tbuckley/cabot-search huggingface dataset:
225. Preserving CD4+ T-Cells Phenotype and Function Upon Ex Vivo Lentiviral Transduction
Authors: Isabelle Hmitou, Amani Ouedrani, Lounes Djerroudi, Cécile Roudaut, Laure Caccavelli, Tayebeh S. Soheili, Isabelle André-Schmutz, Marina Cavazzana, Fabien Touzot
Journal: Molecular Therapy (2016)

Ex vivo gene modification of T-cell is an appealing strategy for the treatment of both immunodeficiencies and neoplasia. Cell activation remains an essential prerequisite to genetic modification by lentiviral transduction. However, most current protocols for T-cell activation alter significantly the phenotype of transduced cells. This phenotypic change can constitute a drawback when the gene modification aims to correct a gene defect while preserving the T cell-subsets diversity. As we plan to conduct an open label phase I/II gene therapy trial for HIV-1 infected patients presenting with lymphoma where the patients will receive autologous hematopoietic stem cells transplantation with gene modified CD34+ cells and CD4+ T-cells, we investigate the use of the TransAct™ reagent (a CD3/CD28 nanoscale activator reagent from Miltenyi Biotec, Bergisch Gladbach, Germany) for the clinical grade transduction of CD4+ T-cells with the LVsh5/C46 lentiviral vector (Cal-1, Calimmune, Inc. Tucson, USA). LVsh5/C46 is a SIN lentiviral vector that inhibits two crucial steps of CD4+ T cell infection by the HIV virus: (i) attachment of the virus to its target by downregulation of CCR5 via a short hairpin RNA, (ii) fusion of the virus to the target cell through expression of the C46 inhibitor. Compared to previously published T-cells transduction protocols, the use of Miltenyi TransAct™ permits an efficient transduction - evaluated by measurement of vector copy number through quantitative PCR - without major phenotypic modification. Indeed, after activation with the TransAct™ reagent, ex vivo transduced CD4+ T-cells display very few changes in their surface markers with conservation of naïve (CCR7+CD62L+CD45RA+), central memory (CCR7+CD62L+CD45RA-) and effector memory (CCR7-CD62L-CD45RA-) subsets in superimposable proportions as initially. Moreover, expression of CD25 remains below 50% of cells suggesting a more "gentle " activation of the transduced CD4+ T-cells. Phenotypic analysis of transduced cells show no overt modification of cell subsets containing TH1, TH2 and TH17 memory T-cells. Furthermore, transduced T-cells retained the ability to be primed towards the TH1, TH2 and TH17 pathways. Cell sorting of ex vivo modified cells demonstrate a preferential transduction of naïve CD31+CCR7+CD62L+CD45RA+ T-cells as compared to other subsets. Besides, we did not find any significant impact of the transduction process on the TCRβ repertoire diversity as evaluated by high-throughput sequencing and analysis of diversity through the Gini-Simpson index or the Shannon index. This optimized protocol could be of valuable use for clinical trials aiming to provide the patient with diversified gene-corrected T-cells.
Phase-Locked Inhibition, but Not Excitation, Underlies Hippocampal Ripple Oscillations in Awake Mice In Vivo
Authors: Jian Gan, Shih-ming Weng, Alejandro J. Pernía-Andrade, Jozsef Csicsvari, Peter Jonas
Journal: Neuron (2016)

Sharp wave-ripple (SWR) oscillations play a key role in memory consolidation during non-rapid eye movement sleep, immobility, and consummatory behavior. However, whether temporally modulated synaptic excitation or inhibition underlies the ripples is controversial. To address this question, we performed simultaneous recordings of excitatory and inhibitory postsynaptic currents (EPSCs and IPSCs) and local field potentials (LFPs) in the CA1 region of awake mice in vivo. During SWRs, inhibition dominated over excitation, with a peak conductance ratio of 4.1 ± 0.5. Furthermore, the amplitude of SWR-associated IPSCs was positively correlated with SWR magnitude, whereas that of EPSCs was not. Finally, phase analysis indicated that IPSCs were phase-locked to individual ripple cycles, whereas EPSCs were uniformly distributed in phase space. Optogenetic inhibition indicated that PV+ interneurons provided a major contribution to SWR-associated IPSCs. Thus, phasic inhibition, but not excitation, shapes SWR oscillations in the hippocampal CA1 region in vivo.
Efficacy and Safety Profile of Long Term Exposure to Lenalidomide in Relapsed Multiple Myeloma.
Authors: Guillemette Fouquet, Stéphanie Tardy, Helene Demarquette, Sarah Bonnet, Julie Gay, Houria Debarri, Charles Herbaux, Jessica Michel, Aurore Perrot, Caroline Serrier, Suzanne K. Robinson, Darko Miljkovic, Pascale Morel, Catherine Boccacio, Herve AvetLoiseau, Thierry Facon, Cyrille Hulin, Xavier Leleu
Journal: Blood (2012)
Abstract AS05: Metabolomic signatures in sera from early stage ovarian cancer patients
Authors: David A. Gaul, Christina M. Jones, Maria Eugenia Monge, Long Q. Tran, Martin M. Matzuk, John F. McDonald, Facundo M. Fernandez
Journal: Clinical Cancer Research (2015)

Abstract PURPOSE: Lack of symptoms as well as the deficiency of highly specific biomarkers has resulted in only a quarter of ovarian cancer cases being diagnosed in stage I. Early detection combined with conventional therapies has resulted in 5-year survival rates up to 90%, while 5-year overall survival is less than 30% for women with advanced stage ovarian cancer. An effective screening strategy for early diagnosis would be particularly advantageous for ovarian cancer patients. Investigation into characteristic metabolomic patterns for disease has the potential to detect changes in cells, tissues, and biofluids that can aid in diagnosis at an early stage. METHODS: Serum samples were collected from early-stage serous papillary or endometrioid ovarian cancer (n=26) and normal patients (n=40) and analyzed using ultra high performance liquid chromatography coupled with high resolution mass spectrometry (UPLC-MS) and tandem mass spectrometry (MS/MS). Metabolites were extracted from blood serum by precipitating proteins with methanol, lyophilization, and solvent reconstitution prior to MS analysis in both positive and negative electrospray ionization modes. Metabolic features were extracted with MZmine software. Untargeted multivariate statistical analysis employing support vector machine (SVM) learning methods, genetic algorithms and recursive feature elimination (RFE) selected a panel of metabolites that differentiates between the age-matched samples with better than 92% sensitivity and 91% specificity in all cases tested. RESULTS: Comparison of metabolic phenotypes of ovarian cancer with normal metabolic signatures revealed unique metabolite patterns for ovarian cancer. From multivariate statistical analysis, panels consisting of 17-35 metabolic features from serum samples were found to differentiate between early stage cancer and normal with very high accuracy, sensitivity, and specificity. CONCLUSIONS: Poor early diagnosis complicates collection of large patient cohorts for more detailed studies. Our preliminary work demonstrated that metabolites in serum samples may be useful for detecting early-stage ovarian cancer and support conducting larger, more focused studies. (Grant support: Marsha Rivkin Ovarian Cancer Challenge Grant; Ovarian Cancer Research Fund (OCRF)) Citation Format: David A. Gaul, Christina M. Jones, Maria Eugenia Monge, Long Q. Tran, Martin M. Matzuk, John F. McDonald*, Facundo M. Fernandez*. Metabolomic signatures in sera from early stage ovarian cancer patients [abstract]. In: Proceedings of the 10th Biennial Ovarian Cancer Research Symposium; Sep 8-9, 2014; Seattle, WA. Philadelphia (PA): AACR; Clin Cancer Res 2015;21(16 Suppl):Abstract nr AS05.
Abstract 4427: Apoptosis, autophagy and ATP: The dynamic interaction of cellular ATP and drug resistance in MET amplified gastric cancer
Authors: Rebecca Dunbar Schroeder, David Hong, David J. McConkey
Journal: Cancer Research (2015)

Abstract Background: MET amplification occurs in 20% of gastric tumors, MET protein overexpression is present in approximately 50% of advanced gastric cancers and activating MET mutations are exceedingly rare in gastric cancer. Several ongoing trials have reported responses in gastric and esophageal patients with MET amplification .Methods: To investigate the effects, of MET inhibition on proliferation and cell death in gastric cancer I used two complementary approaches 1) siRNA mediated knockdown of MET; 2) incubation with crizotinib, a clinically approved small molecule inhibitor of MET. Both resulted in decreased proliferation and increased cell death only in the MET amplified gastric cancer cell lines. Results: The effects on growth arrest were stronger than the effects on cell death. To look for possible resistance mechanisms we performed whole genome mRNA expression profiling. Molecular changes related to autophagy were among the top alterations observed. Consistent with these findings, autophagy levels increased in a concentration dependent manner when exposed to crizotinib. In order to investigate the role of autophagy on cell death, I inhibited autophagy using two approaches 1) siRNA mediated knockdown of ATG5 and ATG7; 2) exposure to chloroquine, a clinically approved agent that inhibits autophagy by raising lysosomal pH. I then measured apoptosis levels with the autophagy inhibitor alone or in combination with MET knockdown or crizotinib. Autophagy inhibition caused a dramatic decrease in apoptosis in one of the MET amplified cell lines (MKN45) but not in the other (SNU-5). Because autophagy provides energy for cells, we explored the effects of MET or autophagy inhibition on cellular ATP levels using the Cell Titer-glo assay. The MKN45 cells had the lowest basal levels of ATP and these levels were further diminished in combination with autophagy inhibition. Conclusions: Overall, our data reveal a novel relationship between low ATP levels and resistance to MET inhibitor-induced cell death. Clinically this is significant because it may discourage the use of combination therapies with autophagy inhibitors in gastric cancer patients whose tumors contain MET amplification. Citation Format: Rebecca Dunbar Schroeder, David Hong, David J. McConkey. Apoptosis, autophagy and ATP: The dynamic interaction of cellular ATP and drug resistance in MET amplified gastric 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 4427. doi:10.1158/1538-7445.AM2015-4427
Abstract 1604: IMI CANCER-ID: Validation of novel blood-based biomarker technologies in clinical settings
Authors: Thomas Schlange, Thomas Krahn, Sabrina Pleier, Klaus Pantel, Leon WMM Terstappen, Barbara Baggiani
Journal: Cancer Research (2015)

Abstract The Innovative Medicines Initiative (IMI) was launched in 2008 as a public-private partnership between the European Union and the European Federation of Pharmaceutical Industries and Associations (EFPIA). IMI aims to facilitate the collaboration of healthcare stakeholders such as academic and clinical researchers, pharmaceutical industry and small and medium-sized enterprises (SMEs) in Europe, in order to address key issues in drug development and patient access to innovative medicines. Tumor heterogeneity and the dynamic changes at the molecular level during disease progression make longitudinal monitoring of malignant disease highly desirable in order to choose the best treatment options and to monitor treatment efficacy. As access to tumor tissue is often the limiting factor and historic samples are not predictive for the current state of the disease, liquid biopsies are explored to support personalized treatment of cancer patients. The CANCER-ID consortium was established in 2014 and aims to validate technologies for blood-based biomarkers such as Circulating Tumor Cells (CTCs), circulating tumor DNA (ctDNA) and microRNAs (miRNAs) to determine the absence/presence of drug targets and to assess the response to treatment. To prove broader applicability and clinical utility of the consortium's technologies and protocols, the validated assays will be deployed in controlled clinical studies (TRACERx, NCT01888601; NVALT17, NTR4410; SPECTAlung, NCT02214134; patients under SoC treatment) in 1) Non-Small Cell Lung Cancer (NSCLC) and 2) anti-Her2-resistant metastatic breast cancer (Her2RMBC). CANCER-ID is a unique network of experts in the fields of tumor biology, biomarker development, clinical sciences and bioinformatics with a total indicative budget of 14 Mio €. The consortium joins forces of 16 academic groups (ten large clinical trial sites), 6 EFPIA companies, 1 multi-national diagnostics company, 5 SMEs with advanced technologies for CTC isolation or for complex data analysis and big data handling, and two non-profit organizations. In order to fully exploit the synergies created by CANCER-ID, regulatory agencies and patient advocacy groups are involved and invited to participate in the IMI project. Citation Format: Thomas Schlange, Thomas Krahn, Sabrina Pleier, Klaus Pantel, Leon WMM Terstappen, Barbara Baggiani. IMI CANCER-ID: Validation of novel blood-based biomarker technologies in clinical settings. [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 1604. doi:10.1158/1538-7445.AM2015-1604
Analysis of Early Mortality of Chronic Lymphocytic Leukemia (CLL) Patients Treated in US Practices in the Connect CLL® Registry
Authors: Charles M. Farber, Anthony Mato, Chadi Nabhan, Thomas J. Kipps, Christopher Flowers, Neil E. Kay, Nicole Lamanna, David L. Grinblatt, Mark Kozloff, Mark Weiss, Kristen Sullivan, E. Dawn Flick, Pavel Kiselev, Shriya Bhushan, Arlene S. Swern, Jeff P. Sharman
Journal: Blood (2015)
High Prevalence of Platelet Dysfunction Among Patients with Chronic Myeloid Leukemia Receiving Tyrosine Kinase Inhibitors
Authors: Wangsuekul Warit, Lalita Norasetthada, Adisak Tantiworawit, Ekarat Rattarittamrong, Chatree Chai-adisaksopha, Sasinee Hantrakool, Wongtagan Ornkamon, Weerasak Nawarawong
Journal: Blood (2014)
Hydroxyurea Treatment of Young Children with Sickle Cell Anemia: Safety and Efficacy of Continued Treatment – the BABY HUG Follow-up Study
Authors: Zora R. Rogers, Billie Fish, Zhaoyu Luo, Rathi V. Iyer, Courtney D. Thornburg, Sharada A. Sarnaik, Sohail R. Rana, Lori Luchtman-Jones, Sherron M. Jackson, Thomas H. Howard, James F. Casella, R. Clark Brown, Ofelia A. Alvarez, Jonathan C. Goldsmith, Scott T. Miller, Winfred C. Wang
Journal: Blood (2011)
Abstract LB-059: Opposing roles for protein tyrosine kinase 6 (PTK6) in colon cancer
Authors: Priya S. Mathur, Jessica J. Gierut, Rosa M. Xicola, Xavier Llor, Angela L. Tyner
Journal: Cancer Research (2015)

Abstract Background: Protein Tyrosine Kinase 6 (PTK6, also called BRK) is a non-receptor tyrosine kinase expressed in differentiated epithelial cells of the skin, gastrointestinal tract, and prostate. Disruption of the Ptk6 gene led to impaired intestinal differentiation and increased intestinal proliferation in mice. However, PTK6 also has a tumor-promoting role in the colon, as disruption of the Ptk6 gene impaired carcinogen-induced STAT3 activation and tumorigenesis in mice. PTK6 also promotes survival of human colon cancer cell lines following DNA damaging treatments including γ-irradiation and chemotherapeutic drugs via STAT3 activation. Results: We examined and manipulated colon cancer cell lines to understand these two seemingly contradictory roles for PTK6 in the colon. The human colon adenocarcinoma cell lines SW480 and SW620 represent a primary colon tumor and a metastasis from the same patient, respectively. PTK6 is highly expressed in SW480 cells and significantly reduced in SW620 cells. Active PTK6, phosphorylated on tyrosine residue 342, is not detectable in either cell line. Stable knockdown of PTK6 in SW480 cells results in an epithelial-to-mesenchymal transition (EMT), evidenced by decreased E-cadherin expression and increased ZEB-1 and Vimentin; as well as increased migration, wound-healing, and anchorage-independent growth of cells in culture. Additionally, knockdown of PTK6 led to increased in vivo tumorigenesis of xenograft cells in nude mice. Ectopic expression of wild-type PTK6 in SW620 cells drives the reverse process (MET), demonstrating a rescue of the EMT phenotype. When a constitutively active PTK6 construct is expressed in SW620 cells, it promotes activation of cytoplasmic oncogenic targets and downstream effectors, STAT3, FAK, BCAR1 and ERK5. Analysis of patient tissues demonstrates a downregulation of mRNA and protein levels, as well as a change in protein localization in tumor versus normal tissues; while PTK6 is detectable in the nuclei of differentiating normal cells it is excluded from nuclei in colon tumors. Conclusions: Our studies indicate that PTK6 promotes the epithelial phenotype to antagonize the EMT in a kinase-independent manner and a kinase switch activates PTK6 to promote oncogenic signaling. PTK6 protein localization may function to regulate its specific role. Further examination of the complex role of this kinase could allow for a more nuanced understanding of colon cancer initiation and progression for the development of novel treatments. Citation Format: Priya S. Mathur, Jessica J. Gierut, Rosa M. Xicola, Xavier Llor, Angela L. Tyner. Opposing roles for protein tyrosine kinase 6 (PTK6) in colon 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 LB-059. doi:10.1158/1538-7445.AM2015-LB-059
757. Stable In Vivo Transduction of Primitive Hematopoietic Stem Cells After Mobilization and Intravenous Injection of an Integrating Gene Transfer Vector
Authors: Maximilian Richter, Roma Yumul, Donna Palmer, Philip Ng, Zsuzsanna Izsvák, Roberto Cattaneo, Jing Liu, Anja Ehrhardt, Wolfgang Uckert, Thalia Papayannopoulou, André Lieber
Journal: Molecular Therapy (2016)

Current protocols for hematopoietic stem cell (HSC) gene therapy involve the collection of HSCs from donors/patients, in vitro culture, transduction with retrovirus vectors, and retransplantation into myelo-conditioned patients. Besides its technical complexity, disadvantages of this approach include the necessity for culture in the presence of multiple cytokines which can affect the pluripotency of HSCs and their engraftment potential. Furthermore, the requirement for myeloablative regimens in patients with non-malignant disorders creates additional risks. We therefore explored the potential for in vivo transduction of HSCs. We developed an approach that involves GCSF/AMD3100-mediated mobilization of HSCs from the bone marrow into the peripheral blood stream, followed by intravenous injection of a Sleeping Beauty transposase-based integrating helper-dependent adenovirus (HD-Ad5/35++) vector system. These vectors target CD46, a receptor that is expressed at higher levels on HSCs than on more differentiated bone marrow and blood cells. We demonstrated in human CD46 transgenic mice and immunodeficient mice with engrafted human CD34+ cells that HSCs transduced in the periphery home back to the bone marrow where they persist and stably express the transgene long-term. In the CD46 transgenic mouse model we showed that our in vivo HSC transduction approach allows for the stable transduction of primitive HSCs, i.e. cells capable of forming multi-lineage progenitor colonies. At 12 weeks after in vivo transduction, we detected GFP marking in bone marrow HSCs in the range of 1 to 2%. Importantly, the proportion of transduced primitive HSCs increased over time. Furthermore, in vivo transduced HSCs were able to repopulate the hematopoietic system of lethally irradiated C57BL/6 mice, showing the functionality of the modified HSCs. Our in vivo HSC transduction approach did not result in innate toxicity or significant transduction of non-hematopoietic tissues. Genome-wide integration site analysis in in vivo transduced HSCs revealed a close-to-random integration pattern without preference for genes and the absence of integration into or near to cancer-associated genes. In conclusion, our novel in vivo transduction approach allows for stable genetic modification of primitive HSCs without the need of ex vivo culture, myelo-conditioning, and transplantation. Thus, our method is relevant for a broader clinical application of gene therapy of inherited diseases as well as infectious diseases and cancer.
Carfilzomib–dexamethasone vs bortezomib–dexamethasone in relapsed or refractory multiple myeloma by cytogenetic risk in the phase 3 study ENDEAVOR
Authors: W-J Chng, H Goldschmidt, M A Dimopoulos, P Moreau, D Joshua, A Palumbo, T Facon, H Ludwig, L Pour, R Niesvizky, A Oriol, L Rosiñol, A Suvorov, G Gaidano, T Pika, K Weisel, V Goranova-Marinova, H H Gillenwater, N Mohamed, S Feng, S Aggarwal, R Hájek
Journal: Leukemia (2016)

The randomized phase 3 study ENDEAVOR demonstrated a statistically significant and clinically meaningful improvement in progression-free survival (PFS) for carfilzomib and dexamethasone (Kd) vs bortezomib and dexamethasone (Vd) in relapsed or refractory multiple myeloma (MM). We conducted a preplanned subgroup analysis of ENDEAVOR to evaluate Kd vs Vd by cytogenetic risk. Of 785 patients with known cytogenetics, 210 (27%) had high-risk cytogenetics (Kd, n=97 (25%); Vd, n=113 (28%)) and 575 (73%) had standard-risk cytogenetics (Kd, n=284 (75%); Vd, n=291 (72%)). Median PFS in the high-risk group was 8.8 months for Kd vs 6.0 months for Vd (hazard ratio (HR), 0.65; 95% confidence interval (CI), 0.45–0.92; P=0.0075). Median PFS in the standard-risk group was not estimable for Kd vs 10.2 months for Vd (HR, 0.44; 95% CI, 0.33–0.58; P<0.0001). Overall response rates were 72.2% (Kd) vs 58.4% (Vd) in the high-risk group and 79.2% (Kd) vs 66.0% (Vd) in the standard-risk group. In the high-risk group, 15.5% (Kd) vs 4.4% (Vd) achieved a complete response (CR) or better. In the standard-risk group, 13.0% (Kd) vs 7.9% (Vd) achieved ⩾CR. This preplanned subgroup analysis found that Kd was superior to Vd in relapsed or refractory MM, regardless of cytogenetic risk.