tbuckley/cabot-search huggingface dataset:
502. Optimization of Intrathecal Delivery of AAV for Targeting the Spinal Compartment
Authors: Adrian P. Kells, Martin Goulet, Justin Aubin, Shipeng Yuan, David Dismuke, Randall P. Reed, Qin Su, Guangping Gao, Dinah W.Y. Sah, Gregory R. Stewart
Journal: Molecular Therapy (2015)

Adeno-associated viral (AAV) vectors are a platform of great potential for therapeutic gene delivery. One of the major challenges regarding AAV gene therapy is to deliver the transgene of interest to target cells at levels that result in expression that is both safe and effective. For diseases of the central nervous system (CNS) such as amyotrophic lateral sclerosis (ALS) and Friedreich's ataxia, it is important to identify a dosing paradigm that provides a relatively homogenous distribution of gene transfer along the rostral-caudal axis of the spinal column in the CNS and is translatable. Intrathecal (IT) administration is a delivery approach that has shown promise for providing such distribution. AAV dosing via the IT route has been reported in large mammals to provide greater CNS distribution, less exposure to peripheral organs and tissues, and reduced impact of immune responses than systemic dosing. However, to-date, IT dosing of AAV in large mammals has been investigated primarily by lumbar bolus administration, with a few studies assessing administration at more rostral sites either alone or in combination with a lumbar site. Parameters that are likely to have a major impact on CNS distribution such as volume, rate and duration of infusion have not been reported previously for IT dosing of AAV. Here, we studied the effects of these parameters as well as site of infusion on distribution of transgene expression in the non-human primate CNS, using AAVrh10 to package a vector genome (vg) containing the human frataxin gene driven by the chicken β-actin promoter. Four weeks after dosing, frataxin (FXN) expression was assessed in spinal cord and dorsal root ganglia (DRG) at multiple rostral-caudal levels, as well as in brain, cerebellum, and peripheral organs such as liver, spleen and heart. Quantitative assessments included measurements of vector genome copy number and mRNA and protein expression levels. Our results showed that the distribution of transgene expression in the spinal cord, DRG, cerebellum and brain were significantly impacted by the site(s) of IT delivery (i.e. cervical vs lumbar), and volume, rate and duration of infusion. As expected, there was transduction of peripheral organs, indicating systemic exposure of the AAV vector following IT delivery. In addition, FXN expression across different cell types is being studied by histological methods. These results will not only guide the optimization of IT delivery of AAV gene therapy for diseases such as ALS and Friedreich's ataxia, but also provide useful information for IT dosing for other CNS disorders.
Genetics of ramucirumab-associated hypertension in the ROSE/TRIO-012 breast cancer trial.
Authors: John Robert Mackey, Oleg N. Lipatov, Miguel Martin, Marc Webster, Roberto Hegg, Sunil Verma, Manuel Ramos Vazquez, Rodrigo Fresco, Francois Thireau, Vincent Houé, Michael F. Press, Ashok Narasimhan, Sambasivarao Damaraju
Journal: Journal of Clinical Oncology (2015)

547 Background: TRIO-012 is a double-blinded multinational phase III trial that randomized 1,144 patients with advanced breast cancer to receive first-line docetaxel in combination with ramucirumab (anti-VEGFR2) or placebo. We investigated the association of genotype (single nucleotide polymorphisms, SNPs) with the phenotype (hypertension, HT as a treatment-emergent adverse event) to seek genetic predispositions to ramucirumab toxicity. Methods: In this study, 220 SNPs were selected from literature related to anti-angiogenic pathways, drug metabolism/transport, immune regulation, and hypertension. SNPs were genotyped using germline DNA on the platforms, Sequenom iPLEX Gold and Pyrosequencing. Genotype data was filtered for deviations from Hardy Weinberg Equilibrium and minor allele frequency of > 0.05. Study subjects provided ethics-committee approved prospective consent for this genetic study. 257 Caucasian subjects were analysed here from the docetaxel-ramucirumab arm. Toxicity grades 0-1 (n = 208 controls; low toxicity) vs. grade > 2 (n = 49 cases, high toxicity) were tested for genetic associations. Dominant genotypic model was assumed; Chi-square test with 10000 permutations were employed (Golden Helix-SVS v8.3) and p < 0.05 considered statistically significant. Results: VEGF-R2 (rs17709898) conferred protection (OR 0.51 [0.26-0.96]) and rs7691507 conferred risk (OR 2.01 [1.07-3.77]). Polymorphism in ABCB1 (MDR1), rs2235067 conferred risk (OR 2.37[1.21-4.64]). SNPs (rs9508033, rs722503 and rs3794405) in VEGF-R1 and NR1I3 (rs2307418 and rs5085) showed association (risk and protection, respectively). Conclusions: The association of VEGF- R2 rs17709898 with HT is consistent with the known mechanism of ramucirumab VEGF-R2–directed antibody. rs17709898 is in linkage disequilibrium with rs1870377, a variant previously shown to be associated with HT. Similarly, the association of VEGF-R1 with HT suggests compensatory pathways may have a role in anti-angiogenic toxicity. None of the polymorphisms in the VEGF ligand (21tagSNPs) were associated with hypertension. Confirmation of these findings in ongoing ramucirumab studies may permit risk stratification of ramucirumab therapy.
Abstract LB-204: Reprogramming inflammatory monocytes to mediate anti-tumor activity in pancreatic carcinoma
Authors: Kristen B. Long, Whitney L. Gladney, Graham M. Tooker, Gregory L. Beatty
Journal: Cancer Research (2015)

Abstract In cancer, increased mobilization of inflammatory monocytes from the bone marrow into the peripheral blood correlates inversely with patient survival. Peripheral blood inflammatory monocytes, which express CCR2, are recruited to tumor tissue by the chemokine CCL2 where they then differentiate into macrophages and support tumor development, growth, and metastasis. While neutralization of CCL2 can block inflammatory monocyte recruitment and inhibit metastasis, this approach has recently been shown to be at risk for lethal outcomes if therapy is interrupted. An alternative approach to inhibiting inflammatory monocyte recruitment to tumors is to reprogram monocytes with anti-tumor activity. Using the KrasG12D/+; Trp53R172H/+; Pdx-1 Cre (KPC) genetically engineered mouse model of pancreatic ductal adenocarcinoma (PDAC), we report that systemic immune activation induced with an agonist CD40 monoclonal antibody can redirect Gr-1+ inflammatory monocytes to infiltrate the tumor microenvironment and degrade tumor-associated fibrosis leading to tumor regression. Extra-tumoral macrophages were found to be necessary for mobilization of inflammatory monocytes from the bone marrow into the peripheral blood. In addition, systemic IFN-γ released in response to anti-CD40 therapy was necessary for reprogramming inflammatory monocytes with anti-tumor activity. Inflammatory monocytes responding to IFN-γ displayed a distinct matrix metalloproteinase gene expression profile necessary for selective degradation of extracellular matrix proteins, including type I collagen and fibronectin, which define fibrosis in PDAC. Therefore, although inflammatory monocytes are commonly associated with pro-tumor activity, our findings demonstrate that they can also be reprogrammed with potent anti-tumor properties. Citation Format: Kristen B. Long, Whitney L. Gladney, Graham M. Tooker, Gregory L. Beatty. Reprogramming inflammatory monocytes to mediate anti-tumor activity in pancreatic 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-204. doi:10.1158/1538-7445.AM2015-LB-204
Clinical Use of Programmed Cell Death-1 and Its Ligand Expression as Discriminatory and Predictive Markers in Ovarian Cancer
Authors: Jayanta Chatterjee, Wei Dai, Nor Haslinda Abd Aziz, Pei Yun Teo, John Wahba, David L. Phelps, Christian J. Maine, Lynsey M. Whilding, Roberto Dina, Giorgia Trevisan, Kirsty J. Flower, Andrew J.T. George, Sadaf Ghaem-Maghami
Journal: Clinical Cancer Research (2016)

Abstract Purpose: We aimed to establish whether programmed cell death-1 (PD-1) and programmed cell death ligand 1 (PD-L1) expression, in ovarian cancer tumor tissue and blood, could be used as biomarkers for discrimination of tumor histology and prognosis of ovarian cancer. Experimental Design: Immune cells were separated from blood, ascites, and tumor tissue obtained from women with suspected ovarian cancer and studied for the differential expression of possible immune biomarkers using flow cytometry. PD-L1 expression on tumor-associated inflammatory cells was assessed by immunohistochemistry and tissue microarray. Plasma soluble PD-L1 was measured using sandwich ELISA. The relationships among immune markers were explored using hierarchical cluster analyses. Results: Biomarkers from the discovery cohort that associated with PD-L1+ cells were found. PD-L1+ CD14+ cells and PD-L1+ CD11c+ cells in the monocyte gate showed a distinct expression pattern when comparing benign tumors and epithelial ovarian cancers (EOCs)—confirmed in the validation cohort. Receiver operating characteristic curves showed PD-L1+ and PD-L1+ CD14+ cells in the monocyte gate performed better than the well-established tumor marker CA-125 alone. Plasma soluble PD-L1 was elevated in patients with EOC compared with healthy women and patients with benign ovarian tumors. Low total PD-1+ expression on lymphocytes was associated with improved survival. Conclusions: Differential expression of immunological markers relating to the PD-1/PD-L1 pathway in blood can be used as potential diagnostic and prognostic markers in EOC. These data have implications for the development and trial of anti–PD-1/PD-L1 therapy in ovarian cancer. Clin Cancer Res; 23(13); 3453–60. ©2016 AACR.
ヨーロッパ心臓リズム協会(EHRA)スコアに従った心房細動の日本人患者の分布と背景の差異
Authors: Saga Akiko, Suzuki Shinya, Otsuka Takayuki, Sagara Koichi, Matsuno Shunsuke, Funada Ryuichi, Uejima Tokuhisa, Oikawa Yuji, Yajima Junji, Koike Akira, Nagashima Kazuyuki, Kirigaya Hajime, Sawada Hitoshi, Aizawa Tadanori, Yamashita Takeshi
Journal: Circulation (2012)
Epstein-Barr virus associated breast cancer as a marker of biological aggressiveness.
Authors: C. Mazouni, F. Fina, S. Romain, L. Ouafik, P. Bonnier, P. Martin
Journal: Journal of Clinical Oncology (2011)

e21028 Background: While a potential role of the Epstein-Barr virus (EBV) in the pathogenesis of breast cancer (BC) has been underlined results remain conflicting. Particularly, the impact of EBV infection on biological markers of BC has received little investigation. Methods: In this study, we established the frequency of EBV-infected BC using real-time quantitative PCR (RT-PCR) in 196 BC specimens. Biological and pathological characteristics according to EBV status were evaluated. Results: EBV DNA was present in 65 of the 196 (33.2%) studied cases. EBV positive BCs tended to be tumours with a more aggressive phenotype, more frequently oestrogen receptor negative (p=0.05), and with high histological grade (p=0.01). Overexpression of thymidine kinase activity was higher in EBV-infected BC (p=0.007). The presence of EBV was weakly associated with HER2 gene amplification (p=0.08). Conclusions: Our study provides evidence for EBV-associated BC undergoing distinct carcinogenic processes, with more aggressive features.
Preliminary Results of a Prospective Randomized Study Comparing First Line Conventional Therapy Versus High Dose Therapy with Autologous CD34+ Purified Progenitor Cell Support in B CLL Patients with B and C Binet Stages: The GOELAMS LLC98 Study.
Authors: Annie Brion, Beatrice Mahe, Brigitte Kolb, Bernard Audhuy, Philippe Colombat, Herve Maisoneuve, Charles Foussard, Alain Bureau, Pierre Feugier
Journal: Blood (2005)
Abstract 3036: The SUMO-targeted ubiquitin ligase RNF4 regulates BLM helicase's function in dormant origin firing
Authors: Nathan A. Ellis, Wei-Chih Yang, Mary Yagle, Jianmei Zhu, Jing Huang, Michael Seidman, Michael J. Matunis
Journal: Cancer Research (2015)

Abstract Regulation of dormant origin firing under conditions of replication stress is poorly understood. The Bloom syndrome DNA helicase BLM functions in maintaining replication fork stability, with sumoylation regulating this function, and BLM deficiency is associated with increased dormant origin firing. We found here that BLM sumoylation levels increase in response to replication stalling by hydroxyurea (HU) and to proteasome inhibition; depletion of the SUMO-targeted ubiquitin ligase RNF4 also causes increased levels of BLM sumoylation. RNF4 directly interacts with BLM and can ubiquitylate sumoylated BLM in vitro. These data indicate that sumoylated BLM is an RNF4 substrate. RNF4 is recruited to DNA repair foci in response to replication stalling. RNF4 depletion causes the accumulation of increased numbers of HU-induced BLM foci, whereas the numbers of RPA, RAD51, and gamma-H2AX foci are unaffected by fork stalling in RNF4-depleted cells. Sister chromatid exchanges are normal in RNF4-depleted cells. These data indicate that RNF4 can regulate BLM retention at stalled forks without affecting repair by homologous recombination. RNF4 depletion reduces cell proliferation and survival of untreated cells, and it confers hypersensitivity to replication stalling by HU. Studies of cell-cycle progression using bromodeoxyuridine incorporation and flow cytometry show that RNF4 depletion causes a delay of re-entry into S phase in HU-treated cells and the replication delay is partially rescued by BLM mutation. The delay is not caused by modification of checkpoint kinase activities. Analysis of replication dynamics using the DNA fiber assay show that RNF4 depletion causes an increase of permanently stalled replication forks and a decrease in activation of dormant origins following recovery from HU-induced replication stress. Co-depletion of RNF4 and BLM partially rescues these defects. Replication dynamics is unaffected by RNF4 depletion in untreated cells. These data indicate that RNF4 regulates BLM's functions in replication fork stability and dormant origin firing, without affecting BLM's roles in homologous recombination. We propose that sumoylation of BLM at stalled replication forks leads to RNF4-mediated ubiquitylation and subsequent proteasome-dependent degradation of BLM, which relieves BLM's active inhibition of dormant origin firing. Citation Format: Nathan A. Ellis, Wei-Chih Yang, Mary Yagle, Jianmei Zhu, Jing Huang, Michael Seidman, Michael J. Matunis. The SUMO-targeted ubiquitin ligase RNF4 regulates BLM helicase's function in dormant origin firing. [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 3036. doi:10.1158/1538-7445.AM2015-3036
Impaired Response to Influenza Vaccination in AML Patients Post-Chemotherapy Associated with a Highly Atypical B-Cell Profile
Authors: Meghali Goswami, Gabrielle T. Prince, Angelique Biancotto, Susan Moir, Foo Cheung, Yuri Kotliarov, Kimberly Dunham, Jinguo Chen, Rongye Shi, Huizhi Zhou, Hana Golding, Jingrong Tang, John S. Tsang, Howard B. Dickler, Kimberly Noonan, B. Douglas Smith, Ivan M. Borrello, Christopher S. Hourigan
Journal: Blood (2015)
Tryptophan Catabolism Is Associated with the Prognosis of Patients with De Novo Acute Myeloid Leukemia,
Authors: Hisashi Tsurumi, Nobuhiro Kanemura, Kenji Fukuno, Junji Nagano, Kengo Ogawa, Soranobu Ninomiya, Naoe Goto, Senji Kasahara, Takeshi Hara, Hisataka Moriwaki
Journal: Blood (2011)
643. Various Forms of CD40L Encoded as an Immune Plasmid Adjuvant Generate Unique Anti-Cancer DNA Vaccine Induced Responses
Authors: Megan Wise, Daniel Villarreal, Lumena Louis, Jian Yan, Matthew Morrow, Niranjan Sardesai, David Weiner
Journal: Molecular Therapy (2016)

The use of immune plasmid adjuvants encoding cytokine, chemokine or immune modulators to tailor the vaccine induced response is a strength of DNA vaccine approaches. This has been established through the recent HVTN080 trial which demonstrated the potency of pIL-12 in increasing cellular responses above that of DNA only vaccination. Due to its role in both innate and adaptive immunity, the co-delivery of plasmid encoded CD40 ligand (CD40L) could increase DNA vaccine responses. In its natural form, CD40L can occur as either a surface bound form or a cleaved/solubilized form. Thus, we sought to determine if different forms of pCD40L can influence cellular and humoral responses when co-delivered with a HPV16 DNA vaccine expressing the oncogenic proteins E6 and E7. Mice were immunized with HPV DNA with or without synthetic optimized plasmids expressing various forms of CD40L. Mice which received the soluble form of CD40L (sCD40L) exhibited significantly higher antigen specific CD8+ T cell responses including IFN-γ, IL-2 and TNF-α expression. These responses were maintained into memory. On the other hand, the surface bound as well as the wild type form blunted the vaccine induced responses compared to vaccine alone. Time course analysis revealed that 11 days after primary immunization, CD8+ tetramer specific (H-2Db HPV16 E7 (RAHYNIVTF)) T cells in mice immunized with sCD40L averaged around 18% compared to vaccine alone at 4%. These responses were partially dependent on CD4+ T cell help. Upon therapeutic tumor challenge, mice immunized with sCD40L displayed significant tumor regression compared to vaccine alone or naïve animals. We have also seen similar vaccine induced immune responses when sCD40L was combined with an HIV Envelope expressing DNA vaccine as well as an H1N1 flu DNA vaccine. These results demonstrate the power of using an immune plasmid adjuvant encoding a synthetic optimized sCD40L in a DNA vaccine. Additional studies in other models are important for this approach to be considered for possible clinical development.
Abstract 3787: EphrinB1 is a novel microtubule associated protein whose expression may predict sensitivity to taxane
Authors: Paola D. Vermeer, Paul L. Colbert, Daniel W. Vermeer, Bryant G. Wieking, John H. Lee
Journal: Cancer Research (2015)

Abstract Mitosis is a complex sequence of highly regulated events that ensures the proper segregation of sister chromatids into daughter cells. At the heart of the mitotic machinery lie the microtubules. Microtubules (MTs) are components of the cytoskeleton made up of polymerized alpha and beta tubulin dimers. MT structure and function must be maintained throughout the cell cycle to ensure proper execution of mitosis and cellular homeostasis. It has previously been reported that the protein tyrosine phosphatase, PTPN13, localizes at centrosomes from interphase, through metaphase and dramatically shifts to the spindle midzone during anaphase. During telophase, PTPN13 accumulates at the midzone, becoming concentrated at the center of the midbody during cytokinesis. We have previously demonstrated that the HPV16 E6 oncoprotein binds PTPN13 and leads to its degradation. Given PTPN13's localization to distinct compartments during mitosis/cytokinesis, we speculated that HPV infection may affect the process of mitosis. In addition, the newly appreciated roles of the PTPN13 phosphatase substrate, EphrinB1, in oncogenesis, further prompted us to define its role in mitosis. Here we report that EphrinB1 co-localizes with MTs during all phases of the cell cycle. Specifically, unphosphorylated EphrinB1 directly binds tubulin, while its phosphorylated form lacks MT binding. These characteristics are hallmarks of microtubule associated proteins (MAPs) and suggest that EphrinB1 is a novel MAP. Importantly, we demonstrate that expression of PTPN13 correlates with sensitivity to taxanes while its absence may confer resistance. In addition, we show that EphrinB1 expression affects taxane response in vitro and in vivo. We speculate that this reflects PTPN13's modulation of EphrinB1 phosphorylation and suggest that EphrinB1 is an important contributor to taxane sensitivity/resistance phenotypes in epithelial cancers. HPV infection or functional mutations of PTPN13 in non-viral cancers may predict taxane sensitivity. Note: This abstract was not presented at the meeting. Citation Format: Paola D. Vermeer, Paul L. Colbert, Daniel W. Vermeer, Bryant G. Wieking, John H. Lee. EphrinB1 is a novel microtubule associated protein whose expression may predict sensitivity to taxane. [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 3787. doi:10.1158/1538-7445.AM2015-3787
89. In Silico Reconstruction of AAV Evolutionary Intermediates To Identify Genetic Determinants of Capsid Function
Authors: Eric M. Zinn, Vadim Khaychuk, Heikki Turunen, Luk H. Vandenberghe
Journal: Molecular Therapy (2015)

Study of naturally occurring isolates of adeno-associated virus has revealed a wide range of phenotypes across several viral characteristics relevant to gene therapy. These fundamental differences in viral properties such as receptor binding, particle assembly, and capsid stability are believed to influence vector properties such as tissue tropism and the efficiency of gene transfer. Although well described, many of these properties of AAV capsids have proven difficult to modulate with traditional biochemical and molecular techniques, such as domain swapping. Epistatic interactions between seemingly disparate mutations along the evolutionary lineage of AAV may be a contributing factor to these difficulties. The goal of our project is to leverage the evolutionary history of AAV towards the end of engineering viral capsids modulated in these viral properties, and in doing so, elucidating novel genetic determinants of capsid function. In this project, our group performed an in-silico, maximum likelihood reconstruction of several putative evolutionary intermediates of AAV. We have predicted, synthesized, and have begun to characterize nine such capsids in vitro, and in vivo. These capsids constitute structurally distinct and phenotypically novel vectors, differing between 1% and 9% in terms of amino acid identity from previously described vectors, and remain capable of gene transfer. The putative evolutionary intermediates demonstrate log-fold differences in particle assembly, producing between 3% and 183% of AAV8 production levels. Moreover, the newly designed and synthesized capsids transduce cells at levels 25% to 851% of AAV8 levels measured through titer-controlled in vitro infectivity experiments. Towards the end of compensating for the uncertainty inherent to our probabilistic methods, we describe a technique for rapidly introducing targeted mutations into an AAV capsid gene, thereby creating well-defined libraries of capsids. Our studies provide novel vector reagents for gene transfer, and are expected to lead to mechanistic and structural insights into AAV biology of transduction and host interaction.