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13 results on '"Saftien, Aurelia"'

1. Metagenome-informed metaproteomics of the human gut microbiome, host, and dietary exposome uncovers signatures of health and inflammatory bowel disease

Author

Valdés-Mas, Rafael, Leshem, Avner, Zheng, Danping, Cohen, Yotam, Kern, Lara, Zmora, Niv, He, Yiming, Katina, Corine, Eliyahu-Miller, Shimrit, Yosef-Hevroni, Tal, Richman, Liron, Raykhel, Barbara, Allswang, Shira, Better, Reut, Shmueli, Merav, Saftien, Aurelia, Cullin, Nyssa, Slamovitz, Fernando, Ciocan, Dragos, Ouyang, Kyanna S., Mor, Uria, Dori-Bachash, Mally, Molina, Shahar, Levin, Yishai, Atarashi, Koji, Jona, Ghil, Puschhof, Jens, Harmelin, Alon, Stettner, Noa, Chen, Minhu, Suez, Jotham, Honda, Kenya, Lieb, Wolfgang, Bang, Corinna, Kori, Michal, Maharshak, Nitsan, Merbl, Yifat, Shibolet, Oren, Halpern, Zamir, Shouval, Dror S., Shamir, Raanan, Franke, Andre, Abdeen, Suhaib K., Shapiro, Hagit, Savidor, Alon, and Elinav, Eran

Published
2025
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4. High-Resolution mRNA and Secretome Atlas of Human Enteroendocrine Cells

Author

Beumer, Joep, Puschhof, Jens, Bauzá-Martinez, Julia, Martínez-Silgado, Adriana, Elmentaite, Rasa, James, Kylie R., Ross, Alexander, Hendriks, Delilah, Artegiani, Benedetta, Busslinger, Georg A., Ponsioen, Bas, Andersson-Rolf, Amanda, Saftien, Aurelia, Boot, Charelle, Kretzschmar, Kai, Geurts, Maarten H., Bar-Ephraim, Yotam E., Pleguezuelos-Manzano, Cayetano, Post, Yorick, Begthel, Harry, van der Linden, Franka, Lopez-Iglesias, Carmen, van de Wetering, Willine J., van der Linden, Reinier, Peters, Peter J., Heck, Albert J.R., Goedhart, Joachim, Snippert, Hugo, Zilbauer, Matthias, Teichmann, Sarah A., Wu, Wei, and Clevers, Hans

Published
2020
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5. Improved detection of colibactin-induced mutations by genotoxic E. coli in organoids and colorectal cancer

Author

CMM Groep Van Mil, CMM, Cancer, Hubrecht Institute with UMC, Rosendahl Huber, Axel, Pleguezuelos-Manzano, Cayetano, Puschhof, Jens, Ubels, Joske, Boot, Charelle, Saftien, Aurelia, Verheul, Mark, Trabut, Laurianne T., Groenen, Niels, van Roosmalen, Markus, Ouyang, Kyanna S., Wood, Henry, Quirke, Phil, Meijer, Gerrit, Cuppen, Edwin, Clevers, Hans, van Boxtel, Ruben, CMM Groep Van Mil, CMM, Cancer, Hubrecht Institute with UMC, Rosendahl Huber, Axel, Pleguezuelos-Manzano, Cayetano, Puschhof, Jens, Ubels, Joske, Boot, Charelle, Saftien, Aurelia, Verheul, Mark, Trabut, Laurianne T., Groenen, Niels, van Roosmalen, Markus, Ouyang, Kyanna S., Wood, Henry, Quirke, Phil, Meijer, Gerrit, Cuppen, Edwin, Clevers, Hans, and van Boxtel, Ruben

Published
2024

8. Colon Tumors in Enterotoxigenic Bacteroides fragilis (ETBF)-Colonized Mice Do Not Display a Unique Mutational Signature but Instead Possess Host-Dependent Alterations in the APC Gene

Author

Allen, Jawara, Rosendahl Huber, Axel, Pleguezuelos-Manzano, Cayetano, Puschhof, Jens, Wu, Shaoguang, Wu, Xinqun, Boot, Charelle, Saftien, Aurelia, O'Hagan, Heather M, Wang, Hao, van Boxtel, Ruben, Clevers, Hans, Sears, Cynthia L, Allen, Jawara, Rosendahl Huber, Axel, Pleguezuelos-Manzano, Cayetano, Puschhof, Jens, Wu, Shaoguang, Wu, Xinqun, Boot, Charelle, Saftien, Aurelia, O'Hagan, Heather M, Wang, Hao, van Boxtel, Ruben, Clevers, Hans, and Sears, Cynthia L

Abstract

Enterotoxigenic Bacteroides fragilis (ETBF) is consistently found at higher frequency in individuals with sporadic and hereditary colorectal cancer (CRC) and induces tumorigenesis in several mouse models of CRC. However, whether specific mutations induced by ETBF lead to colon tumor formation has not been investigated. To determine if ETBF-induced mutations impact the Apc gene, and other tumor suppressors or proto-oncogenes, we performed whole-exome sequencing and whole-genome sequencing on tumors isolated after ETBF and sham colonization of Apcmin/+ and Apcmin/+Msh2fl/flVC mice, as well as whole-genome sequencing of organoids cocultured with ETBF. Our results indicate that ETBF-induced tumor formation results from loss of heterozygosity (LOH) of Apc, unless the mismatch repair system is disrupted, in which case, tumor formation results from new acquisition of protein-truncating mutations in Apc. In contrast to polyketide synthase-positive Escherichia coli (pks+ E. coli), ETBF does not produce a unique mutational signature; instead, ETBF-induced tumors arise from errors in DNA mismatch repair and homologous recombination DNA damage repair, established pathways of tumor formation in the colon, and the same genetic mechanism accounting for sham tumors in these mouse models. Our analysis informs how this procarcinogenic bacterium may promote tumor formation in individuals with inherited predispositions to CRC, such as Lynch syndrome or familial adenomatous polyposis (FAP). IMPORTANCE Many studies have shown that microbiome composition in both the mucosa and the stool differs in individuals with sporadic and hereditary colorectal cancer (CRC). Both human and mouse models have established a strong association between particular microbes and colon tumor induction. However, the genetic mechanisms underlying putative microbe-induced colon tumor formation are not well established. In this paper, we applied whole-exome sequencing and whole-genome sequencing to investigate

Published
2022

9. Colon Tumors in Enterotoxigenic Bacteroides fragilis (ETBF)Colonized Mice Do Not Display a Unique Mutational Signature but Instead Possess Host-Dependent Alterations in the APC Gene

Author

CMM, Cancer, Hubrecht Institute with UMC, Allen, Jawara, Huber, Axel Rosendahl, Pleguezuelos-Manzano, Cayetano, Puschhof, Jens, Wu, Shaoguang, Wu, Xinqun, Boot, Charelle, Saftien, Aurelia, O’Hagan, Heather M., Wang, Hao, van Boxtel, Ruben, Clevers, Hans, Sears, Cynthia L., CMM, Cancer, Hubrecht Institute with UMC, Allen, Jawara, Huber, Axel Rosendahl, Pleguezuelos-Manzano, Cayetano, Puschhof, Jens, Wu, Shaoguang, Wu, Xinqun, Boot, Charelle, Saftien, Aurelia, O’Hagan, Heather M., Wang, Hao, van Boxtel, Ruben, Clevers, Hans, and Sears, Cynthia L.

Published
2022

10. Colon Tumors in Enterotoxigenic Bacteroides fragilis (ETBF)-Colonized Mice Do Not Display a Unique Mutational Signature but Instead Possess Host-Dependent Alterations in the APC Gene

Author

Allen, Jawara, primary, Rosendahl Huber, Axel, additional, Pleguezuelos-Manzano, Cayetano, additional, Puschhof, Jens, additional, Wu, Shaoguang, additional, Wu, Xinqun, additional, Boot, Charelle, additional, Saftien, Aurelia, additional, O’Hagan, Heather M., additional, Wang, Hao, additional, van Boxtel, Ruben, additional, Clevers, Hans, additional, and Sears, Cynthia L., additional

Published
2022
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11. Intestinal organoid cocultures with microbes

Author

Hubrecht Institute with UMC, Puschhof, Jens, Pleguezuelos-Manzano, Cayetano, Martinez-Silgado, Adriana, Akkerman, Ninouk, Saftien, Aurelia, Boot, Charelle, de Waal, Amy, Beumer, Joep, Dutta, Devanjali, Heo, Inha, Clevers, Hans, Hubrecht Institute with UMC, Puschhof, Jens, Pleguezuelos-Manzano, Cayetano, Martinez-Silgado, Adriana, Akkerman, Ninouk, Saftien, Aurelia, Boot, Charelle, de Waal, Amy, Beumer, Joep, Dutta, Devanjali, Heo, Inha, and Clevers, Hans

Published
2021

12. High-Resolution mRNA and Secretome Atlas of Human Enteroendocrine Cells

Author

CMM Groep Snippert, Cancer, CMM Sectie Molecular Cancer Research, Child Health, Regenerative Medicine and Stem Cells, Hubrecht Institute with UMC, Beumer, Joep, Puschhof, Jens, Bauzá-Martinez, Julia, Martínez-Silgado, Adriana, Elmentaite, Rasa, James, Kylie R, Ross, Alexander, Hendriks, Delilah, Artegiani, Benedetta, Busslinger, Georg A, Ponsioen, Bas, Andersson-Rolf, Amanda, Saftien, Aurelia, Boot, Charelle, Kretzschmar, Kai, Geurts, Maarten H, Bar-Ephraim, Yotam E, Pleguezuelos-Manzano, Cayetano, Post, Yorick, Begthel, Harry, van der Linden, Franka, Lopez-Iglesias, Carmen, van de Wetering, Willine J, van der Linden, Reinier, Peters, Peter J, Heck, Albert J R, Goedhart, Joachim, Snippert, Hugo, Zilbauer, Matthias, Teichmann, Sarah A, Wu, Wei, Clevers, Hans, CMM Groep Snippert, Cancer, CMM Sectie Molecular Cancer Research, Child Health, Regenerative Medicine and Stem Cells, Hubrecht Institute with UMC, Beumer, Joep, Puschhof, Jens, Bauzá-Martinez, Julia, Martínez-Silgado, Adriana, Elmentaite, Rasa, James, Kylie R, Ross, Alexander, Hendriks, Delilah, Artegiani, Benedetta, Busslinger, Georg A, Ponsioen, Bas, Andersson-Rolf, Amanda, Saftien, Aurelia, Boot, Charelle, Kretzschmar, Kai, Geurts, Maarten H, Bar-Ephraim, Yotam E, Pleguezuelos-Manzano, Cayetano, Post, Yorick, Begthel, Harry, van der Linden, Franka, Lopez-Iglesias, Carmen, van de Wetering, Willine J, van der Linden, Reinier, Peters, Peter J, Heck, Albert J R, Goedhart, Joachim, Snippert, Hugo, Zilbauer, Matthias, Teichmann, Sarah A, Wu, Wei, and Clevers, Hans

Published
2020

13. Intestinal organoid cocultures with microbes

Author

Puschhof, Jens, Pleguezuelos-Manzano, Cayetano, Martinez-Silgado, Adriana, Akkerman, Ninouk, Saftien, Aurelia, Boot, Charelle, de Waal, Amy, Beumer, Joep, Dutta, Devanjali, Heo, Inha, and Clevers, Hans

Subjects
stem-cells, expansion, host, responses, rna, in-vitro
Abstract

This protocol comprises various methods to coculture organoids (particularly human small intestinal and colon organoids) with microbes, including microinjection into the lumen and periphery of 3D organoids and exposure of organoids to microbes in a 2D layer., Adult-stem-cell-derived organoids model human epithelial tissues ex vivo, which enables the study of host-microbe interactions with great experimental control. This protocol comprises methods to coculture organoids with microbes, particularly focusing on human small intestinal and colon organoids exposed to individual bacterial species. Microinjection into the lumen and periphery of 3D organoids is discussed, as well as exposure of organoids to microbes in a 2D layer. We provide detailed protocols for characterizing the coculture with regard to bacterial and organoid cell viability and growth kinetics. Spatial relationships can be studied by fluorescence live microscopy, as well as scanning electron microscopy. Finally, we discuss considerations for assessing the impact of bacteria on gene expression and mutations through RNA and DNA sequencing. This protocol requires equipment for standard mammalian tissue culture, or bacterial or viral culture, as well as a microinjection device.

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