tbuckley/cabot-search huggingface dataset:
Abstract B40: Characterization of <i>TP53</i> mutations in Pap test DNA of women with and without serous ovarian cancer
Authors: Jeffrey D. Krimmel-Morrison, Shenyi Lian, Yuezheng Zhang, Jeanne Fredrickson, Daniela Nachmanson, Kathryn T. Baker, Marc R. Radke, Enna Hun, Barbara Norquist, Mary J. Emond, Elizabeth M. Swisher, Rosa Ana Risques
Journal: Clinical Cancer Research (2020)

Abstract Objective: The development of Pap tests as a molecular diagnostic for serous ovarian cancer is a promising concept, but previous studies reported limited sensitivity. In addition, the presence of cancer-associated somatic mutations in normal tissue is increasingly recognized as a specificity challenge for mutational tests. We aimed to determine the diagnostic performance of Pap tests for ovarian cancer detection using ultra-accurate deep sequencing. Methods: We used CRISPR-DS, a novel duplex sequencing method that employs CRISPR-based target enrichment to increase efficiency and reduce DNA input. We performed ultra-accurate deep sequencing (mean 2000x) of the TP53 gene in 30 Pap tests from 21 women without cancer and 9 women with serous ovarian cancer with known TP53 driver mutations. Mutations were annotated using the Seshat web service and compared to those in the UMD TP53 cancer database. Results: The tumor-derived mutation was identified in 3 of 9 Pap tests from women with ovarian cancer (33% sensitivity). In addition, 221 low-frequency (≲0.001) mutations were identified in the coding region of TP53 in Pap tests from women with ovarian cancer (94 mutations) and without ovarian cancer (127 mutations). In both groups these mutations showed evidence of positive selection as indicated by clustering in exons 5 to 8, preferential location in hotspot codons and CpG dinucleotides, common presence in cancer database, impact on protein activity, and predicted pathogenicity. These “cancer-like” features were significantly more frequent in mutations identified in women with ovarian cancer than in women without cancer. Conclusions: Pap tests have low sensitivity for ovarian cancer detection and carry abundant low-frequency TP53 mutations. These mutations are more frequently pathogenic in women with ovarian cancer and determining whether their presence is associated with an increased gynecologic cancer risk warrants further study. Citation Format: Jeffrey D. Krimmel-Morrison, Shenyi Lian, Yuezheng Zhang, Jeanne Fredrickson, Daniela Nachmanson, Kathryn T. Baker, Marc R. Radke, Enna Hun, Barbara Norquist, Mary J. Emond, Elizabeth M. Swisher, Rosa Ana Risques. Characterization of TP53 mutations in Pap test DNA of women with and without serous ovarian cancer [abstract]. In: Proceedings of the AACR Special Conference on Advances in Ovarian Cancer Research; 2019 Sep 13-16, 2019; Atlanta, GA. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(13_Suppl):Abstract nr B40.
A personalized approach to guide allogeneic stem cell transplantation in younger adults with acute myeloid leukemia
Authors: Laurène Fenwarth, Xavier Thomas, Stéphane de Botton, Nicolas Duployez, Jean-Henri Bourhis, Auriane Lesieur, Gael Fortin, Paul-Arthur Meslin, Ibrahim Yakoub-Agha, Pierre Sujobert, Pierre-Yves Dumas, Christian Récher, Delphine Lebon, Céline Berthon, Mauricette Michallet, Arnaud Pigneux, Stéphanie Nguyen, Sylvain Chantepie, Norbert Vey, Emmanuel Raffoux, Karine Celli-Lebras, Claude Gardin, Juliette Lambert, Jean-Valère Malfuson, Denis Caillot, Sébastien Maury, Benoît Ducourneau, Pascal Turlure, Emilie Lemasle, Cécile Pautas, Sylvie Chevret, Christine Terré, Nicolas Boissel, Gérard Socié, Hervé Dombret, Claude Preudhomme, Raphael Itzykson
Journal: Blood (2020)
Abstract 3247: Development of CAR-T cell therapy for B-ALL using a point-of-care approach
Authors: Luiza Abdo, Luciana Rodrigues Barros, Mariana Saldanha Viegas, Luisa Vieira Marques, Priscila de Sousa Ferreira, Leonardo Chicaybam, Martín Hernán Bonamino
Journal: Cancer Research (2020)

Abstract Introduction: CD19-targeted CAR-T cell immunotherapy is now an approved treatment for B cell leukemias and lymphomas. Current protocols for producing CAR-T cells use viral vectors for genetic modification and take 12-15 days to expand sufficient numbers of T cells, constituting an important bottleneck for the widespread use of this therapy. The development of non-viral, plasmid-based systems like Sleeping Beauty (SB) transposons, coupled with the emergence of large scale, closed electroporation devices, present the opportunity of generating high numbers of CAR-T cells in a short period of time and transforming this in a point-of-care (POC) therapy. Methods and Results: In this work, mononuclear cells were isolated using Ficoll and electroporated using Nucleofector IIb electroporator combined with plasmids encoding 19BBz CAR (in the pT3 SB transposon backbone) and SB100x transposase. Cells were rested for 24h and used for in vitro and in vivo experiments. The phenotype was assessed by flow cytometry. The in vitro cytotoxicity assay was performed using Calcein-AM dye on target cells incubated with different ratios of effector cells. 8-12-week-old-female-NSG were injected iv. 5 × 106 RS4;11 GFP or 105 Nalm-6 GFP and after 3 days were treated with different doses of recently electroporated CAR-T cells. CAR expression on day 1 following electroporation ranged between 5-15% and in vitro cytotoxic activity against RS4;11 or Nalm-6 CD19+ B cell precursor leukemia lines was low or absent. NSG mice engrafted with RS4;11 and treated with 1 × 105 19BBz+ cells showed improved survival when compared to mice treated with mock electroporated cells. POC approach was also efficient against Nalm-6, where 19BBz+CAR-T cells (7 × 105 per mice) improved the survival of mice. In both models, decreased tumor burden in blood and spleen was observed in mice treated with 19BBz. Head to head comparison of 19BBz cells used in POC approach or expanded for 8-12 days in vitro showed similar antitumor activity in vivo against RS4;11 cells, leading to equivalent improvements in mice survival. Conclusion: In summary, we show that the POC strategy is a viable approach for the use of CAR-T cells, obviating the need for T cell expansion while having the potential to greatly decrease the total cost and time of CAR-T cell therapy manufacturing. Citation Format: Luiza Abdo, Luciana Rodrigues Barros, Mariana Saldanha Viegas, Luisa Vieira Marques, Priscila de Sousa Ferreira, Leonardo Chicaybam, Martín Hernán Bonamino. Development of CAR-T cell therapy for B-ALL using a point-of-care approach [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 3247.
Precore and Basal Core Promoter Hepatitis B Virus (HBV) Variants Are Present From a Young Age and Differ Across HBV Genotypes
Authors: Daryl T.Y. Lau, Lilia Ganova‐Raeva, Junyao Wang, Douglas Mogul, Raymond T. Chung, Mauricio Lisker‐Melman, Kyong‐Mi Chang, Obaid S. Shaikh, Harry L.A. Janssen, Abdus S. Wahed, Anna S. Lok
Journal: Hepatology (2020)

Background and Aims Hepatitis B virus (HBV) precore (PC) and dual basal core promoter (BCP) mutations halt and down‐regulate hepatitis B e antigen (HBeAg) production respectively. PC mutation is rarely associated with HBV genotype A. We sought to examine the association of these variants with HBV genotypes, age, and HBeAg status in a racially diverse population in North America. Prospective study included 1,036 (808 adults, 228 children) participants in the Hepatitis B Research Network. PC and BCP variants were determined by Sanger sequencing, and dominant HBV species (&gt;50%) were reported. Approach and Results Median age was 36.3 years (range, 2‐80), 44.6% HBeAg(+), 74.2% Asians, 13.3% black, and 9.7% white. The dominant PC variant was present in 29.4% participants, including 20 with subgenotype A1 or A2. Seventeen of 20 participants with genotype A and PC had a compensatory C1858T mutation. In the HBeAg(+) cohort, the prevalence of PC and/or BCP variants increased from 14.4% in the first two decades to 51% after 40 years of age. Among those aged 2‐18, 52% and 83% with dominant PC and BCP variants were HBeAg(+) compared to 3.8% and 29% in the &gt;40 years age group. HBeAg clearance rates were significantly higher for those with dominant PC or BCP variants: 24.4 and 15.0 per 100 person‐years compared to 6.0 in wild‐type HBV ( P &lt; 0.0001). Conclusions PC variants can be present in HBV genotype A and are usually associated with C1858T, which preserves the pregenome encapsidation sequence. Selection of PC and BCP variants occurred at a young age, with increasing prevalence across age groups. HBeAg(+) participants with dominant PC and BCP variants progressed to the HBeAg(−) phase of chronic HBV infection significantly faster. This finding has potential clinical and therapeutic implications.
Weight Gain Induced by Continuous Positive Airway Pressure in Patients with Obstructive Sleep Apnea Is Mediated by Fluid Accumulation: A Randomized Crossover Controlled Trial
Authors: Sara Herculano, Gustavo F. Grad, Luciano F. Drager, André L. P. de Albuquerque, Camila M. Melo, Geraldo Lorenzi-Filho, Pedro R. Genta
Journal: American Journal of Respiratory and Critical Care Medicine (2020)
<i>In Vivo</i> Generation of Lung and Thyroid Tissues from Embryonic Stem Cells Using Blastocyst Complementation
Authors: Bingqiang Wen, Enhong Li, Vladimir Ustiyan, Guolun Wang, Minzhe Guo, Cheng-Lun Na, Gregory T. Kalin, Veronica Galvan, Yan Xu, Timothy E. Weaver, Tanya V. Kalin, Jeffrey A. Whitsett, Vladimir V. Kalinichenko
Journal: American Journal of Respiratory and Critical Care Medicine (2020)

Rationale: The regeneration and replacement of lung cells or tissues from induced pluripotent stem cell- or embryonic stem cell-derived cells represent future therapies for life-threatening pulmonary disorders but are limited by technical challenges to produce highly differentiated cells able to maintain lung function. Functional lung tissue-containing airways, alveoli, vasculature, and stroma have never been produced via directed differentiation of embryonic stem cells (ESCs) or induced pluripotent stem cells. We sought to produce all tissue components of the lung from bronchi to alveoli by embryo complementation.Objectives: To determine whether ESCs are capable of generating lung tissue in Nkx2-1-/- mouse embryos with lung agenesis.Methods: Blastocyst complementation was used to produce chimeras from normal mouse ESCs and Nkx2-1-/- embryos, which lack pulmonary tissues. Nkx2-1-/- chimeras were examined using immunostaining, transmission electronic microscopy, fluorescence-activated cell sorter analysis, and single-cell RNA sequencing.Measurements and Main Results: Although peripheral pulmonary and thyroid tissues are entirely lacking in Nkx2-1 gene-deleted embryos, pulmonary and thyroid structures in Nkx2-1-/- chimeras were restored after ESC complementation. Respiratory epithelial cell lineages in restored lungs of Nkx2-1-/- chimeras were derived almost entirely from ESCs, whereas endothelial, immune, and stromal cells were mosaic. ESC-derived cells from multiple respiratory cell lineages were highly differentiated and indistinguishable from endogenous cells based on morphology, ultrastructure, gene expression signatures, and cell surface proteins used to identify cell types by fluorescence-activated cell sorter.Conclusions: Lung and thyroid tissues were generated in vivo from ESCs by blastocyst complementation. Nkx2-1-/- chimeras can be used as "bioreactors" for in vivo differentiation and functional studies of ESC-derived progenitor cells.
A network of immune and microbial modifications underlies viral persistence in the gastrointestinal tract
Authors: Bethany L. Macleod, Heidi J. Elsaesser, Laura M. Snell, Russell J. Dickson, Mengdi Guo, Kebria Hezaveh, Wenxi Xu, Akash Kothari, Tracy L. McGaha, Cynthia J. Guidos, David G. Brooks
Journal: The Journal of Experimental Medicine (2020)

Many pathogens subvert intestinal immunity to persist within the gastrointestinal tract (GIT); yet, the underlying mechanisms that enable sanctuary specifically in this reservoir are unclear. Using mass cytometry and network analysis, we demonstrate that chronic LCMV infection of the GIT leads to dysregulated microbial composition, a cascade of metabolic alterations, increased susceptibility to GI disease, and a system-wide recalibration of immune composition that defines viral persistence. Chronic infection led to outgrowth of activated Tbet–expressing T reg cell populations unique to the GIT and the rapid erosion of pathogen-specific CD8 tissue-resident memory T cells. Mechanistically, T reg cells and coinhibitory receptors maintained long-term viral sanctuary within the GIT, and their targeting reactivated T cells and eliminated this viral reservoir. Thus, our data provide a high-dimensional definition of the mechanisms of immune regulation that chronic viruses implement to exploit the unique microenvironment of the GIT and identify T reg cells as key modulators of viral persistence in the intestinal tract.
Arrb2 promotes endothelial progenitor cell-mediated postischemic neovascularization
Authors: Xuelian Wang, Gaojian Huang, Jiaxin Mu, Zhilei Cong, Shuyan Chen, Dong Fu, Jia Qi, Zhen Li
Journal: Theranostics (2020)

Background and aim: Modulating biological functions of endothelial progenitor cells (EPCs) is essential for therapeutic angiogenesis in ischemic vascular diseases. This study aimed to explore the role and molecular mechanisms of β-arrestin 2 (Arrb2) in EPCs biology and angiogenic therapy. Methods: The influence of Arrb2 on postischemic neovascularization was evaluated in Arrb2-deficient mice. The proliferation, apoptosis, and various functions of EPCs were analyzed in vitro by manipulating the expression of Arrb2. Finally, the in vivo effect of Arrb2 on EPC-mediated neovascularization was investigated in a mouse model of hind-limb ischemia (HLI). Results: Arrb2-deficient mice exhibited impaired blood flow recovery based on laser Doppler measurements and reduced capillary density in the adductor muscle after unilateral HLI. Arrb2-deficient mice also showed restricted intraplug angiogenesis in subcutaneously implanted Matrigel plugs. In vitro, lentivirus-mediated Arrb2 overexpression promoted EPC proliferation, migration, adhesion, and tube formation, whereas Arrb2 knockdown had opposite effects. In addition, the overexpression of Arrb2 in EPCs protected them from hypoxia-induced apoptosis and improved intraplug angiogenesis ex vivo. Mechanistically, Arrb2 interacted with and activated extracellular signal-regulated kinase (ERK)1/2 and protein kinase B (Akt) signaling pathways. Finally, the transplantation of EPCs overexpressing Arrb2 resulted in a significantly higher blood flow restoration in ischemic hind limb and higher capillary density during histological analysis compared with control or Arrb2-knockdown EPC-treated nude mice. Conclusions: The data indicated that Arrb2 augmented EPC-mediated neovascularization through the activation of ERK and Akt signaling pathways. This novel biological function of Arrb2 might provide a potential therapeutic option to promote EPCs in the treatment of ischemic vascular diseases.
Abstract 2190: Engineering off-the-shelf T cell receptor fusion construct (TRuC) T cells
Authors: Julie Donaghey, Philippe Kieffer-Kwon, Troy Patterson, Tiffany Chan, Holly Horton, Robert Tighe, Dario A. Gutierrez, Daniel Getts, Robert Hofmeister
Journal: Cancer Research (2020)

Abstract The T-Cell Receptor (TCR) can be functionally split into antigen recognition mediated by the TCRα/β heterodimer and signal transduction triggered by the CD3 complex comprising CD3ϵ/γ, CD3ϵ/δ and CD3ζ/ζ dimers. Unlike antibodies, the TCR recognizes its cognate peptide antigen only when presented on human leukocyte antigen (HLA) molecules. Recently, we reported that tethering an antibody-derived binder to one of the TCR subunits redirects T cells to specifically kill tumor cells independent of HLA. Different from CAR-T cells, the T cell receptor fusion constructs (TRuC™) are integrated into the natural TCR and require all TCR subunits for receptor translocation to the cell surface. The development of off-the-shelf TRuC-T cells is desirable to shorten the vein-to-vein production time and reduce manufacturing costs. Here, we describe the generation of TRuC-T cells expressing a fully functional TRuC TCR without alloreactivity. Inactivation of the endogenous TRAC gene employing CRISPR/Cas9 endonuclease disrupts natural TCR formation. Yet, replacing the endogenous TCRα subunit with a human TCRα constant region without variable domain to avoid alloreactivity is insufficient for TRuC TCR expression. A functional TRuC TCR, however, can be created by substituting the following constructs for the inactivated TRAC gene: (i) murine TCRα and β constant domains without variable domains, (ii) chimeric human/murine TCRα and β constant regions or (iii) TCRγ and δ constant domains. Off-the-shelf TRuC-T cells upregulate activation markers, secrete cytokines, and kill tumor cells in an antigen-specific manner. Importantly, the genome-engineered TRuC-T cells lack alloreactivity as demonstrated in mixed lymphocyte reactions and clear tumors in NSG xenograft models without signs of Graft versus host disease (GvHD). Our findings warrant further development of allogeneic TRuC-T cells for cancer therapy. Citation Format: Julie Donaghey, Philippe Kieffer-Kwon, Troy Patterson, Tiffany Chan, Holly Horton, Robert Tighe, Dario A. Gutierrez, Daniel Getts, Robert Hofmeister. Engineering off-the-shelf T cell receptor fusion construct (TRuC) T cells [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 2190.
Abstract 2276: Preclinical development and mechanism of action studies of NM21-1480, a PD-L1/4-1BB/HSA trispecific MATCH3 therapeutic clinical candidate
Authors: Daniel Snell, Tea Gunde, Stefan Warmuth, Peter Lichtlen, Julia Tietz, Matthias Brock, Alexandre Simonin, Christian Hess, Weinert Christopher, Robin Heiz, Naomi Flueckiger, Julia Zeberer, Dania Diem, Dana Mahler, Diego Morenzoni, Belinda Wickihalder, Simone Muntwiler, Antonia Poelderl, Benjamin Kuettner, Sandro Wagen, Sebastian Meyer, Timothy Egan, David Urech
Journal: Cancer Research (2020)

Abstract Antagonistic molecules targeting the PD-1/PD-L1 axis have shown excellent activity in the clinic. However the majority of patients do not respond to the therapy due to multifaceted reasons implicating a non-effective activation of the immune system in those patients. The co-stimulatory molecule 4-1BB has been shown to be a key signalling component of T cells and the combination of 4-1BB activation and PD-1/PD-L1 antagonism has been shown to be highly active in preclinical models. Systemic application of first generation anti-4-1BB antibodies however have resulted in dose limiting hepatic toxicities. We have generated a novel 4-1BB/PD-L1/HSA trispecific MATCH3 immunomodulatory drug candidate (NM21-1480) that agonizes 4-1BB conditionally upon PD-L1 binding / blockade. Here we show the preclinical development data package for NM21-1480 demonstrating exquisite tumour-specific T cell activation associated with both 4-1BB agonism as well as PD-L1/PD-1 antagonism. We also demonstrate tumour specific localisation and accumulation of NM21-1480 in a mouse xenograft model. We report on the toxicity profile and pharmacokinetic properties of the molecule in non-human primates. We plan to initiate a first-in-human clinical study in the second half of 2020 to determine the safety, tolerability and first signs of clinical activity of the molecule. Citation Format: Daniel Snell, Tea Gunde, Stefan Warmuth, Peter Lichtlen, Julia Tietz, Matthias Brock, Alexandre Simonin, Christian Hess, Weinert Christopher, Robin Heiz, Naomi Flueckiger, Julia Zeberer, Dania Diem, Dana Mahler, Diego Morenzoni, Belinda Wickihalder, Simone Muntwiler, Antonia Poelderl, Benjamin Kuettner, Sandro Wagen, Sebastian Meyer, Timothy Egan, David Urech. Preclinical development and mechanism of action studies of NM21-1480, a PD-L1/4-1BB/HSA trispecific MATCH3 therapeutic clinical candidate [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 2276.
Abstract 6072: MUC16-Cter cleavage increases the metastatic potential in pancreatic cancer
Authors: Saravanakumar Marimuthu, Imayavaramban Lakshmanan, Sakthivel Muniyan, Pranita Atri, Maneesh Jain, Moorthy P. Ponnusamy, Surinder K. Batra
Journal: Cancer Research (2020)

Abstract Pancreatic cancer (PC) is one of the most lethal malignant tumors. Several membrane-bound mucins are overexpressed in PC, including MUC16. The role and molecular mechanism of MUC16 mucin, particularly carboxyl-terminal domain (MUC16-Cter) in metastasis of pancreatic cancer, are poorly understood. Therefore, we hypothesize that the “MUC16-Cter domain plays a vital role in facilitating metastasis in pancreatic cancer”. Here, we knockout MUC16 in Capan 1 PC cells and overexpressed MUC16-Cter (F114AA) domain in MiaPaCa2 PC cells to study its functional impact in PC. Capan-1 MUC16 knockout cells displayed a significant decrease in colony-forming by in vitro tumorigenicity assay, endothelial binding, and P-selectin binding ability compared to control cells. Whereas, MUC16-Cter domain overexpressed MiaPaCa2 cells showed a significant increase in colony formation as compared to vector control cells. These results suggest that MUC16 plays a role in promoting in vitro tumorigenicity and facilitating intravasation and circulation of PC cell by interacting with endothelial cells during the metastatic spread of PC cells. Interestingly, we observed that chemotherapeutic drug (gemcitabine) induces MUC16-Cter cleavage in PC cells. We generated a genetically engineered mouse model Muc16-/- with KrasG12D, Trp53R172H/+, Pdx1-Cre (KPCM) background to study the role of Muc16 in PC tumorigenesis and metastasis with existing KPC model. KPCM showed decreased the early onset of cancer formation compared to KPC. Further, the Kaplan Meier test showed an increased survival rate in Muc16 -/- with KPC background as compared to KPC mice. EMT markers showed decreased expression in KPCM compared to KPC tumors. KPCM cells showed a significant decreased in migratory potential, endothelial, and P-selectin binding ability KPC PC cells. In conclusion, our in vitro and in vivo findings confirm that MUC16 and its Cter domain might play an essential role during the PC tumorigenesis and metastasis. Therefore, targeting MUC16-Cter might be an ideal therapeutic strategy for inhibiting tumorigenesis and metastasis of PC. Citation Format: Saravanakumar Marimuthu, Imayavaramban Lakshmanan, Sakthivel Muniyan, Pranita Atri, Maneesh Jain, Moorthy P. Ponnusamy, Surinder K. Batra. MUC16-Cter cleavage increases the metastatic potential in pancreatic cancer [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 6072.