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Article: Strain-level characterization of foodborne pathogens without culture enrichment for outbreak investigation using shotgun metagenomics facilitated with nanopore adaptive sampling.

Buytaers, Florence E / Verhaegen, Bavo / Van Nieuwenhuysen, Tom / Roosens, Nancy H C / Vanneste, Kevin / Marchal, Kathleen / De Keersmaecker, Sigrid C J

Frontiers in microbiology

2024 Volume 15, Page(s) 1330814

Abstract: Introduction: Shotgun metagenomics has previously proven effective in the investigation of foodborne outbreaks by providing rapid and comprehensive insights into the microbial contaminant. However, culture enrichment of the sample has remained a ... ...

Abstract	Introduction: Shotgun metagenomics has previously proven effective in the investigation of foodborne outbreaks by providing rapid and comprehensive insights into the microbial contaminant. However, culture enrichment of the sample has remained a prerequisite, despite the potential impact on pathogen detection resulting from the growth competition. To circumvent the need for culture enrichment, we explored the use of adaptive sampling using various databases for a targeted nanopore sequencing, compared to shotgun metagenomics alone. Methods: The adaptive sampling method was first tested on DNA of mashed potatoes mixed with DNA of a Results: Overall, the adaptive sampling outperformed the shotgun sequencing. While the use of a host removal DNA extraction kit and targeted sequencing using a database of foodborne pathogens allowed rapid detection of the pathogen, the most complete characterization was achieved when using solely a database of Discussion: This method shows great potential for strain-level analysis of foodborne outbreaks without the need for culture enrichment, thereby enabling faster investigations and facilitating precise pathogen characterization. The integration of adaptive sampling with metagenomics presents a valuable strategy for more efficient and targeted analysis of microbial communities in foodborne outbreaks, contributing to improved food safety and public health.
Language	English
Publishing date	2024-03-01
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2587354-4
ISSN	1664-302X
ISSN	1664-302X
DOI	10.3389/fmicb.2024.1330814
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Article ; Online: Validation of a Targeted LC-MS/MS Method for Cereulide and Application in Food and Faeces.

Masquelier, Julien / Segers, Céline / Jacobs, Bram / Van Nieuwenhuysen, Tom / Delbrassinne, Laurence / Van Hoeck, Els

Toxins

2023 Volume 16, Issue 1

Abstract: Cereulide is an emetic toxin produced by some strains ... ...

Abstract	Cereulide is an emetic toxin produced by some strains of
MeSH term(s)	Humans ; Chromatography, Liquid ; Liquid Chromatography-Mass Spectrometry ; Reproducibility of Results ; Tandem Mass Spectrometry ; Feces ; Depsipeptides
Chemical Substances	cereulide ; Depsipeptides
Language	English
Publishing date	2023-12-27
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2518395-3
ISSN	2072-6651 ; 2072-6651
ISSN (online)	2072-6651
ISSN	2072-6651
DOI	10.3390/toxins16010013
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Article ; Online: Targeted Genome Engineering in Xenopus Using the Transcription Activator-Like Effector Nuclease (TALEN) Technology.

Van Nieuwenhuysen, Tom / Vleminckx, Kris

Methods in molecular biology (Clifton, N.J.)

2018 Volume 1865, Page(s) 55–65

Abstract: Targeted genome engineering technologies are revolutionizing the field of functional genomics and have been extensively used in a variety of model organisms, including X. tropicalis and X. laevis. The original methods based on Zn-finger proteins coupled ... ...

Abstract	Targeted genome engineering technologies are revolutionizing the field of functional genomics and have been extensively used in a variety of model organisms, including X. tropicalis and X. laevis. The original methods based on Zn-finger proteins coupled to endonuclease domains were initially replaced by the more efficient and straightforward transcription activator-like effector nucleases (TALENs), adapted from plant pathogenic Xanthomonas species. Although functional genomics are more recently dominated by the even faster and more convenient CRISPR/Cas9 technology, the use of TALENs may still be preferred in a number of cases. We have successfully implemented this technology in Xenopus and in this chapter we describe our working protocol for targeted genome editing in X. tropicalis using TALENs.
MeSH term(s)	Animals ; Base Sequence ; Genetic Engineering/methods ; Genome ; Microinjections ; RNA, Messenger/biosynthesis ; Transcription Activator-Like Effector Nucleases/metabolism ; Xenopus/genetics
Chemical Substances	RNA, Messenger ; Transcription Activator-Like Effector Nucleases (EC 3.1.-)
Language	English
Publishing date	2018-08-27
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-4939-8784-9_4
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Article: Engraftment of Allotransplanted Tumor Cells in Adult

Tulkens, Dieter / Dimitrakopoulou, Dionysia / Boelens, Marthe / Van Nieuwenhuysen, Tom / Demuynck, Suzan / Toussaint, Wendy / Creytens, David / Van Vlierberghe, Pieter / Vleminckx, Kris

Cancers

2022 Volume 14, Issue 19

Abstract: Modeling human genetic diseases and cancer in lab animals has been greatly aided by the emergence of genetic engineering tools such as TALENs and CRISPR/Cas9. We have previously demonstrated the ease with which genetically ... ...

Abstract	Modeling human genetic diseases and cancer in lab animals has been greatly aided by the emergence of genetic engineering tools such as TALENs and CRISPR/Cas9. We have previously demonstrated the ease with which genetically engineered
Language	English
Publishing date	2022-09-20
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2527080-1
ISSN	2072-6694
ISSN	2072-6694
DOI	10.3390/cancers14194560
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Article: Retrospective surveillance of viable

Bogaerts, Bert / Fraiture, Marie-Alice / Huwaert, Astrid / Van Nieuwenhuysen, Tom / Jacobs, Bram / Van Hoorde, Koenraad / De Keersmaecker, Sigrid C J / Roosens, Nancy H C / Vanneste, Kevin

Frontiers in microbiology

2023 Volume 14, Page(s) 1173594

Abstract: ... Bacillus ... ...

Abstract	Bacillus cereus
Language	English
Publishing date	2023-06-21
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2587354-4
ISSN	1664-302X
ISSN	1664-302X
DOI	10.3389/fmicb.2023.1173594
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Article ; Online: TALENs and CRISPR/Cas9 fuel genetically engineered clinically relevant Xenopus tropicalis tumor models.

Naert, Thomas / Van Nieuwenhuysen, Tom / Vleminckx, Kris

Genesis (New York, N.Y. : 2000)

2017 Volume 55, Issue 1-2

Abstract: The targeted nuclease revolution (TALENs, CRISPR/Cas9) now allows Xenopus researchers to rapidly generate custom on-demand genetic knockout models. These novel methods to perform reverse genetics are unprecedented and are fueling a wide array of human ... ...

Abstract	The targeted nuclease revolution (TALENs, CRISPR/Cas9) now allows Xenopus researchers to rapidly generate custom on-demand genetic knockout models. These novel methods to perform reverse genetics are unprecedented and are fueling a wide array of human disease models within the aquatic diploid model organism Xenopus tropicalis (X. tropicalis). This emerging technology review focuses on the tools to rapidly generate genetically engineered X. tropicalis models (GEXM), with a focus on establishment of genuine genetic and clinically relevant cancer models. We believe that due to particular advantageous characteristics, outlined within this review, GEXM will become a valuable alternative animal model for modeling human cancer. Furthermore, we provide perspectives of how GEXM will be used as a platform for elucidation of novel therapeutic targets and for preclinical drug validation. Finally, we also discuss some future prospects on how the recent expansions and adaptations of the CRISPR/Cas9 toolbox might influence and push forward X. tropicalis cancer research.
MeSH term(s)	Animals ; CRISPR-Cas Systems/genetics ; Disease Models, Animal ; Gene Targeting ; Genetic Engineering ; Humans ; Neoplasms/genetics ; Neoplasms/pathology ; Transcription Activator-Like Effector Nucleases/genetics ; Xenopus/genetics
Chemical Substances	Transcription Activator-Like Effector Nucleases (EC 3.1.-)
Language	English
Publishing date	2017-01
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	2004544-X
ISSN	1526-968X ; 1526-954X
ISSN (online)	1526-968X
ISSN	1526-954X
DOI	10.1002/dvg.23005
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Zs.A 2772: Show issues

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Article ; Online: CRISPR-SID: Identifying EZH2 as a druggable target for desmoid tumors via in vivo dependency mapping.

Naert, Thomas / Tulkens, Dieter / Van Nieuwenhuysen, Tom / Przybyl, Joanna / Demuynck, Suzan / van de Rijn, Matt / Al-Jazrawe, Mushriq / Alman, Benjamin A / Coucke, Paul J / De Leeneer, Kim / Vanhove, Christian / Savvides, Savvas N / Creytens, David / Vleminckx, Kris

Proceedings of the National Academy of Sciences of the United States of America

2021 Volume 118, Issue 47

Abstract: Cancer precision medicine implies identification of tumor-specific vulnerabilities associated with defined oncogenic pathways. Desmoid tumors are soft-tissue neoplasms strictly driven by Wnt signaling network hyperactivation. Despite this clearly defined ...

Abstract	Cancer precision medicine implies identification of tumor-specific vulnerabilities associated with defined oncogenic pathways. Desmoid tumors are soft-tissue neoplasms strictly driven by Wnt signaling network hyperactivation. Despite this clearly defined genetic etiology and the strict and unique implication of the Wnt/β-catenin pathway, no specific molecular targets for these tumors have been identified. To address this caveat, we developed fast, efficient, and penetrant genetic
MeSH term(s)	Abdominal Neoplasms/genetics ; Adenomatous Polyposis Coli/genetics ; Animals ; CRISPR-Cas Systems ; Carcinogenesis/genetics ; Cell Line, Tumor ; Clustered Regularly Interspaced Short Palindromic Repeats ; Cyclic AMP Response Element-Binding Protein ; Enhancer of Zeste Homolog 2 Protein/genetics ; Enhancer of Zeste Homolog 2 Protein/isolation & purification ; Enhancer of Zeste Homolog 2 Protein/metabolism ; Fibromatosis, Aggressive/genetics ; Gene Editing/methods ; Gene Expression Regulation, Neoplastic ; Humans ; Neoplasm Proteins/genetics ; Neoplasm Proteins/metabolism ; Nerve Tissue Proteins ; Oncogenes ; Polycomb Repressive Complex 2/metabolism ; Transcription Factors/genetics ; Transcription Factors/metabolism ; Wnt Signaling Pathway ; Xenopus ; beta Catenin
Chemical Substances	CREB3L1 protein, human ; CTNNB1 protein, human ; Cyclic AMP Response Element-Binding Protein ; Neoplasm Proteins ; Nerve Tissue Proteins ; SUZ12 protein, human ; Transcription Factors ; beta Catenin ; EZH2 protein, human (EC 2.1.1.43) ; Enhancer of Zeste Homolog 2 Protein (EC 2.1.1.43) ; Polycomb Repressive Complex 2 (EC 2.1.1.43)
Language	English
Publishing date	2021-11-18
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.2115116118
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Zs.A 1148: Show issues

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Article ; Online: TLR2 activation causes no morbidity or cardiovascular failure, despite excessive systemic nitric oxide production.

Cauwels, Anje / Vandendriessche, Benjamin / Bultinck, Jennyfer / Descamps, Benedicte / Rogge, Elke / Van Nieuwenhuysen, Tom / Sips, Magdalena / Vanhove, Christian / Brouckaert, Peter

Cardiovascular research

2013 Volume 100, Issue 1, Page(s) 28–35

Abstract: Aims: Septic shock is the leading cause of death in intensive care units worldwide, resulting from a progressive systemic inflammatory reaction causing cardiovascular and organ failure. Nitric oxide (NO) is a potent vasodilator and inhibition of NO ... ...

Abstract	Aims: Septic shock is the leading cause of death in intensive care units worldwide, resulting from a progressive systemic inflammatory reaction causing cardiovascular and organ failure. Nitric oxide (NO) is a potent vasodilator and inhibition of NO synthases (NOS) can increase blood pressure in septic shock. However, NOS inhibition does not improve outcome, on the contrary, and certain NO donors may even provide protection. In addition, NOS produce superoxide in case of substrate or cofactor deficiency or oxidation. We hypothesized that excessive systemic iNOS-derived NO production is insufficient to trigger cardiovascular failure and shock. Methods and results: We found that the systemic injection with various synthetic Toll-like receptor-2 (TLR2), TLR3, or TLR9 agonists triggered systemic NO production identical to that of lipopolysaccharide (LPS) or tumour necrosis factor. In contrast to the latter, however, these agonists did not cause hypothermia or any other signs of discomfort or morbidity, and inflammatory cytokine production was low. TLR2 stimulation with the triacylated lipopeptide Pam3CSK4 not only caused identical NO levels in circulation, but also identical iNOS expression patterns as LPS. Nevertheless, Pam3CSK4 did not cause hypotension, bradycardia, reduced blood flow, or inadequate tissue perfusion in the kidney or the liver. Conclusion: We demonstrate that excessive iNOS-derived NO in circulation is not necessarily linked to concomitant cardiovascular collapse, morbidity, or mortality. As such, our data indicate that the central role of iNOS-derived NO in inflammation-associated cardiovascular failure may be overestimated.
MeSH term(s)	Animals ; Cytokines/physiology ; Female ; Lipopolysaccharides/pharmacology ; Mice ; Mice, Inbred C57BL ; Morbidity ; Nitric Oxide/biosynthesis ; Nitric Oxide Synthase/physiology ; Shock, Septic/etiology ; Systemic Inflammatory Response Syndrome/etiology ; Toll-Like Receptor 2/physiology
Chemical Substances	Cytokines ; Lipopolysaccharides ; Tlr2 protein, mouse ; Toll-Like Receptor 2 ; Nitric Oxide (31C4KY9ESH) ; Nitric Oxide Synthase (EC 1.14.13.39)
Language	English
Publishing date	2013-10-01
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	80340-6
ISSN	1755-3245 ; 0008-6363
ISSN (online)	1755-3245
ISSN	0008-6363
DOI	10.1093/cvr/cvt168
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Zs.A 565: Show issues

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Article ; Online: CRISPR/Cas9 mediated knockout of rb1 and rbl1 leads to rapid and penetrant retinoblastoma development in Xenopus tropicalis.

Naert, Thomas / Colpaert, Robin / Van Nieuwenhuysen, Tom / Dimitrakopoulou, Dionysia / Leoen, Jannick / Haustraete, Jurgen / Boel, Annekatrien / Steyaert, Wouter / Lepez, Trees / Deforce, Dieter / Willaert, Andy / Creytens, David / Vleminckx, Kris

Scientific reports

2016 Volume 6, Page(s) 35264

Abstract: Retinoblastoma is a pediatric eye tumor in which bi-allelic inactivation of the Retinoblastoma 1 (RB1) gene is the initiating genetic lesion. Although recently curative rates of retinoblastoma have increased, there are at this time no molecular targeted ... ...

Abstract	Retinoblastoma is a pediatric eye tumor in which bi-allelic inactivation of the Retinoblastoma 1 (RB1) gene is the initiating genetic lesion. Although recently curative rates of retinoblastoma have increased, there are at this time no molecular targeted therapies available. This is, in part, due to the lack of highly penetrant and rapid retinoblastoma animal models that facilitate rapid identification of targets that allow therapeutic intervention. Different mouse models are available, all based on genetic deactivation of both Rb1 and Retinoblastoma-like 1 (Rbl1), and each showing different kinetics of retinoblastoma development. Here, we show by CRISPR/Cas9 techniques that similar to the mouse, neither rb1 nor rbl1 single mosaic mutant Xenopus tropicalis develop tumors, whereas rb1/rbl1 double mosaic mutant tadpoles rapidly develop retinoblastoma. Moreover, occasionally presence of pinealoblastoma (trilateral retinoblastoma) was detected. We thus present the first CRISPR/Cas9 mediated cancer model in Xenopus tropicalis and the first genuine genetic non-mammalian retinoblastoma model. The rapid kinetics of our model paves the way for use as a pre-clinical model. Additionally, this retinoblastoma model provides unique possibilities for fast elucidation of novel drug targets by triple multiplex CRISPR/Cas9 gRNA injections (rb1 + rbl1 + modifier gene) in order to address the clinically unmet need of targeted retinoblastoma therapy.
Language	English
Publishing date	2016-10-14
Publishing country	England
Document type	Journal Article
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/srep35264
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Article: TALEN-mediated apc mutation in Xenopus tropicalis phenocopies familial adenomatous polyposis.

Van Nieuwenhuysen, Tom / Naert, Thomas / Tran, Hong Thi / Van Imschoot, Griet / Geurs, Sarah / Sanders, Ellen / Creytens, David / Van Roy, Frans / Vleminckx, Kris

Oncoscience

2015 Volume 2, Issue 5, Page(s) 555–566

Abstract: Truncating mutations in the tumor suppressor gene adenomatous polyposis coli (APC) are the initiating step in the vast majority of sporadic colorectal cancers, and they underlie familial adenomatous polyposis (FAP) syndromes. Modeling of APC- driven ... ...

Abstract	Truncating mutations in the tumor suppressor gene adenomatous polyposis coli (APC) are the initiating step in the vast majority of sporadic colorectal cancers, and they underlie familial adenomatous polyposis (FAP) syndromes. Modeling of APC- driven tumor formation in the mouse has contributed substantially to our mechanistic understanding of the associated disease, but additional models are needed to explore therapeutic opportunities and overcome current limitations of mouse models. We report on a novel and penetrant genetic cancer model in Xenopus tropicalis, an aquatic tetrapod vertebrate with external development, diploid genome and short life cycle. Tadpoles and froglets derived from embryos injected with TAL effector nucleases targeting the apc gene rapidly developed intestinal hyperplasia and other neoplasms observed in FAP patients, including desmoid tumors and medulloblastomas. Bi-allelic apc mutations causing frame shifts were detected in the tumors, which displayed activation of the Wnt/β-catenin pathway and showed increased cellular proliferation. We further demonstrate that simultaneous double bi-allelic mutation of apc and a non-relevant gene is possible in the neoplasias, opening the door for identification and characterization of effector or modifier genes in tumors expressing truncated apc. Our results demonstrate the power of modeling human cancer in Xenopus tropicalis using mosaic TALEN-mediated bi-allelic gene disruption.
Language	English
Publishing date	2015-05-19
Publishing country	United States
Document type	Journal Article
ISSN	2331-4737
ISSN	2331-4737
DOI	10.18632/oncoscience.166
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