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104. Microbiota, not host origin drives ex vivo intestinal epithelial responses

Author

Arnauts, Kaline, Sudhakar, Padhmanand, Verstockt, Sare, Lapierre, Cynthia, Potche, Selina, Caenepeel, Clara, Verstockt, Bram, Raes, Jeroen, Vermeire, Séverine, Sabino, João, Verfaillie, Catherine, and Ferrante, Marc

Subjects
Microbiology (medical), Microbiota, Gastroenterology, Inflammatory Bowel Diseases, digestive system, Microbiology, epithelial cells, Gastrointestinal Microbiome, Infectious Diseases, Ulcerative colitis, RNA, Ribosomal, 16S, Dysbiosis, Humans, Colitis, Ulcerative, Intestinal Mucosa, organoids
Abstract

Microbial dysbiosis is an established finding in patients with inflammatory bowel disease (IBD), but host-microbial interactions are poorly understood. We aimed to unravel the effect of microbiota exposure on intestinal epithelial cells. Confluent Transwell® organoid monolayers of eight UC patients and eight non-IBD controls were co-cultured for six hours with microbiota (3x108 cells) of UC patients or a healthy volunteer (HV), in the presence or absence of an inflammatory cytokine mix. Transepithelial electrical resistance (TEER), fluorescein isothiocyanate (FITC) dextran measurements, and RNA sequencing were performed on epithelial cells, and 16S rRNA sequencing on microbiota samples before and after co-culture. Transcriptomic response following microbiota exposure was not different between epithelial cells from UC patients or non-IBD controls. Following UC microbiota exposure, but not HV microbiota, a strong decrease in epithelial barrier integrity was observed in both UC and HV epithelial cells by TEER and FITC dextran measurements. Exposure of inflamed epithelium to UC microbiota induced transcriptomic stress pathways including activation of EGR1, MAPK and JAK/STAT signaling, as well as AP-1 family and FOSL transcripts. Stress responses after HV microbiota stimulation were milder. We conclude that not the epithelial cell origin (UC versus non-IBD) but the microbial donor drives transcriptomic responses, as exposure to UC microbiota was sufficient to induce stress responses in all epithelial cells. Further research on therapies to restore the microbial balance, to remove the constant trigger of dysbiosis, is required. ispartof: GUT MICROBES vol:14 issue:1 ispartof: location:United States status: Published online

Published
2022
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105. Hipsc-derived hepatocyte-like cells can be used as a model for transcriptomics-based study of chemical toxicity

Author

Ghosh, Sreya, De Smedt, Jonathan, Tricot, Tine, Proença, Susana, Kumar, Manoj, Nami, Fatemeharefeh, Vanwelden, Thomas, Vidal, Niels, Jennings, Paul, Kramer, Nynke I., Verfaillie, Catherine M., Ghosh, Sreya, De Smedt, Jonathan, Tricot, Tine, Proença, Susana, Kumar, Manoj, Nami, Fatemeharefeh, Vanwelden, Thomas, Vidal, Niels, Jennings, Paul, Kramer, Nynke I., and Verfaillie, Catherine M.

Abstract

Traditional toxicity risk assessment approaches have until recently focussed mainly on histochemical readouts for cell death. Modern toxicology methods attempt to deduce a mechanistic understanding of pathways involved in the development of toxicity, by using transcriptomics and other big data-driven methods such as high-content screening. Here, we used a recently described optimised method to differentiate human induced pluripotent stem cells (hiPSCs) to hepatocyte-like cells (HLCs), to assess their potential to classify hepatotoxic and non-hepatotoxic chemicals and their use in mechanistic toxicity studies. The iPSC-HLCs could accurately classify chemicals causing acute hepatocellular injury, and the transcriptomics data on treated HLCs obtained by TempO-Seq technology linked the cytotoxicity to cellular stress pathways, including oxidative stress and unfolded protein response (UPR). Induction of these stress pathways in response to amiodarone, diclofenac, and ibuprofen, was demonstrated to be concentration and time dependent. The transcriptomics data on diclofenac-treated HLCs were found to be more sensitive in detecting differentially expressed genes in response to treatment, as compared to existing datasets of other diclofenac-treated in vitro hepatocyte models. Hence iPSC-HLCs generated by transcription factor overexpression and in metabolically optimised medium appear suitable for chemical toxicity detection as well as mechanistic toxicity studies.

Published
2022

108. Mesodermal iPSC-derived progenitor cells functionally regenerate cardiac and skeletal muscle

Author

Quattrocelli, Mattia, Swinnen, Melissa, Giacomazzi, Giorgia, Camps, Jordi, Barthelemy, Ines, Ceccarelli, Gabriele, Caluwe, Ellen, Grosemans, Hanne, Thorrez, Lieven, Pelizzo, Gloria, Muijtjens, Manja, Verfaillie, Catherine M., Blot, Stephane, Janssens, Stefan, and Sampaolesi, Maurilio

Subjects
Medical research, Medicine, Experimental, Muscles -- Regeneration, Stem cells -- Health aspects, Cell differentiation -- Health aspects, Health care industry
Abstract

Conditions such as muscular dystrophies (MDs) that affect both cardiac and skeletal muscles would benefit from therapeutic strategies that enable regeneration of both of these striated muscle types. Protocols have been developed to promote induced pluripotent stem cells (iPSCs) to differentiate toward cardiac or skeletal muscle; however, there are currently no strategies to simultaneously target both muscle types. Tissues exhibit specific epigenetic alterations; therefore, source-related lineage biases have the potential to improve iPSC-driven multilineage differentiation. Here, we determined that differential myogenic propensity influences the commitment of isogenic iPSCs and a specifically isolated pool of mesodermal iPSC-derived progenitors (MiPs) toward the striated muscle lineages. Differential myogenic propensity did not influence pluripotency, but did selectively enhance chimerism of MiP-derived tissue in both fetal and adult skeletal muscle. When injected into dystrophic mice, MiPs engrafted and repaired both skeletal and cardiac muscle, reducing functional defects. Similarly, engraftment into dystrophic mice of canine MiPs from dystrophic dogs that had undergone TALEN-mediated correction of the MD-associated mutation also resulted in functional striatal muscle regeneration. Moreover, human MiPs exhibited the same capacity for the dual differentiation observed in murine and canine MiPs. The findings of this study suggest that MiPs should be further explored for combined therapy of cardiac and skeletal muscles., Introduction Induced pluripotent stem cells (iPSCs) represent a promising contribution to regenerative medicine (1). Despite the regulatory hurdles and safety issues involved, reprogramming patients' cells into iPSCs for autologous cell [...]

Published
2015
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113. Rectal Organoid Morphology Analysis (ROMA): A Diagnostic Assay in Cystic Fibrosis

Author

Cuyx, Senne, primary, Ramalho, Anabela S., primary, Corthout, Nikky, primary, Fieuws, Steffen, primary, Fürstová, Eva, primary, Arnauts, Kaline, primary, Ferrante, Marc, primary, Verfaillie, Catherine, primary, Munck, Sebastian, primary, Boon, Mieke, primary, Proesmans, Marijke, primary, Dupont, Lieven, primary, De Boeck, Kris, primary, and Vermeulen, François, primary

Published
2022
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114. Tu1485: EXPOSURE TO MICROBIOTA FROM ULCERATIVE COLITIS PATIENTS IS INDUCING STRESS RESPONSES IN EPITHELIAL CELLS

Author

Arnauts, Kaline, primary, Sudhakar, Padhmanand, additional, Verstockt, Sare, additional, Lapierre, Cynthia, additional, Potche, Selina, additional, Caenepeel, Clara, additional, Verstockt, Bram, additional, Raes, Jeroen, additional, Vermeire, Séverine, additional, Sabino, João, additional, Verfaillie, Catherine, additional, and Ferrante, Marc, additional

Published
2022
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115. List of Contributors

Author

Ascheim, Deborah D., primary, Balkan, Wayne, additional, Bareja, Akshay, additional, Bartlett, Courtney E., additional, Behfar, Atta, additional, Blackbourn, Lisle, additional, Bolli, Roberto, additional, Buja, L. Maximilian, additional, Castellanos, Angela, additional, Chaanine, Antoine H., additional, Chau, Eric, additional, Chen, Zhen, additional, Christman, Karen L., additional, Chung, Amy, additional, Cole, Robert M., additional, Cooke, John P., additional, Duckers, H.J., additional, Dzau, Victor J., additional, Ebert, Ray F., additional, Fujita, Jun, additional, Fukuda, Keiichi, additional, Gaetani, Roberto, additional, Gahremanpour, Amir, additional, Gathier, W., additional, Gelijns, Annetine C., additional, Gobin, Andrea S., additional, Gomez, José A., additional, Hajjar, Roger J., additional, Hare, Joshua M., additional, Hariharan, Nirmala, additional, Henry, Timothy D., additional, Hiesinger, William, additional, Hirsch, Alan T., additional, Hodgkinson, Conrad P., additional, Hong, Kimberly N., additional, Hong, Kyung U., additional, Ichim, Thomas E., additional, Jolicoeur, E. Marc, additional, Kodo, Kazuki, additional, Krishnan, Sandeep K., additional, Kutryk, Michael J.B., additional, Lee, David S., additional, Lee, Randall J., additional, Losordo, Douglas W., additional, Migliati, Elton, additional, Miller, Leslie W., additional, Misra, Vivek, additional, Moyé, Lem, additional, Nguyen, Nathalie, additional, Ong, Sang-Ging, additional, Orozco, Aaron, additional, Patel, Amit N., additional, Penn, Brittany M., additional, Penn, Marc S., additional, Perin, Emerson C., additional, Raval, Amish N., additional, Resende, Micheline, additional, Roelandt, Philip R., additional, Roobrouck, Valerie D., additional, Sampaio, Luiz C., additional, Savitz, Sean I., additional, Schmuck, Eric G., additional, Schulman, Ivonne Hernandez, additional, Simari, Robert D., additional, Smidt, Luis Felipe Silva, additional, Smith, Rachel Ruckdeschel, additional, Stewart, Duncan J., additional, Sussman, Mark A., additional, Swaminath, Deephak, additional, Taldone, Sabrina, additional, Taylor, Doris A., additional, Terzic, Andre, additional, Traverse, Jay H., additional, Türktaş, Z., additional, Ungerleider, Jessica, additional, Vela, Deborah, additional, Verfaillie, Catherine M., additional, Vrtovec, Bojan, additional, Weber, Thomas, additional, Woo, Y. Joseph, additional, Willerson, James T., additional, Wu, Joseph C., additional, Yaroshinsky, Alex, additional, Zangi, Lior, additional, and Zhang, Jianyi (Jay), additional

Published
2016
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118. Loss or Inhibition of Stromal-Derived PlGF Prolongs Survival of Mice with Imatinib-Resistant Bcr-Abl1 + Leukemia

Author

Schmidt, Thomas, Masouleh, Behzad Kharabi, Loges, Sonja, Cauwenberghs, Sandra, Fraisl, Peter, Maes, Christa, Jonckx, Bart, De Keersmaecker, Kim, Kleppe, Maria, Tjwa, Marc, Schenk, Thomas, Vinckier, Stefan, Fragoso, Rita, De Mol, Maria, Beel, Karolien, Dias, Sérgio, Verfaillie, Catherine, Clark, Richard E., Brümmendorf, Tim H., Vandenberghe, Peter, Rafii, Shahin, Holyoake, Tessa, Hochhaus, Andreas, Cools, Jan, Karin, Michael, Carmeliet, Geert, Dewerchin, Mieke, and Carmeliet, Peter

Published
2011
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124. A Novel UPLC-MS Metabolomic Analysis-Based Strategy to Monitor the Course and Extent of iPSC Differentiation to Hepatocytes

Author

Moreno-Torres, Marta, primary, Kumar, Manoj, additional, García-Llorens, Guillem, additional, Quintás, Guillermo, additional, Tricot, Tine, additional, Boon, Ruben, additional, Tolosa, Laia, additional, Toprakhisar, Burak, additional, Chesnais, Francois, additional, Verfaillie, Catherine, additional, and Castell, José V., additional

Published
2022
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129. A FACILE METHOD TO GENERATE CEREBRAL ORGANOIDS FROM HUMAN PLURIPOTENT STEM CELLS.

Author

Simorgh, Susan, Mousavi, Seyed Ahmad, To, San Kit, Pasque, Vincent, Wierda, Keimpe, Vervliet, Tim, Yeganeh, Meghdad, Pooyan, Paria, Chai, Yoke Chin, Verfaillie, Catherine, and Baharvand, Hossein

Subjects
HUMAN stem cells, NEUROGLIA, ORGANOIDS, PLURIPOTENT stem cells, NEURAL development, CELL culture
Abstract

Human cerebral organoids (COs) are self-organizing three-dimensional (3D) neural structures that provide a human-specific platform to study the cellular and molecular processes that underlie different neurological events. The first step of CO generation from human pluripotent stem cells (hPSCs) is neural induction, which is an in vitro simulation of neural ectoderm development. Several signaling pathways cooperate during neural ectoderm development and in vitro differentiation of hPSCs toward neural cell lineages is also affected by them. In this study, we considered some of the known sources of these variable signaling cues arising from cell culture media components and sought to modulate their effects by applying a comprehensive combination of small molecules and growth factors for CO generation. Histological analysis demonstrated that these COs recapitulate the neural progenitor zone and early cortical layer organization, containing different types of neuronal and glial cells which was in accordance with single-nucleus transcriptome profiling results. Moreover, patch clamp and intracellular Ca2+ dynamic studies demonstrated that the COs behave as a functional neural network. Thus, this method serves as a facile protocol for generating hPSC-derived COs that faithfully mimic the features of their in vivo counterparts in the developing human brain. [ABSTRACT FROM AUTHOR]

Published
2023
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134. List of Contributors

Author

Addis, Russell C., primary, Anversa, Piero, additional, Arcidiacono, Judith, additional, Atala, Anthony, additional, Axelman, Joyce, additional, Batra, Ashok, additional, Blau, Helen M., additional, Bonner-Weir, Susan, additional, Brittan, Mairi, additional, Broxmeyer, Hal E., additional, Cananzi, Mara, additional, Cepko, Constance, additional, Cheng, Tao, additional, Chuva de Sousa Lopes, Susana M., additional, Clark, Gregory O., additional, Colehour, Maegen, additional, de Coppi, Paolo, additional, Cossu, Giulio, additional, Daley, George Q., additional, Dang, Jiyoung M., additional, Direkze, Natalie, additional, Dor, Yuval, additional, Dressler, Gregory R., additional, Durfor, Charles N., additional, Ellis, Ewa C.S., additional, Evans, Martin, additional, Fekete, Donna M., additional, Fink, Donald, additional, Fuchs, Elaine, additional, Fuller, Margaret T., additional, Gardner, Richard L., additional, Gazit, Zulma, additional, Gazit, Dan, additional, Gearhart, John D., additional, Goldberg, Victor M., additional, Gonzalez, Rodolfo, additional, Grayeski, Deborah Lavoie, additional, Green, Ronald M., additional, Grompe, Markus, additional, Hilbert, Stephen L., additional, Horb, Marko E., additional, Huang, Jerry I., additional, Imitola, Jaimie, additional, Jones, D. Leanne, additional, Kajstura, Jan, additional, Kaplan, David S., additional, Kaur, Pritinder, additional, Kent, Kathleen C., additional, Kerr, Candace L., additional, Khademhosseini, Ali, additional, Kimelman, Nadav, additional, Klimanskaya, Irina, additional, Kraszewski, Jennifer N., additional, LaBarge, Mark A., additional, Langer, Robert, additional, Lanza, Robert, additional, Lazarus, Ellen, additional, Lee, Jean Pyo, additional, Lee, Mark H., additional, Leri, Annarosa, additional, Levenberg, Shulamit, additional, Levine, S. Robert, additional, Littlefield, John W., additional, McFarland, Richard, additional, McMahon, Jill, additional, Melton, Douglas A., additional, Moore, Mary Tyler, additional, Mueller, Franz-Josef, additional, Mummery, Christine L., additional, Nadal-Ginard, Bernardo, additional, Niwa, Hitoshi, additional, Okita, Keisuke, additional, Ourednik, Jitka, additional, Ourednik, Vaclav, additional, Park, Kook I., additional, Patterson, Ethan S., additional, Pelled, Gadi, additional, Potten, Christopher S., additional, Preston, Sean, additional, Roelandt, Philip R., additional, Roobrouck, Valerie D., additional, Rosenthal, Nadia, additional, Rossant, Janet, additional, Sampaolesi, Maurilio, additional, Santini, Maria Paola, additional, Scadden, David T., additional, Schlüter, Holger, additional, Schuch, Gunter, additional, Shamblott, Michael J., additional, Sheyn, Dima, additional, Sidman, Richard L., additional, Snyder, Evan Y., additional, Soker, Shay, additional, Strom, Stephen C., additional, Studer, Lorenz, additional, Surani, M. Azim, additional, Tedesco, Francesco Saverio, additional, Teng, Yang D., additional, Tosh, David, additional, Trounson, Alan, additional, Tumbar, Tudorita, additional, Upjohn, Edward, additional, Varigos, George, additional, Verfaillie, Catherine M., additional, Wang, Zhan, additional, Weir, Gordon C., additional, Whittlesey, Kevin J., additional, Williams, J. Koudy, additional, Wilson, James W., additional, Witten, Celia, additional, Wright, Nicholas A., additional, Yamanaka, Shinya, additional, and Yoo, Jung U., additional

Published
2014
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137. Fluorescent tagging of endogenous Heme oxygenase-1 in human induced pluripotent stem cells for high content imaging of oxidative stress in various differentiated lineages

Author

Snijders, Kirsten E., primary, Fehér, Anita, additional, Táncos, Zsuzsanna, additional, Bock, István, additional, Téglási, Annamária, additional, van den Berk, Linda, additional, Niemeijer, Marije, additional, Bouwman, Peter, additional, Le Dévédec, Sylvia E., additional, Moné, Martijn J., additional, Van Rossom, Rob, additional, Kumar, Manoj, additional, Wilmes, Anja, additional, Jennings, Paul, additional, Verfaillie, Catherine M., additional, Kobolák, Julianna, additional, ter Braak, Bas, additional, Dinnyés, András, additional, and van de Water, Bob, additional

Published
2021
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142. MMP2 Modulates Inflammatory Response during Axonal Regeneration in the Murine Visual System

Author

Andries, Lien, primary, Masin, Luca, additional, Salinas-Navarro, Manuel, additional, Zaunz, Samantha, additional, Claes, Marie, additional, Bergmans, Steven, additional, Brouwers, Véronique, additional, Lefevere, Evy, additional, Verfaillie, Catherine, additional, Movahedi, Kiavash, additional, De Groef, Lies, additional, and Moons, Lieve, additional

Published
2021
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144. Fast and efficient generation of oligodendrocytes from human induced pluripotent stem cells (hiPSCs)

Author

García León, Juan Antonio, Cáceres Palomo, Laura, Davila, Jose Carlos, Vitorica, Javier, Verfaillie, Catherine, and Gutierrez-Perez, Antonia

Subjects
iPSC, nervous system, Oligodendrocytes, Alzheimer, Neuroglia
Abstract

Acknowledgments: This study was supported by Instituto de Salud Carlos III (ISCiii) of Spain, co-financed by FEDER funds from European Union, through grants PI18/01557 (to AG), PI18/01556 (to JV), and CIBERNED (CB06/05/1116 to AG and CB06/05/0094 to JV); by Junta de Andalucia through Consejería de Economía y Conocimiento grants UMA18-FEDERJA-211 (to AG), PY18-RT-2233 (to AG) and US-1262734 (to JV) co-financed by Programa Operativo FEDER 2014-2020 and Consejeria de Salud grant PI-0276-2018 (to JAGL). Oligodendrocytes (OLs) are highly specialized cells of the central nervous system responsible for myelin production and metabolic support of neurons. Defects in OLs are crucial in several neurodegenerative diseases including multiple sclerosis (MS) and amyotrophic lateral sclerosis (ALS). Scarce access to primary samples and lack of efficient protocols to generate OLs from human pluripotent stem cells (hPSCs) are hampering our understanding of OL biology and the development of novel therapies. To promote the conversion of hPSCs into OLs, we have screened for a number of transcription factors (TFs) previously reported to be involved in OL generation. We found that the overexpression of SOX10 was sufficient to generate O4+ oligodendrocyte precursor cells (OPCs) from hPSCs only 10 days after SOX10 induction. Generated OPCs expressed mature OL proteins as MBP or MOG. At the transcriptome level, generated OPCs resembled primary OPCs. To test the functionality of generated OPCs, O4+ cells were co-cultured together with neurons, finding that O4+ cells were able to myelinate the neurons. Moreover, O4+ cells were injected intracerebrally in newborn shiverer RAG2-/- mice, finding that generated OLs extended within the corpus callosum and generated functional myelin, demonstrating the functionality of generated cells also in vivo. The protocol also describes an alternative for viral transduction, by incorporating an inducible SOX10 in the safe harbor locus AAVS1, yielding ~100% pure OPCs. O4+ OPCs can be co-cultured with maturing hPSC-derived neurons in 96/384-well- format plates, allowing the screening of pro-myelinating compounds. We have developed a novel methodology for a fast (20 days from hPSC stage) and efficient generation of functional OLs, which allow testing of compounds involved in myelination. This technology will allow further studies to better understand human OL biology and the screening of potential compounds involved in myelination in a human setting. Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech.

Published
2021

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