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1. Modulation of nonsense mediated decay by rapamycin

Author

Martinez-Nunez, Rocio T, Wallace, Andrew, Coyne, Doyle, Jansson, Linnea, Rush, Miles, Ennajdaoui, Hanane, Katzman, Sol, Bailey, Joanne, Deinhardt, Katrin, Sanchez-Elsner, Tilman, and Sanford, Jeremy R

Subjects
Biological Sciences, Stem Cell Research, Genetics, Underpinning research, 1.1 Normal biological development and functioning, Alternative Splicing, Codon, Nonsense, Eukaryotic Initiation Factors, HEK293 Cells, Humans, Nonsense Mediated mRNA Decay, Phosphoproteins, Polyribosomes, RNA Helicases, RNA Isoforms, RNA, Messenger, Serine-Arginine Splicing Factors, Sirolimus, Trans-Activators, Environmental Sciences, Information and Computing Sciences, Developmental Biology, Biological sciences, Chemical sciences, Environmental sciences
Abstract

Rapamycin is a naturally occurring macrolide whose target is at the core of nutrient and stress regulation in a wide range of species. Despite well-established roles as an inhibitor of cap-dependent mRNA translation, relatively little is known about its effects on other modes of RNA processing. Here, we characterize the landscape of rapamycin-induced post-transcriptional gene regulation. Transcriptome analysis of rapamycin-treated cells reveals genome-wide changes in alternative mRNA splicing and pronounced changes in NMD-sensitive isoforms. We demonstrate that despite well-documented attenuation of cap-dependent mRNA translation, rapamycin can augment NMD of certain transcripts. Rapamycin-treatment significantly reduces the levels of both endogenous and exogenous Premature Termination Codon (PTC)-containing mRNA isoforms and its effects are dose-, UPF1- and 4EBP-dependent. The PTC-containing SRSF6 transcript exhibits a shorter half-life upon rapamycin-treatment as compared to the non-PTC isoform. Rapamycin-treatment also causes depletion of PTC-containing mRNA isoforms from polyribosomes, underscoring the functional relationship between translation and NMD. Enhanced NMD activity also correlates with an enrichment of the nuclear Cap Binding Complex (CBC) in rapamycin-treated cells. Our data demonstrate that rapamycin modulates global RNA homeostasis by NMD.

Published
2017

2. IGF2BP3 Modulates the Interaction of Invasion-Associated Transcripts with RISC.

Author

Ennajdaoui, Hanane, Howard, Jonathan M, Sterne-Weiler, Timothy, Jahanbani, Fereshteh, Coyne, Doyle J, Uren, Philip J, Dargyte, Marija, Katzman, Sol, Draper, Jolene M, Wallace, Andrew, Cazarez, Oscar, Burns, Suzanne C, Qiao, Mei, Hinck, Lindsay, Smith, Andrew D, Toloue, Masoud M, Blencowe, Benjamin J, Penalva, Luiz OF, and Sanford, Jeremy R

Subjects
Cell Line, Tumor, Hela Cells, Focal Adhesions, Humans, Adenocarcinoma, Carcinoma, Pancreatic Ductal, Neoplasm Invasiveness, RNA-Induced Silencing Complex, RNA-Binding Proteins, MicroRNAs, RNA, Messenger, RNA, Neoplasm, Gene Expression Regulation, Neoplastic, Polymorphism, Single Nucleotide, Argonaute Proteins, HeLa Cells, Cell Line, Tumor, Carcinoma, Pancreatic Ductal, RNA, Messenger, Neoplasm, Gene Expression Regulation, Neoplastic, Polymorphism, Single Nucleotide, Pancreatic Cancer, Rare Diseases, Biotechnology, Digestive Diseases, Cancer, Genetics, 2.1 Biological and endogenous factors, Biochemistry and Cell Biology, Medical Physiology
Abstract

Insulin-like growth factor 2 mRNA binding protein 3 (IGF2BP3) expression correlates with malignancy, but its role(s) in pathogenesis remains enigmatic. We interrogated the IGF2BP3-RNA interaction network in pancreatic ductal adenocarcinoma (PDAC) cells. Using a combination of genome-wide approaches, we have identified 164 direct mRNA targets of IGF2BP3. These transcripts encode proteins enriched for functions such as cell migration, proliferation, and adhesion. Loss of IGF2BP3 reduced PDAC cell invasiveness and remodeled focal adhesion junctions. Individual nucleotide resolution crosslinking immunoprecipitation (iCLIP) revealed significant overlap of IGF2BP3 and microRNA (miRNA) binding sites. IGF2BP3 promotes association of the RNA-induced silencing complex (RISC) with specific transcripts. Our results show that IGF2BP3 influences a malignancy-associated RNA regulon by modulating miRNA-mRNA interactions.

Published
2016

3. A reference map of the human binary protein interactome

Author

Luck, Katja, Kim, Dae-Kyum, Lambourne, Luke, Spirohn, Kerstin, Begg, Bridget E., Bian, Wenting, Brignall, Ruth, Cafarelli, Tiziana, Campos-Laborie, Francisco J., Charloteaux, Benoit, Choi, Dongsic, Coté, Atina G., Daley, Meaghan, Deimling, Steven, Desbuleux, Alice, Dricot, Amélie, Gebbia, Marinella, Hardy, Madeleine F., Kishore, Nishka, Knapp, Jennifer J., Kovács, István A., Lemmens, Irma, Mee, Miles W., Mellor, Joseph C., Pollis, Carl, Pons, Carles, Richardson, Aaron D., Schlabach, Sadie, Teeking, Bridget, Yadav, Anupama, Babor, Mariana, Balcha, Dawit, Basha, Omer, Bowman-Colin, Christian, Chin, Suet-Feung, Choi, Soon Gang, Colabella, Claudia, Coppin, Georges, D’Amata, Cassandra, De Ridder, David, De Rouck, Steffi, Duran-Frigola, Miquel, Ennajdaoui, Hanane, Goebels, Florian, Goehring, Liana, Gopal, Anjali, Haddad, Ghazal, Hatchi, Elodie, Helmy, Mohamed, Jacob, Yves, Kassa, Yoseph, Landini, Serena, Li, Roujia, van Lieshout, Natascha, MacWilliams, Andrew, Markey, Dylan, Paulson, Joseph N., Rangarajan, Sudharshan, Rasla, John, Rayhan, Ashyad, Rolland, Thomas, San-Miguel, Adriana, Shen, Yun, Sheykhkarimli, Dayag, Sheynkman, Gloria M., Simonovsky, Eyal, Taşan, Murat, Tejeda, Alexander, Tropepe, Vincent, Twizere, Jean-Claude, Wang, Yang, Weatheritt, Robert J., Weile, Jochen, Xia, Yu, Yang, Xinping, Yeger-Lotem, Esti, Zhong, Quan, Aloy, Patrick, Bader, Gary D., De Las Rivas, Javier, Gaudet, Suzanne, Hao, Tong, Rak, Janusz, Tavernier, Jan, Hill, David E., Vidal, Marc, Roth, Frederick P., and Calderwood, Michael A.

Published
2020
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4. Splicing factor TRA2B is required for neural progenitor survival

Author

Roberts, Jacqueline M, Ennajdaoui, Hanane, Edmondson, Carina, Wirth, Brunhilde, Sanford, Jeremy R, and Chen, Bin

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Genetics, Stem Cell Research, Stem Cell Research - Nonembryonic - Non-Human, Pediatric, Mental Health, Neurosciences, 1.1 Normal biological development and functioning, Neurological, Alternative Splicing, Animals, Blotting, Western, Cell Survival, Cerebral Cortex, Immunoprecipitation, In Situ Hybridization, Mice, Mice, Knockout, Neural Stem Cells, Neurogenesis, Neurons, Nuclear Proteins, RNA-Binding Proteins, Serine-Arginine Splicing Factors, TRA2B, cerebral cortex, development, splicing, neural progenitor, SR protein, Zoology, Medical Physiology, Neurology & Neurosurgery
Abstract

Alternative splicing of pre-mRNAs can rapidly regulate the expression of large groups of proteins. The RNA binding protein TRA2B (SFRS10) plays well-established roles in developmentally regulated alternative splicing during Drosophila sexual differentiation. TRA2B is also essential for mammalian embryogenesis and is implicated in numerous human diseases. Precise regulation of alternative splicing is critical to the development and function of the central nervous system; however, the requirements for specific splicing factors in neurogenesis are poorly understood. This study focuses on the role of TRA2B in mammalian brain development. We show that, during murine cortical neurogenesis, TRA2B is expressed in both neural progenitors and cortical projection neurons. Using cortex-specific Tra2b mutant mice, we show that TRA2B depletion results in apoptosis of the neural progenitor cells as well as disorganization of the cortical plate. Thus, TRA2B is essential for proper development of the cerebral cortex.

Published
2014

5. CD8-Targeted, Integrating Viral Vectors Transduce Resting T Cells and Enable Extracorporeal Delivery (ECD) for Rapid CAR T Cell Therapies

Author

Green, Jesse, primary, Johnson, Adam, additional, Granger, Brian, additional, Liang, Ouwen, additional, Moreno, Jesus, additional, Tucker, Andrew, additional, Wright, Hallee, additional, Dolinski, Brian, additional, Ennajdaoui, Hanane, additional, Tareen, Semih, additional, van Hoeven, PhD, Neal, additional, Shah, Jagesh, additional, Elpek, Kutlu, additional, Foster, Aaron, additional, and Fry, Terry J., additional

Published
2022
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6. In Vivo Delivery of a CD20 CAR Using a CD8-Targeted Fusosome in Southern Pig-Tail Macaques (M. nemestrina) Results in B Cell Depletion

Author

Cunningham, Justine, primary, Chandra, Sundeep, additional, Emmanuel, Akinola, additional, Mazzarelli, Allyse, additional, Passaro, Carmela, additional, Baldwin, Paige, additional, Nguyen-McCarty, Michelle, additional, Rocca, Carrie, additional, Joyce, Shannon, additional, Kim, Joohwan, additional, Vagin, Vasily, additional, Kaczmarek, James, additional, Chavan, Hemant, additional, Jewell, Heather, additional, Lipsitz, Yonatan, additional, Shamashkin, Misha, additional, Hlavaty, Kelan, additional, Rodriguez, Jason, additional, Co, Carl, additional, Cruite, Pattie, additional, Ennajdaoui, Hanane, additional, Duback, Victoria, additional, Elman, Jess, additional, Amatya, Shirisha, additional, Harding, Caspian, additional, Lyubinetsky, Sergey, additional, Patel, Vidur, additional, Pepper, Lauren, additional, Ruzo, Albert, additional, Iovino, Salvatore, additional, Varghese, Bindu, additional, Foster, Aaron E., additional, Gorovits, Boris, additional, Elpek, Kutlu, additional, Laska, Michael, additional, McGill, Trevor, additional, Shah, Jagesh V, additional, Fry, Terry J., additional, and Dambach, Donna, additional

Published
2021
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7. Abstract LB105: In vivo CAR T therapy: targeted in vivo gene delivery of a CAR using a CD8-specific fusogen results in tumor eradication

Author

Emmanuel, Akinola, primary, Cruite, Patty, additional, Ennajdaoui, Hanane, additional, Passaro, Carmela, additional, Baldwin, Paige, additional, Duback, Victoria, additional, Liang, Anna, additional, Elman, Jess, additional, Crocker, Samantha, additional, Amatya, Shirisha, additional, Harding, Caspian, additional, Mazarelli, Allyse, additional, Lyubinetsky, Sergey, additional, Patel, Vidur, additional, Parikh, Avani, additional, Hlavaty, Kelan, additional, Rodriguez, Jason, additional, Pepper, Lauren, additional, Ruzo, Albert, additional, Iovino, Salvatore, additional, Elpek, Kutlu, additional, Laska, Michael, additional, McGill, Trevor, additional, Dambach, Donna, additional, Fry, Terry, additional, and Shah, Jagesh, additional

Published
2021
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9. A reference map of the human protein interactome

Author

Luck, Katja, primary, Kim, Dae-Kyum, additional, Lambourne, Luke, additional, Spirohn, Kerstin, additional, Begg, Bridget E., additional, Bian, Wenting, additional, Brignall, Ruth, additional, Cafarelli, Tiziana, additional, Campos-Laborie, Francisco J., additional, Charloteaux, Benoit, additional, Choi, Dongsic, additional, Cote, Atina G., additional, Daley, Meaghan, additional, Deimling, Steven, additional, Desbuleux, Alice, additional, Dricot, Amélie, additional, Gebbia, Marinella, additional, Hardy, Madeleine F., additional, Kishore, Nishka, additional, Knapp, Jennifer J., additional, Kovács, István A., additional, Lemmens, Irma, additional, Mee, Miles W., additional, Mellor, Joseph C., additional, Pollis, Carl, additional, Pons, Carles, additional, Richardson, Aaron D., additional, Schlabach, Sadie, additional, Teeking, Bridget, additional, Yadav, Anupama, additional, Babor, Mariana, additional, Balcha, Dawit, additional, Basha, Omer, additional, Bowman-Colin, Christian, additional, Chin, Suet-Feung, additional, Choi, Soon Gang, additional, Colabella, Claudia, additional, Coppin, Georges, additional, D’Amata, Cassandra, additional, De Ridder, David, additional, De Rouck, Steffi, additional, Duran-Frigola, Miquel, additional, Ennajdaoui, Hanane, additional, Goebels, Florian, additional, Goehring, Liana, additional, Gopal, Anjali, additional, Haddad, Ghazal, additional, Hatchi, Elodie, additional, Helmy, Mohamed, additional, Jacob, Yves, additional, Kassa, Yoseph, additional, Landini, Serena, additional, Li, Roujia, additional, van Lieshout, Natascha, additional, MacWilliams, Andrew, additional, Markey, Dylan, additional, Paulson, Joseph N., additional, Rangarajan, Sudharshan, additional, Rasla, John, additional, Rayhan, Ashyad, additional, Rolland, Thomas, additional, San-Miguel, Adriana, additional, Shen, Yun, additional, Sheykhkarimli, Dayag, additional, Sheynkman, Gloria M., additional, Simonovsky, Eyal, additional, Taşan, Murat, additional, Tejeda, Alexander, additional, Twizere, Jean-Claude, additional, Wang, Yang, additional, Weatheritt, Robert J., additional, Weile, Jochen, additional, Xia, Yu, additional, Yang, Xinping, additional, Yeger-Lotem, Esti, additional, Zhong, Quan, additional, Aloy, Patrick, additional, Bader, Gary D., additional, De Las Rivas, Javier, additional, Gaudet, Suzanne, additional, Hao, Tong, additional, Rak, Janusz, additional, Tavernier, Jan, additional, Tropepe, Vincent, additional, Hill, David E., additional, Vidal, Marc, additional, Roth, Frederick P., additional, and Calderwood, Michael A., additional

Published
2019
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10. Analyse fonctionnelle du promoteur de la cembranetriène- diol-synthase spécifique des trichomes de Nicotiana sylvestris

Author

Ennajdaoui, Hanane, Laboratoire genomique des plantes (LGP), Université Joseph Fourier - Grenoble 1 (UJF), Université de Grenoble, Université Joseph-Fourier - Grenoble I, Pr Michel Herzog(michel.herzog@ujf-grenoble.fr), and Ennajdaoui, Hanane

Subjects
secretion, promoter, [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, element cis et facteur trans, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Trichomes, N.sylverstris
Abstract

In tobacco, secretory glandular trichomes (SGTs) are specifically producing volatiles compounds. This specificity is the consequence of the specific transcriptional expression of Terpenes synthases genes in SGTs. Promoters of those genes are of significant interest because they may be used in plant bioengineering to produce high value biomolecules (taxol, artemisinine) in SGTs. The promoter of a Cembrane-diol-sytnhase (P1.1NsTPSO2a), active in the SGTs heads, was isolated and transfected in transgenic N. sylvestris. Deletion analysis of P1.1NsTPSO2a shown 4c (100pb) and 400c (400pb) region required in trichome specificity. We next performed GUS fusion with the 4c region placed upstream of the minimum 35S promoter (-46) and demonstrate that 4c is sufficient to mimic the full-length promoter. Finally, we isolated a putative trichome transcription factor (NsZnf) that potentially binds the 400pb domain in yeast one-hybrid assay. NsZnf belongs to the GATA-ZincFinger III family. NsZnf possess a single zinc finger domain, a CCT domain and Tify domain. NsZnf nuclear localization was demonstrated by transient expression in N.benthamiana consistent with its role as transcription factor., Chez le tabac, les trichomes glandulaires sécréteurs (TGSs) sont des structures pluricellulaires où s'effectuent la synthèse et la sécrétion de nombreux composés volatiles. Cette production spécifique dans les TGSs est la conséquence de la spécificité de l'expression transcriptionnelle des gènes des Terpènes synthases. Les promoteurs de ces gènes sont intéressants parce qu'ils peuvent être utilisés en bioingénieurie pour produire des biomolécules à forte valeur ajoutées (taxol, l'artémisinine) dans TGSs. L'un d'eux, le promoteur de la Cembratriène-diol-synthase (P1.1NsTPSO2a), actif dans les cellules de têtes des TGSs, a été isolé et transfecté dans N.sylvestris. L'analyse par délétions de P1.1NsTPSO2a a montré que deux fragments, 4c (100pb) et 400c (360 pb) sont importants pour l'expression spécifique dans les têtes de trichomes. La région 4c a été placée en amont du promoteur 35S minimum (-46) et du gène rapporteur GUS. Nous avons démontré que 4c est nécessaire et suffisant pour une expression dans les têtes de TGSs. Le fragment 400c pourrait jouer un rôle dans la répression du P1.1NsTPSO2a dans les cellules épidermiques et dans certaines parties des racines. Enfin, nous avons isolé par crible simple-hybride dans la levure un facteur de transcription putatif du trichome (NsZnF) pouvant reconnaître le fragment 400c. NsZnf appartient à la famille des facteurs de transcription GATA-ZincFinger III. Cette protéine possède un doigt de zinc, un domaine CCT et un domaine TIFY. L'expression transitoire dans N.benthamiana montre une localisation nucléaire de NsZnf compatible avec son rôle de facteur de transcription.

Published
2009

11. Modulation of nonsense mediated decay by rapamycin

Author

Martinez-Nunez, Rocio T., primary, Wallace, Andrew, additional, Coyne, Doyle, additional, Jansson, Linnea, additional, Rush, Miles, additional, Ennajdaoui, Hanane, additional, Katzman, Sol, additional, Bailey, Joanne, additional, Deinhardt, Katrin, additional, Sanchez-Elsner, Tilman, additional, and Sanford, Jeremy R., additional

Published
2016
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13. Splicing Factor TRA2B Is Required for Neural Progenitor Survival

Author

Roberts, Jacqueline M., Ennajdaoui, Hanane, Edmondson, Carina, Wirth, Brunhilde, Sanford, Jeremy R., Chen, Bin, Roberts, Jacqueline M., Ennajdaoui, Hanane, Edmondson, Carina, Wirth, Brunhilde, Sanford, Jeremy R., and Chen, Bin

Abstract

Alternative splicing of pre-mRNAs can rapidly regulate the expression of large groups of proteins. The RNA binding protein TRA2B (SFRS10) plays well-established roles in developmentally regulated alternative splicing during Drosophila sexual differentiation. TRA2B is also essential for mammalian embryogenesis and is implicated in numerous human diseases. Precise regulation of alternative splicing is critical to the development and function of the central nervous system; however, the requirements for specific splicing factors in neurogenesis are poorly understood. This study focuses on the role of TRA2B in mammalian brain development. We show that, during murine cortical neurogenesis, TRA2B is expressed in both neural progenitors and cortical projection neurons. Using cortex-specific Tra2b mutant mice, we show that TRA2B depletion results in apoptosis of the neural progenitor cells as well as disorganization of the cortical plate. Thus, TRA2B is essential for proper development of the cerebral cortex. (c) 2013 Wiley Periodicals, Inc.

Published
2014

15. In VivoDelivery of a CD20 CAR Using a CD8-Targeted Fusosome in Southern Pig-Tail Macaques (M. nemestrina) Results in B Cell Depletion

Author

Cunningham, Justine, Chandra, Sundeep, Emmanuel, Akinola, Mazzarelli, Allyse, Passaro, Carmela, Baldwin, Paige, Nguyen-McCarty, Michelle, Rocca, Carrie, Joyce, Shannon, Kim, Joohwan, Vagin, Vasily, Kaczmarek, James, Chavan, Hemant, Jewell, Heather, Lipsitz, Yonatan, Shamashkin, Misha, Hlavaty, Kelan, Rodriguez, Jason, Co, Carl, Cruite, Pattie, Ennajdaoui, Hanane, Duback, Victoria, Elman, Jess, Amatya, Shirisha, Harding, Caspian, Lyubinetsky, Sergey, Patel, Vidur, Pepper, Lauren, Ruzo, Albert, Iovino, Salvatore, Varghese, Bindu, Foster, Aaron E., Gorovits, Boris, Elpek, Kutlu, Laska, Michael, McGill, Trevor, Shah, Jagesh V, Fry, Terry J., and Dambach, Donna

Abstract

Introduction: Ex vivomanufactured chimeric antigen receptor (CAR) T cell therapies are highly effective for treating B cell malignancies. However, the complexity, cost and time required to manufacture CAR T cells limits access. To overcome conventional ex vivoCAR T limitations, a novel gene therapy platform has been developed that can deliver CAR transgenes directly to T cells through systemic administration of a fusosome, an engineered, target-directed novel paramyxovirus-based integrating vector that binds specific cell surface receptors for gene delivery through membrane fusion. Here, we demonstrate that systemic administration of a CD8a-targeted, integrating vector envelope (i.e., fusogen) encoding an anti-CD20 CAR into Southern pig-tail macaques (M. nemestrina), which is a species permissive to the integrating vector-mediated transduction, results in T cell transduction and B cell depletion with no treatment-related toxicities.

Published
2021
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