tumor, with poor survival despite standard therapy. Genetic profiling of tumor tissue can identify targeted therapies to increase treatment options, though such testing presents with limitations. Cell-free circulating tumor DNA (ctDNA) testing was recently developed and carries remarkable diagnostic potential for targeted therapy. CtDNA testing needs to be further characterized in glioma patients to establish its utility. METHODS: 133 consecutive samples of gliomas (15 grade II, 20 grade III and 98 grade IV) were tested prospectively at a CLIA-certified, CAP-accredited clinical laboratory with Guardant360 ctDNA panel. Testing is sensitive to 1-2 molecules of mutated ctDNA in a 10 mL blood sample with 99.9999% specificity. Samples were analyzed for amplifications in 3 genes (EGFR, ERBB2, MET) and single nucleotide variants (SNVs) by a 54 or expanded 68-gene panel, with a combination of comprehensive and critical exon sequencing. RESULTS: 2/15 (13.3%) samples from patients with grade II gliomas harbored detectable genomic alterations, whereas 6/20 (30.0%) of grade III and 38/98 (38.8%) of grade IV samples contained alterations. The most common genes with detectable alterations in the 98 glioblastoma samples were p53 (15), APC (8), EGFR (5), and MET (5). Data for date of next progression was available for 40 of the 98 glioblastoma samples. 16 of the 40 samples were tested within 30 days of the next recurrence; 9/16 (56%) detected genomic alterations. The remaining 24 samples were tested more than 30 days before the next recurrence; only 5/24 (21%) had detectable alterations. CONCLUSIONS: CtDNA testing is more sensitive to detecting genetic variations in glioblastomas as opposed to lower grade gliomas. The presence of detectable alterations was increased in the 30 days prior to the next documented recurrence. This increased sensitivity may suggest the utility of ctDNA as an early detector of progression.
OC-038 Pellino 1: a novel regulator of Toll-like receptor-mediated signalling in response to<i>Helicobacter pylori</i>lipopolysaccharide
Authors: S M Smith, A P Moran, P N Moynagh, D P Kelleher
Journal: Gut (2010)

<h3>Introduction</h3> Toll-like receptors (TLRs) play a key role in host defence against invading pathogens by functioning as primary sensors for conserved microbial structures known as pathogen-associated molecular patterns (PAMPs). Recognition of PAMPs by a particular TLR results in the activation of transcription factors such as NF-κB, AP-1 and interferon regulatory factors, culminating in the induction of gene expression necessary for the co-ordination of the innate immune response. This study set out to identify novel regulators of TLR signalling in response to the gastric pathogen <i>Helicobacter pylori</i>. We investigated the role of the interacting protein Pellino 1 (PELI1) during the TLR2-mediated response to <i>H pylori</i> lipopolysaccharide (LPS). PELI1 has recently been suggested to interact with components of the TLR signalling pathway (IRAKs 1 and 4, TRAF6), thereby regulating NF-κB activation. <h3>Methods</h3> PELI1 expression in response to <i>H pylori</i> infection or <i>H pylori</i> LPS was monitored by quantitative real-time PCR in HEK-TLR2 cells and MKN45 gastric epithelial cells. In order to determine the involvement of PELI1 during TLR2-mediated signalling, HEK-TLR2 cells were co-transfected with increasing quantities of an expression vector for PELI1, and either an NF-κB-reporter construct or promoter-reporter constructs for interleukin 8 (IL-8) and chemokine (C-C) motif ligand 20 (CCL20). Forty-eight hours post-transfection, cells were stimulated with either <i>H pylori</i> LPS or the synthetic TLR2 ligand Pam<sub>2</sub>CSK<sub>4</sub> for 8 h. Additionally, co-transfection experiments were carried out using small interfering RNA (siRNA) for PELI1. <h3>Results</h3> Stimulation of HEK-TLR2 and MKN45 cells with both intact <i>H pylori</i> or LPS resulted in a significant increase in PELI1 mRNA expression. PELI1 over-expression in HEK-TLR2 cells resulted in a dose-dependent increase in NF-κB activity in response to both Pam<sub>2</sub>CSK<sub>4</sub> and <i>H pylori</i> LPS. Additionally, increased PELI1 expression led to transcriptional activation of the IL-8 and CCL20 promoters in <i>H pylori</i> LPS-treated cells. Furthermore, PELI1 knock-down using siRNA inhibited the TLR2-mediated activating properties of Pam<sub>2</sub>CSK<sub>4</sub> and <i>H pylori</i> LPS. <h3>Conclusion</h3> PELI1 expression positively regulates TLR2-mediated signalling in response to <i>H pylori</i> LPS, resulting in increased NF-κB activation and pro-inflammatory chemokine induction. Thus, modulation of PELI1 by <i>H pylori</i> and/or its products may be an important mechanism during <i>H pylori</i>-associated pathogenesis.
Echocardiography and Cardiopulmonary Exercise Testing for Early Detection of Pulmonary Hypertension in Primary Myelofibrosis
Authors: Alessandra Iurlo, Mariarita Sciumè, Veronica Mattiello, Daniele Cattaneo, Nicola Orofino, Ivan Cortinovis, Umberto Gianelli, Alberto Pierini, Agostino Cortelezzi
Journal: Blood (2015)
Serum α1-Acid Glycoprotein Level Associate with Imatinib Trough Plasma Concentration and Clinical Outcome in CML Patients Treated with Imatinib: Blood Level Testing of Imatinib in Nagoya (BINGO) Study.
Authors: Yuichi Ishikawa, Hitoshi Kiyoi, Keisuke Watanabe, Yasuyuki Nakano, Kunio Kitamura, Akio Kohno, Toshiya Yokozawa, Isamu Sugiura, Akitoshi Hanamura, Hiroatsu Iida, Kazuhito Yamamoto, Ritsuro Suzuki, Koichi Miyamura, Nobuhiko Emi, Kazunori Ohnishi, Tomoki Naoe
Journal: Blood (2009)
Abstract 5433: Discovery and development of novel USP2 inhibitors for cancer therapy
Authors: Suresh Kumar, James P. LaRocque, Jeffrey G. Marblestone, Jian Wu, Joseph Weinstock, David E. Sterner, Michael R. Mattern
Journal: Cancer Research (2015)

Abstract Ubiquitylation and deubiquitylation control the stability, localization and activity of many cellular proteins. Deubiquitylation is performed by a family of ∼80 enzymes (DUBs) and many of these DUBs have been implicated in a wide range of diseases including cancer. In particular, USP2 removes ubiquitin selectively from Cyclin D1, Cyclin A1, Aurora A, MDM2 and FAS which are all implicated in oncogenic processes. Importantly, USP2 is overexpressed in prostate and ovarian cancers and inhibition of USP2 has been shown to sensitize prostate carcinoma cells to apoptosis. Therefore USP2 is an attractive therapeutic target. Progenra's unique UbiProTM discovery platform was utilized to screen ∼200K member diversity based library of small molecules for identifying novel USP2 inhibitors. Hits from the screen were subjected to orthogonal selectivity assays to identify USP2 specific inhibitors. Here we report discovery and hit to lead optimization of novel USP2 inhibitors showing cellular efficacy and anti-cancer activities against relevant cancer cell models. The most promising compounds are being further developed as novel anti-cancer agents. Citation Format: Suresh Kumar, James P. LaRocque, Jeffrey G. Marblestone, Jian Wu, Joseph Weinstock, David E. Sterner, Michael R. Mattern. Discovery and development of novel USP2 inhibitors for cancer therapy. [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 5433. doi:10.1158/1538-7445.AM2015-5433
Abstract 2443: Optides (optimized peptides), a new knottin-based cancer drug discovery platform
Authors: James M. Olson, Roland Strong, Christopher Mehlin, Colin Correnti
Journal: Cancer Research (2015)

Abstract Some of the highest value targets in cancer therapeutics involve protein:protein interactions that are difficult to inhibit with small molecule therapeutics. Peptide drug candidates offer an alternative, but many peptide drugs have poor pharmacokinetic properties and some are immunogenic. Knottin peptides have long been promoted as scaffolds for human drug discovery efforts because the exquisitely tight knot formed by disulfide bridges creates resistance to proteolytic and other forms of degradation. Furthermore, some knottins cross the blood brain barrier, the gut wall, or cell membranes which is ideal for certain targets. Unfortunately, creating knottins synthetically or in bacteria results in a large number of disulfide isomers, which has hampered research. We have created a mammalian expression system that enables production of most knottin scaffolds and variants of native knottins encoded in plant and animal genomes. The platform routinely produces approximately 10 mg/liter of near pure naked peptide, which is sufficient to conduct in vivo studies without major scale-up. The system is endotoxin free. In addition to building the platform, we identified over 200,000 new potential knottin peptides in various genomes, creating a rich collection of scaffolds from which to establish diversity libraries of native and optimized variants. These candidates have potential for targeting therapeutics to cancer cells as a solid tumor penetrating alternative to antibody drug conjugates. Optides also have potential to be developed as anti-cancer drugs themselves. The fact that knottin peptides are not substrates for resistance mechanisms such as p-glycoprotein pumps underscores the potential importance of this class of drugs for those with previously treated cancer. Citation Format: James M. Olson, Roland Strong, Christopher Mehlin, Colin Correnti. Optides (optimized peptides), a new knottin-based cancer drug discovery platform. [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 2443. doi:10.1158/1538-7445.AM2015-2443