tbuckley/cabot-search huggingface dataset:
282. A scFv-Based CAR To Redirect T Cells To IL13Ra2-Positive Glioma
Authors: Giedre Krenciute, Simone Krebs, David Torres, Maciej Lesniak, Irina Balyasnikova, Stephen Gottschalk
Journal: Molecular Therapy (2015)

BACKGROUND: Glioblastoma (GBM) is the most aggressive primary brain tumor in humans, and is virtually incurable with conventional therapies. Immunotherapy with T cells expressing chimeric antigen receptors (CARs) is an attractive approach to improve outcomes. IL13Ra2 is aberrantly expressed in GBM therefore it is a promising target for CAR T-cell immunotherapy. The antigen recognition domain of CARs normally consists of a single chain variable fragment (scFv), however current IL13Ra2-specific CARs use IL13 muteins as an antigen recognition domain. We have previously shown that IL13 mutein-based CARs also recognize IL13Ra1, raising significant safety concerns. To overcome this obstacle we have recently generated a high affinity IL13Ra2-specific scFv. The goal of this project is now to develop a scFv-based IL13Ra2-specific CAR (IL13Ra2-CAR) and evaluate the effector function of IL13Ra2-CAR T cells. METHODS: We constructed a panel of IL13Ra2-CARs that contain our new IL13Ra2-specific scFv (m47) as an ectodomain, a short hinge (SH) or long hinge (LH), a CD28 transmembrane domain, and endodomains that contain signaling domains derived from CD3ζ and co-stimulatory molecules (CD28.ζ, CD137.ζ, CD28.CD137.ζ, CD28.CD134.ζ). IL13Ra2-CAR T cells were generated by retroviral transduction, and we determined their effector function in vitro, in co-culture and cytotoxicity assays, and in vivo, in the U373 brain xenograft model. RESULTS: Expression of all CARs in T cells was similar as judged by Western blot analysis. However, cell surface expression varied depending on used hinge and endodomain. In cytotoxicity assays, T cells expressing the different IL13Ra2-CARs only killed target cells expressing IL13Ra2, but not IL13Ra1 thus confirming the specificity of receptor-CAR interaction. While all IL13Ra2-CAR T cells secreted significant levels of IFNγ in co-culture assays with the IL13Ra2+ glioma cell line U373, only short hinge CAR T cells secreted significant amounts of IL2. T cells expressing IL13Ra2-CARs with a deleted endodomain (IL13Ra2.Δ-CAR) secreted no cytokines confirming that cytokine production depends on the presence of a functional IL 13Ra2-CAR. In vivo, injection of IL13Ra2.SH.CD28.ζ-CAR T cells into U373-bearing mice resulted in regression of gliomas as judged by bioluminescence imaging. IL13Ra2.LH.CD28.ζ- or IL13Ra2.Δ-CAR T cells had no antitumor effects. CONCLUSION: For the first time we have generated a CAR that only recognizes IL13Ra2 and not IL13Ra1. Comparison of several IL13Ra2-CARs revealed so far that a CAR with a SH and a CD28.ζ endodomain results in optimal T-cell activation as judged by IL2 production and in vivo anti-glioma activity. Our results warrant further active exploration of IL13Ra2-specific scFv-based CAR T cells for the adoptive immunotherapy of high grade glioma.
CEBOPP/VIML Followed by Radiotherapy for Intermediate- and Advanced-Stage Hodgkin’s Disease: A Long-Term Analysis.
Authors: M.R. Nowrousian, S. Ernst, C. Beling, U. Wiefelspuetz, P. Schuett, M. Poser, S. Mueller, P. Ebeling, A. Welt, M. Flasshove, T. Moritz, K.A. Metz, M. Stuschke, S. Seeber
Journal: Blood (2005)
NFκB-Mediated Up-Regulation of Transcription Factors Related to More Primitive State of Hematopoietic Progenitor Cells.
Authors: Rodrigo A. Panepucci, Lucila H.B. Oliveira, Dalila L. Zanette, Greice A. Molfetta, Rita C.V. Carrara, Amelia G. Araujo, Maristela Orellana, Dimas T. Covas, Marco A. Zago
Journal: Blood (2007)
Abstract 621: Serum circulating DNA and nucleosomes increase in response to neoadjuvant chemoradiation and surgical resection for pancreatic cancer
Authors: Ibtehaj A. Naqvi, Ruwan Gunaratne, David Pisetsky, Rebekah White
Journal: Cancer Research (2015)

Abstract Introduction: Pancreatic cancer (PC) is the deadliest of the major cancers, and response rates to standard therapies are low. Tumor cells release circulating extracellular DNA (exDNA) and nucleosomes (short segments of DNA in complex with histone proteins). These factors have been evaluated as markers of disease burden for prognosis and response to therapy. We hypothesized that exDNA and nucleosome (NUC) levels would correlate with each other and decrease in patients (pts) undergoing neoadjuvant chemoradiation (CRT) and surgical resection for localized PC. Methods: Blood was collected from pts with radiographically localized PC before and 4-6 weeks after CRT (N = 8), intraop and 1 week postop in pts with resectable tumors (N = 4), as well as from pts with advanced disease (N = 3) and normal volunteers (N = 6) to create a spectrum of data for disease burden. ExDNA and NUC were isolated from serum samples and quantified using a fluorescent DNA-specific stain (Picogreen) and ELISA, respectively. Results: Normal volunteers had the lowest exDNA/NUC levels while patients with advanced disease had the highest levels. Overall, exDNA/NUC levels increased ∼3-fold in patients who underwent CRT to levels similar to those of patients with advanced disease, regardless of whether they had radiographic partial response (N = 4), stable disease (N = 4), or progressive disease (N = 2) on restaging nor whether they were subsequently able to undergo resection. ExDNA and NUC levels correlated well except in pts who underwent resection, when exDNA but not NUC levels peaked intraop at &amp;gt;5-fold post-CRT levels. Both exDNA and NUC levels remained elevated at least one week postop. Discussion: Contrary to our hypothesis, exDNA and NUC levels increased following neoadjuvant CRT regardless of radiographic response to therapy. ExDNA and NUC levels correlated well except during the intraop period, when exDNA but not NUC levels were dramatically elevated. These data suggest that exDNA and NUC are not simply markers of disease burden. We postulate that exDNA and NUC are released by tumor cells and also by host immune cells in response to CRT and surgical trauma. In order to put this into a broader context, we are expanding our dataset to include more patients and time points. We are evaluating other specific forms of exDNA as well as DNA-associated proteins as markers of cell death that may be more useful for monitoring response to therapy. Citation Format: Ibtehaj A. Naqvi, Ruwan Gunaratne, David Pisetsky, Rebekah White. Serum circulating DNA and nucleosomes increase in response to neoadjuvant chemoradiation and surgical resection for pancreatic cancer. [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 621. doi:10.1158/1538-7445.AM2015-621
Qualitative and Quantitative PCR Monitoring of MRD: Practical Implications of a Surrogate Marker for GVL Effect after RIC Allogeneic Transplantation in Relapsed Chronic Lymphocytic Leukemia.
Authors: Lucia Farina, Cristiana Carniti, Anna Dodero, Antonio Vendramin, Anna Raganato, Francesca Patriarca, Franco Narni, Vittorio Montefusco, Fabio Benedetti, Attilio Olivieri, Paolo Corradini
Journal: Blood (2007)
Abstract 3183: Role of danger signals in tumor elicited inflammation
Authors: Ralph Francescone, Debora Vendramini-Costa, Oxana Dmitrieva, Vivi Hou, David Posocco, Sergei Grivennikov
Journal: Cancer Research (2015)

Abstract Spontaneous colon cancer (CRC) is traditionally thought to arise from a series of genetic mutations to key tumor suppressors and oncogenes that drive its progression. Recently, however, the importance of the immune system and inflammation in exacerbating CRC development has been demonstrated, as seemingly non-inflammatory tumors have massive infiltration of immune cells. This phenomenon has been deemed “Tumor elicited inflammation” (TEI), whereby the tumor cells recruit immune cells to the tumor, promoting tumor development. Danger Associated Molecular Patterns (DAMPs), proteins that are released during cellular stress or oncogenic transformation, promote a robust immune response and are often up-regulated in cancer. Thus, DAMPs may serve as an initial cue to induce TEI. The precise mechanisms of these so-called “danger signals” in CRC development and TEI have not been fully elucidated. Using a number of in vitro and in vivo models, we sought to uncover the major cellular producers of danger signals in the tumor microenvironment, how these danger signals recruit various immune cells to the tumor, and finally their effects on tumor progression. We found an up-regulation of three danger signals, S100A8, S100A9, and HMGB-1, in tumor tissue from mouse models of spontaneous CRC, at the RNA and protein levels. In addition, using FACS, the myeloid compartment of sorted immune cells demonstrated the highest expression levels of S100A8 and S100A9, as measured by qPCR. In order to further explore role of danger signals, lentiviral overexpression of S100A8, S100A9, and HMGB-1 was performed in MC38 colon cancer cells. Subsequently, these new cell lines were injected subcutaneously into C57BL/6 mice and tumor development was followed. S100A8 and S100A9 overexpressing tumors showed accelerated development and a greater influx of myeloid cells into the tumor when compared to GFP overexpressing control cells. Future work will focus on the crosstalk between cancer cells and immune cells, the key cellular pathways affected in cancer cells and immune cells, and finally if blockade of these signals has any therapeutic benefit in the treatment of CRC. Citation Format: Ralph Francescone, Debora Vendramini-Costa, Oxana Dmitrieva, Vivi Hou, David Posocco, Sergei Grivennikov. Role of danger signals in tumor elicited inflammation. [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 3183. doi:10.1158/1538-7445.AM2015-3183
ATPS-60COMPREHENSIVE IDENTIFICATION OF GLIOBLASTOMA MULTIFORME THERAPEUTIC TARGETS AND GROWTH SUPPRESSOR GENES USING GENE EDITING
Authors: Chad Toledo, Yu Ding, Pia Hoellerbauer, Ryan Davis, Ryan Basom, Emily Girard, Philip Corrin, Jeffery Delrow, Bruce Clurman, James Olson, Patrick Paddison
Journal: Neuro-Oncology (2015)

Glioblastoma multiforme (GBM) is the most aggressive and common form of brain cancer in adults and is currently incurable. To identify new therapeutic targets for GBM, we performed genome-wide CRISPR-Cas9 knockout (KO) screens in patient-derived GBM stem-like cells (GSCs) and human neural stem cells (NSCs), non-neoplastic tissue of origin controls. These screens revealed thousands of gene candidates acting to promote or limit expansion of GSCs and NSCs. In vitro and in vivo validation studies revealed several novel therapeutic targets, including the wee1-like kinase, PKMYT1/Myt1. Mechanistic studies revealed that PKMYT1 acts redundantly with WEE1 to facilitate mitosis in NSCs, but that this redundancy is lost in most GBM isolates and in NSCs harboring activated alleles of EGFR and AKT1. In addition to lethal genes, KOs promoting in vitro expansion of NSCs were also examined. For this category, we validated multiple genes, including: ARID1A, ARID1B, CREBBP, EP300, NF2, PDCD10, PTPN14, TAOK1, TGFBR2, and TP53, whose inhibition shortens NSC cell cycle transit times, causing dramatic growth advantages, and, in the case of CREBBP KO, dramatic deregulation of cell cycle gene expression and precocious S-phase entry. Taken together, these results demonstrate the use of CRISPR-Cas9 gene editing to identify novel cancer therapeutic targets and growth suppressor genes in human GBM isolates and NSCs. The results also inform precision medicine approaches for GBM, since most, if not all, candidate therapeutic targets could not be predicted from mutation, CNV, or gene expression analysis of the patient isolates alone.
Targeting PKCtheta Inhibits Alloreactivity and Graft-Versus-Host Disease While Preserving Graft-Versus-Leukemia and Anti-Infection Activities.
Authors: Xue-Zhong Yu, Javier Valenzuela, Cristina Iclozan, Mohammad Hossain, Emily Hopewell, Crystina Bronk, Junmei Wang, Esteban Celis, Robert Engelman, Edmund K. Waller, Bruce R. Blazar, Amer Beg
Journal: Blood (2009)
300. AAV Vector-Mediated In Vivo Reprogramming of Various Cell Types in Adult Mice
Authors: Elena Senís, Lluc Mosteiro, Stefan Wilkening, Manfred Schmidt, Manuel Serrano, Dirk Grimm
Journal: Molecular Therapy (2015)

The 2006/7 discovery that somatic cells of different tissue origins can be converted into induced pluripotent stem cells (iPSC) by mere introduction of a cocktail of "reprogramming" factors, such as Oct4, Klf4, Sox2 and c-Myc (OKSM), has revolutionized the field of regenerative medicine. A major part of this success story is due to the fact that delivery of the OKSM combination (or variants thereof) to cultured target cells can be accomplished using virtually any of the existing non-viral or viral gene transfer systems. Here, we specifically engineered Adeno-associated viral (AAV) vectors for OKSM delivery, based on their superior safety profile and their typical persistence as episomal DNA that is lost during cell division, which we considered beneficial for reprogramming. A third advantage is that AAV vectors can be pseudotyped with natural or synthetic viral capsids exhibiting high specificities and efficiencies in a given cell. Indeed, we reproducibly found that OKSM expression from four AAV vectors – each encoding a single factor under the strong and ubiquitous SFFV promoter, and pseudotyped with the potent chimeric AAV-DJ capsid – resulted in reprogramming of murine embryonic fibroblasts. Notably, the up to 0.2% reprogramming efficiency obtained with our AAV vectors is comparable to the best lentiviral system. Curiously, and defying our original prediction, we observed by PCR that the AAV vector DNA persisted in the reprogrammed cells even after extended cultivation for up to 21 passages. Using a combination of LAM-PCR and SureSelect technologies, we were then able to identify a variety of OKSM vector integration sites in the mouse genome, including a previously reported hot spot for AAV vector insertion. We speculate that the unusual high frequency of genomic AAV integration in iPSC is either related to mutational inactivation of genes that inhibit reprogramming, or merely a by-product of the relaxation of the chromatin structure triggered by OKSM expression. Based on the robust ex vivo efficiency, we next asked whether our OKSM vectors could also mediate reprogramming in vivo, and therefore applied different doses of AAV8-pseudotyped variants to adult mice via tail vein injection. Strikingly, four to eight weeks later, we found various small and large teratomas in their livers that we identified through histological analysis and isolation of residual iPSC. Moreover, by week eight, one mouse showed signs of extra-hepatic reprogramming in the pancreas and the thoracic cavity, congruent with the in vivo tropism of AAV serotype 8. These features make our novel AAV vector-mediated in vivo reprogramming strategy comparable to our previously published OKSM-transgenic mice (Nature 2013, 502:340-5), with the added benefits that AAV vectors can be applied in any mouse strain or other animals, and can be re-targeted to specific tissues, which opens up entirely novel avenues for stem cell research.
369. Therapeutic Effectiveness of AAV-Mediated Iduronidase Delivery to the CNS Following Intravenous Administration in a Murine Model of Mucopolysaccharidosis Type I
Authors: Lalitha Belur, Thuy An Tran, Kelly M. Pedersen, Maureen Riedl, Lucy Vulchanova, Karen Kozarsky, Walter C. Low, R. Scott McIvor
Journal: Molecular Therapy (2016)

Mucopolysaccharidosis type I (MPS I) is an inherited metabolic disease caused by deficiency of alpha-L-iduronidase (IDUA), resulting in accumulation of heparin and dermatan sulfate glycosaminoglycans (GAGs). Individuals with the most severe form of the disease (Hurler syndrome) suffer from neurodegeneration, mental retardation, and death by age 10. Current treatments for this disease include allogeneic hematopoietic stem cell transplantation (HSCT) and enzyme replacement therapy (ERT). However, these treatments are insufficiently effective in addressing CNS manifestations of the disease. Our goal is to improve therapy for severe MPS I by supplementing current ERT and HSCT with IDUA gene transfer to the CNS, thereby preventing neurological manifestations of the disease. In this study we tested the ability of intravenously administered AAV serotypes 9 and rh10 (AAV9 and AAVrh10) to cross the blood brain barrier for delivery and expression of the IDUA gene in the CNS. 4-5 month old adult MPS I animals were infused intravenously via the tail vein with either an AAV9 or AAVrh10 vector encoding the human IDUA gene. Blood and urine samples were collected on a weekly basis until the animals were sacrificed at 10 weeks post-injection. Plasma IDUA activities in treated animals were close to 1000-fold higher than that of heterozygote controls at 3 weeks post-injection. Brains, spinal cords, and peripheral organs were analyzed for IDUA activity, clearance of GAG accumulation, and IDUA immunofluorescence of tissue sections. Treated animals demonstrated widespread restoration of IDUA enzyme activity in all organs including the CNS. High levels of IDUA enzyme activity were observed in the brain and spinal cord, which ranged from 40 to 300-fold higher than heterozygote controls, while levels in peripheral organs were also high, ranging from 100 to 1000-fold higher than control animals. Levels of urinary and tissue GAGs were significantly reduced starting at 3 weeks after vector infusion, with restoration of normal GAG levels by the end of the study. These data demonstrate the non-invasive effectiveness of systemic intravenous AAV9 and AAVrh10 vector infusion in counteracting CNS manifestations of MPS I.
Abstract 4897: Accurate variant detection using molecular barcodes
Authors: Charmian Cher, Henrik Johansson, Javelin Chi, Katie Zobeck, Linus Forsmark, Magnus Isaksson, Holly Hogrefe
Journal: Cancer Research (2015)

Abstract HaloPlex is an amplicon based method for targeted sequencing. The protocol utilizes specificity gained from restriction enzyme recognition, hybridization and DNA ligation to capture molecules originating from the target region to be sequenced. The target region is fully customizable from a single gene up to several thousand discrete regions. Amplicon based methods for multiplex target enrichment are, in general, convenient methods for capturing a wide range of target region sizes. However, in contrast to hybridization capture methods where random shearing is deployed, it is not possible for Haloplex or other amplicon based techniques to use the start point of paired end reads to identify duplicate reads. Duplicate read information can be useful for improving base calling accuracy and to monitor sampling to determine the degree of confidence to assign calls at different presumed allelic fractions. For somatic variants, which are generally present at a lower than 50% allelic fraction, it is even more advantageous to know how many molecules have been sampled when calling a particular base. To enable identification of duplicate reads from libraries prepared with Haloplex, we have added a molecular barcode to the introduced primer cassette. The molecular barcode consists of ten degenerate bases allowing for over one million unique sequences to be present for tagging of molecules. Using information derived from the molecular barcode sequences we demonstrate observation of variants down to 5% allelic fraction in multiple molecules tagged with different molecular barcodes. The new protocol has, besides the introduction of molecular barcodes, been optimized in a few additional aspects. Due to improved reagent formulations and streamlining of workflow, complete target enrichment can now be completed in less than 5 hours. Using 50 ng input we demonstrate &amp;gt;85% specificity and above 90% of target regions being covered at &amp;gt;10% of average depth. Citation Format: Charmian Cher, Henrik Johansson, Javelin Chi, Katie Zobeck, Linus Forsmark, Magnus Isaksson, Holly Hogrefe. Accurate variant detection using molecular barcodes. [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 4897. doi:10.1158/1538-7445.AM2015-4897
The Poor Prognosis Value of High Intra-Tumoral Macrophages Counts in Follicular Lymphoma Patients Requires Selection of Appropriate Cut-Off and Can Be Circumvented by Rituximab Therapy.
Authors: Danielle Canioni, Gilles Salles, Nicolas Mounier, Nicole Brousse, Marie Keuppens, Frank Morchauser, Marion Fournier, Thierry Lamy, Marie-Christine Rousselet, Charles Foussard, Luc Xerri
Journal: Blood (2006)
Route of Delivery Modulates the Efficacy of Mesenchymal Stem Cell Therapy for Myocardial Infarction
Authors: Anthony J. Kanelidis, Courtney Premer, Juan Lopez, Wayne Balkan, Joshua M. Hare
Journal: Circulation Research (2016)

Accumulating data support a therapeutic role for mesenchymal stem cell (MSC) therapy; however, there is no consensus on the optimal route of delivery.We tested the hypothesis that the route of MSC delivery influences the reduction in infarct size and improvement in left ventricular ejection fraction (LVEF).We performed a meta-analysis investigating the effect of MSC therapy in acute myocardial infarction (AMI) and chronic ischemic cardiomyopathy preclinical studies (58 studies; n=1165 mouse, rat, swine) which revealed a reduction in infarct size and improvement of LVEF in all animal models. Route of delivery was analyzed in AMI swine studies and clinical trials (6 clinical trials; n=334 patients). In AMI swine studies, transendocardial stem cell injection reduced infarct size (n=49, 9.4% reduction; 95% confidence interval, -15.9 to -3.0), whereas direct intramyocardial injection, intravenous infusion, and intracoronary infusion indicated no improvement. Similarly, transendocardial stem cell injection improved LVEF (n=65, 9.1% increase; 95% confidence interval, 3.7 to 14.5), as did direct intramyocardial injection and intravenous infusion, whereas intracoronary infusion demonstrated no improvement. In humans, changes of LVEF paralleled these results, with transendocardial stem cell injection improving LVEF (n=46, 7.0% increase; 95% confidence interval, 2.7 to 11.3), as did intravenous infusion, but again intracoronary infusion demonstrating no improvement.MSC therapy improves cardiac function in animal models of both AMI and chronic ischemic cardiomyopathy. The route of delivery seems to play a role in modulating the efficacy of MSC therapy in AMI swine studies and clinical trials, suggesting the superiority of transendocardial stem cell injection because of its reduction in infarct size and improvement of LVEF, which has important implications for the design of future studies.
iCAGES: integrated CAncer GEnome Score for comprehensively prioritizing driver genes in personal cancer genomes
Authors: Chengliang Dong, Yunfei Guo, Hui Yang, Zeyu He, Xiaoming Liu, Kai Wang
Journal: Genome Medicine (2016)

Cancer results from the acquisition of somatic driver mutations. Several computational tools can predict driver genes from population-scale genomic data, but tools for analyzing personal cancer genomes are underdeveloped. Here we developed iCAGES, a novel statistical framework that infers driver variants by integrating contributions from coding, non-coding, and structural variants, identifies driver genes by combining genomic information and prior biological knowledge, then generates prioritized drug treatment. Analysis on The Cancer Genome Atlas (TCGA) data showed that iCAGES predicts whether patients respond to drug treatment (P = 0.006 by Fisher’s exact test) and long-term survival (P = 0.003 from Cox regression). iCAGES is available at http://icages.wglab.org .