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Your search keyword '"Abdallah, Ali T."' showing total 26 results
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26 results on '"Abdallah, Ali T."'

1. LYN kinase programs stromal fibroblasts to facilitate leukemic survival via regulation of c-JUN and THBS1

Author

vom Stein, Alexander F., Rebollido-Rios, Rocio, Lukas, Anna, Koch, Maximilian, von Lom, Anton, Reinartz, Sebastian, Bachurski, Daniel, Rose, France, Bozek, Katarzyna, Abdallah, Ali T., Kohlhas, Viktoria, Saggau, Julia, Zölzer, Rebekka, Zhao, Yue, Bruns, Christiane, Bröckelmann, Paul J., Lohneis, Philipp, Büttner, Reinhard, Häupl, Björn, Oellerich, Thomas, Nguyen, Phuong-Hien, and Hallek, Michael

Published
2023
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3. Adult human kidney organoids originate from CD24+ cells and represent an advanced model for adult polycystic kidney disease

Author

Xu, Yaoxian, Kuppe, Christoph, Perales-Patón, Javier, Hayat, Sikander, Kranz, Jennifer, Abdallah, Ali T., Nagai, James, Li, Zhijian, Peisker, Fabian, Saritas, Turgay, Halder, Maurice, Menzel, Sylvia, Hoeft, Konrad, Kenter, Annegien, Kim, Hyojin, van Roeyen, Claudia R. C., Lehrke, Michael, Moellmann, Julia, Speer, Thimoteus, Buhl, Eva M., Hoogenboezem, Remco, Boor, Peter, Jansen, Jitske, Knopp, Cordula, Kurth, Ingo, Smeets, Bart, Bindels, Eric, Reinders, Marlies E. J., Baan, Carla, Gribnau, Joost, Hoorn, Ewout J., Steffens, Joachim, Huber, Tobias B., Costa, Ivan, Floege, Jürgen, Schneider, Rebekka K., Saez-Rodriguez, Julio, Freedman, Benjamin S., and Kramann, Rafael

Published
2022
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5. Single-cell RNA sequencing identifies a population of human liver-type ILC1s

Author

Krämer, Benjamin, Nalin, Ansel P., Ma, Feiyang, Eickhoff, Sarah, Lutz, Philipp, Leonardelli, Sonia, Goeser, Felix, Finnemann, Claudia, Hack, Gudrun, Raabe, Jan, ToVinh, Michael, Ahmad, Sarah, Hoffmeister, Christoph, Kaiser, Kim M., Manekeller, Steffen, Branchi, Vittorio, Bald, Tobias, Hölzel, Michael, Hüneburg, Robert, Nischalke, Hans Dieter, Semaan, Alexander, Langhans, Bettina, Kaczmarek, Dominik J., Benner, Brooke, Lordo, Matthew R., Kowalski, Jesse, Gerhardt, Adam, Timm, Jörg, Toma, Marieta, Mohr, Raphael, Türler, Andreas, Charpentier, Arthur, van Bremen, Tobias, Feldmann, Georg, Sattler, Arne, Kotsch, Katja, Abdallah, Ali T., Strassburg, Christian P., Spengler, Ulrich, Carson, William E., III, Mundy-Bosse, Bethany L., Pellegrini, Matteo, O’Sullivan, Timothy E., Freud, Aharon G., and Nattermann, Jacob

Published
2023
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8. Cyclin E1 and cyclin-dependent kinase 2 are critical for initiation, but not for progression of hepatocellular carcinoma

Author

Sonntag, Roland, Giebeler, Nives, Nevzorova, Yulia, Bangen, Jörg-Martín, Fahrenkamp, Dirk, Lambertz, Daniela, Haas, Ute, Hu, Wei, Gassler, Nikolaus, Cubero Palero, Francisco Javier, Müller-Newen, Gerhard, Abdallah, Ali T, Weiskirchen, Ralf, Ticconi, Fabio, Costa, Ivan G, Barbacid, Mariano, Trautwein, Christian, Liedtke, Christian, Sonntag, Roland, Giebeler, Nives, Nevzorova, Yulia, Bangen, Jörg-Martín, Fahrenkamp, Dirk, Lambertz, Daniela, Haas, Ute, Hu, Wei, Gassler, Nikolaus, Cubero Palero, Francisco Javier, Müller-Newen, Gerhard, Abdallah, Ali T, Weiskirchen, Ralf, Ticconi, Fabio, Costa, Ivan G, Barbacid, Mariano, Trautwein, Christian, and Liedtke, Christian

Abstract

E-type cyclins E1 (CcnE1) and E2 (CcnE2) are regulatory subunits of cyclin-dependent kinase 2 (Cdk2) and thought to control the transition of quiescent cells into the cell cycle. Initial findings indicated that CcnE1 and CcnE2 have largely overlapping functions for cancer development in several tumor entities including hepatocellular carcinoma (HCC). In the present study, we dissected the differential contributions of CcnE1, CcnE2, and Cdk2 for initiation and progression of HCC in mice and patients. To this end, we tested the HCC susceptibility in mice with constitutive deficiency for CcnE1 or CcnE2 as well as in mice lacking Cdk2 in hepatocytes. Genetic inactivation of CcnE1 largely prevented development of liver cancer in mice in two established HCC models, while ablation of CcnE2 had no effect on hepatocarcinogenesis. Importantly, CcnE1-driven HCC initiation was dependent on Cdk2. However, isolated primary hepatoma cells typically acquired independence on CcnE1 and Cdk2 with increasing progression in vitro, which was associated with a gene signature involving secondary induction of CcnE2 and up-regulation of cell cycle and DNA repair pathways. Importantly, a similar expression profile was also found in HCC patients with elevated CcnE2 expression and poor survival. In general, overall survival in HCC patients was synergistically affected by expression of CcnE1 and CcnE2, but not through Cdk2. Our study suggests that HCC initiation specifically depends on CcnE1 and Cdk2, while HCC progression requires expression of any E-cyclin, but no Cdk2., German Research Foundation, Ramón y Cajal Fellowship, Ministerio de Economía, Comercio y Empresa. Retos, Genomics Facility and by the Confocal Microscopy Facility of the Interdisciplinary Center for Clinical Research (IZKF), Faculty of Medicine at RWTH Aachen University, Depto. de Inmunología, Oftalmología y ORL, Fac. de Medicina, TRUE, pub

Published
2024

9. Revealing Genetic Dynamics: scRNA-seq Unravels Modifications in Human PDL Cells across In Vivo and In Vitro Environments.

Author

Abdallah, Ali T., Peitz, Michael, and Konermann, Anna

Subjects
*GENETIC profile, *PERIODONTAL ligament, *CELL populations, *CELL culture, *RNA sequencing, *CELL analysis
Abstract

The periodontal ligament (PDL) is a highly specialized fibrous tissue comprising heterogeneous cell populations of an intricate nature. These complexities, along with challenges due to cell culture, impede a comprehensive understanding of periodontal pathophysiology. This study aims to address this gap, employing single-cell RNA sequencing (scRNA-seq) technology to analyze the genetic intricacies of PDL both in vivo and in vitro. Primary human PDL samples (n = 7) were split for direct in vivo analysis and cell culture under serum-containing and serum-free conditions. Cell hashing and sorting, scRNA-seq library preparation using the 10x Genomics protocol, and Illumina sequencing were conducted. Primary analysis was performed using Cellranger, with downstream analysis via the R packages Seurat and SCORPIUS. Seven distinct PDL cell clusters were identified comprising different cellular subsets, each characterized by unique genetic profiles, with some showing donor-specific patterns in representation and distribution. Formation of these cellular clusters was influenced by culture conditions, particularly serum presence. Furthermore, certain cell populations were found to be inherent to the PDL tissue, while others exhibited variability across donors. This study elucidates specific genes and cell clusters within the PDL, revealing both inherent and context-driven subpopulations. The impact of culture conditions—notably the presence of serum—on cell cluster formation highlights the critical need for refining culture protocols, as comprehending these influences can drive the creation of superior culture systems vital for advancing research in PDL biology and regenerative therapies. These discoveries not only deepen our comprehension of PDL biology but also open avenues for future investigations into uncovering underlying mechanisms. [ABSTRACT FROM AUTHOR]

Published
2024
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11. Insight into the mechanism of AML del(9q) progression: hnRNP K targets the myeloid master regulators CEBPA (C/EBPα) and SPI1 (PU.1)

Author

Rahn, Kerstin, primary, Abdallah, Ali T., additional, Gan, Lin, additional, Herbrich, Shelley, additional, Sonntag, Roland, additional, Benitez, Oscar, additional, Malaney, Prerna, additional, Zhang, Xiaorui, additional, Rodriguez, Ashely G., additional, Brottem, Jared, additional, Marx, Gernot, additional, Brümmendorf, Tim H., additional, Ostareck, Dirk H., additional, Ostareck-Lederer, Antje, additional, Crysandt, Martina, additional, Post, Sean M., additional, and Naarmann-de Vries, Isabel S., additional

Published
2023
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13. Identification and characterization of a hepatic IL-13–producing ILC3-like population potentially involved in liver fibrosis

Author

Raabe, Jan, primary, Kaiser, Kim M., additional, ToVinh, Michael, additional, Finnemann, Claudia, additional, Lutz, Philipp, additional, Hoffmeister, Christoph, additional, Bischoff, Jenny, additional, Goeser, Felix, additional, Kaczmarek, Dominik J., additional, Glowka, Tim R., additional, Manekeller, Steffen, additional, Charpentier, Arthur, additional, Langhans, Bettina, additional, Nischalke, Hans Dieter, additional, Toma, Marieta, additional, Strassburg, Christian P., additional, Spengler, Ulrich, additional, Abdallah, Ali T., additional, Krämer, Benjamin, additional, and Nattermann, Jacob, additional

Published
2023
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17. Adult human kidney organoids originate from CD24+cells and represent an advanced model for adult polycystic kidney disease

Author

Xu, Yaoxian, Kuppe, Christoph, Perales-Patón, Javier, Hayat, Sikander, Kranz, Jennifer, Abdallah, Ali T., Nagai, James, Li, Zhijian, Peisker, Fabian, Saritas, Turgay, Halder, Maurice, Menzel, Sylvia, Hoeft, Konrad, Kenter, Annegien, Kim, Hyojin, van Roeyen, Claudia R. C., Lehrke, Michael, Moellmann, Julia, Speer, Thimoteus, Buhl, Eva M., Hoogenboezem, Remco, Boor, Peter, Jansen, Jitske, Knopp, Cordula, Kurth, Ingo, Smeets, Bart, Bindels, Eric, Reinders, Marlies E. J., Baan, Carla, Gribnau, Joost, Hoorn, Ewout J., Steffens, Joachim, Huber, Tobias B., Costa, Ivan, Floege, Jürgen, Schneider, Rebekka K., Saez-Rodriguez, Julio, Freedman, Benjamin S., and Kramann, Rafael

Abstract

Adult kidney organoids have been described as strictly tubular epithelia and termed tubuloids. While the cellular origin of tubuloids has remained elusive, here we report that they originate from a distinct CD24+epithelial subpopulation. Long-term-cultured CD24+cell-derived tubuloids represent a functional human kidney tubule. We show that kidney tubuloids can be used to model the most common inherited kidney disease, namely autosomal dominant polycystic kidney disease (ADPKD), reconstituting the phenotypic hallmark of this disease with cyst formation. Single-cell RNA sequencing of CRISPR–Cas9 gene-edited PKD1-and PKD2-knockout tubuloids and human ADPKD and control tissue shows similarities in upregulation of disease-driving genes. Furthermore, in a proof of concept, we demonstrate that tolvaptan, the only approved drug for ADPKD, has a significant effect on cyst size in tubuloids but no effect on a pluripotent stem cell-derived model. Thus, tubuloids are derived from a tubular epithelial subpopulation and represent an advanced system for ADPKD disease modeling.

Published
2022
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18. Bioavailability and impacts of estrogenic compounds from suspended sediment on rainbow trout (Oncorhynchus mykiss)

Author

Müller, Anne-Katrin, primary, Markert, Nele, additional, Leser, Katharina, additional, Kämpfer, David, additional, Schiwy, Sabrina, additional, Riegraf, Carolin, additional, Buchinger, Sebastian, additional, Gan, Lin, additional, Abdallah, Ali T., additional, Denecke, Bernd, additional, Segner, Helmut, additional, Brinkmann, Markus, additional, Crawford, Sarah E., additional, and Hollert, Henner, additional

Published
2021
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20. Myeloid cells in liver and bone marrow acquire a functionally distinct inflammatory phenotype during obesity-related steatohepatitis

Author

Krenkel, Oliver, primary, Hundertmark, Jana, additional, Abdallah, Ali T, additional, Kohlhepp, Marlene, additional, Puengel, Tobias, additional, Roth, Tilmann, additional, Branco, Diogo Philippini Pontual, additional, Mossanen, Jana C, additional, Luedde, Tom, additional, Trautwein, Christian, additional, Costa, Ivan G, additional, and Tacke, Frank, additional

Published
2019
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21. Role of hnRNP K and Interacting mRNAs in Pathogenesis of AML with 9q Deletion

Author

Rahn, Kerstin, primary, Naarmann-de Vries, Isabel, additional, Sackmann, Yvonne, additional, Klein, Felicitas, additional, Ostareck-Lederer, Antje, additional, Ostareck, Dirk, additional, Jost, Edgar, additional, Abdallah, Ali T, additional, Denecke, Bernd, additional, Gan, Lin, additional, Ehninger, Gerhard, additional, Brümmendorf, Tim H, additional, Marx, Gernot, additional, Rollig, Christoph, additional, Thiede, Christian, additional, and Crysandt, Martina, additional

Published
2018
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22. Myeloid cells in liver and bone marrow acquire a functionally distinct inflammatory phenotype during obesity-related steatohepatitis.

Author

Krenkel, Oliver, Hundertmark, Jana, Abdallah, Ali T., Kohlhepp, Marlene, Puengel, Tobias, Roth, Tilmann, Branco, Diogo Philippini Pontual, Mossanen, Jana C., Luedde, Tom, Trautwein, Christian, Costa, Ivan G., and Tacke, Frank

Subjects
BONE marrow cells, CALPROTECTIN, LECTINS, ADVANCED glycation end-products, LIVER cells, METHIONINE sulfoxide reductase, NF-kappa B
Published
2020
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23. Therapeutic inhibition of inflammatory monocyte recruitment reduces steatohepatitis and liver fibrosis

Author

Krenkel, Oliver, primary, Puengel, Tobias, additional, Govaere, Olivier, additional, Abdallah, Ali T., additional, Mossanen, Jana C., additional, Kohlhepp, Marlene, additional, Liepelt, Anke, additional, Lefebvre, Eric, additional, Luedde, Tom, additional, Hellerbrand, Claus, additional, Weiskirchen, Ralf, additional, Longerich, Thomas, additional, Costa, Ivan G., additional, Anstee, Quentin M., additional, Trautwein, Christian, additional, and Tacke, Frank, additional

Published
2018
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24. CoNCoS: Copy number estimation in cancer with controlled support

Author

Abdallah, Ali T., Fischer, Matthias, Nuernberg, Peter, Nothnagel, Michael, Frommolt, Peter, Abdallah, Ali T., Fischer, Matthias, Nuernberg, Peter, Nothnagel, Michael, and Frommolt, Peter

Abstract

Somatic copy number (CN) alterations are major drivers of tumorigenesis and growth. Although next-generation sequencing (NGS) technologies enable a deep genomic analysis of cancers, the analysis of the data remains subject to biases and multiple sources of error, including varying local read coverage. The currently existing algorithms for NGS-based detection of CN abberations do not incorporate information on the local coverage quality. We have developed a new algorithm, copy number estimation with controlled support (CoNCoS) that increases the accuracy of CN estimation in paired tumor/normal exome sequencing data sets by assessing and optimizing the support for a site-specific CN estimate. We show by simulations and in a benchmarking study against single nucleotide polymorphism (SNP) microarray data that our approach outperforms the commonly used methods CNAnorm and VarScan2. Our algorithm is suitable to increase the accuracy of somatic CN analysis by a support-optimized estimation approach.

Published
2015

26. Cognate recognition of microbial antigens defines constricted CD4 + T cell receptor repertoires in the inflamed colon.

Author

Muschaweck M, Kopplin L, Ticconi F, Schippers A, Iljazovic A, Gálvez EJC, Abdallah AT, Wagner N, Costa IG, Strowig T, and Pabst O

Subjects
Adoptive Transfer, Biomarkers, Colitis pathology, Colitis therapy, Disease Management, Disease Susceptibility, Humans, T-Lymphocyte Subsets immunology, T-Lymphocyte Subsets metabolism, CD4-Positive T-Lymphocytes immunology, CD4-Positive T-Lymphocytes metabolism, Colitis etiology, Colitis metabolism, Gastrointestinal Microbiome immunology, Host-Pathogen Interactions immunology, Receptors, Antigen, T-Cell metabolism
Abstract

Key aspects of intestinal T cells, including their antigen specificity and their selection by the microbiota and other intestinal antigens, as well as the contribution of individual T cell clones to regulatory and effector functions, remain unresolved. Here we tracked adoptively transferred T cell populations to specify the interrelation of T cell receptor repertoire and the gut antigenic environment. We show that dominant TCRα clonotypes were shared between interferon-γ- and interleukin-17-producing but not regulatory Foxp3 + T cells. Identical TCRα clonotypes accumulated in the colon of different individuals, whereas antibiotics or defined colonization correlated with the expansion of distinct expanded T cell clonotypes. Our results demonstrate key aspects of intestinal CD4 + T cell activation and suggest that few microbial species exert a dominant effect on the intestinal T cell repertoire during colitis. We speculate that dominant proinflammatory T cell clones might provide a therapeutic target in human inflammatory bowel disease., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2021 The Authors. Published by Elsevier Inc. All rights reserved.)

Published
2021
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