Flemish Institute for Biotechnology

Gent, Belgium

Flemish Institute for Biotechnology

Gent, Belgium
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Vanacker L.,Laboratory of Molecular Oncology | Smeets D.,Flemish Institute for Biotechnology | Smeets D.,Catholic University of Leuven | Teugels E.,Laboratory of Molecular Oncology | And 5 more authors.
Anticancer Research | Year: 2014

Background/Aim: We report a case of a mixed adenoneuroendocrine carcinoma developed in a colorectal adenocarcinoma with lymph node and liver metastases exclusively emanating from the neuroendocrine carcinoma component. The patient underwent right hemicolectomy and postoperatively received chemotherapy with cisplatin and etoposide and subsequent high-dose induction chemotherapy, followed by autologous stem cell transplantation. Following this treatment, there was a complete remission. Currently, thirthy months after treatment, the patient is in unmaintained complete remission. Comparative exome sequencing of germline DNA and DNA from the two separate malignant components revealed six somatic changes in cancer consensus genes. Both components shared somatic mutations in Adenomatous polyposis coli (APC), Kirsten rat sarcoma viral oncogene homolog (KRAS), B-cell CLL/lymphoma 9 (BCL9) and Forkhead Box P1 (FOXP1) genes. Mutation in SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4 (SMARCA4 ) was only found in the neuroendocrine carcinoma component. The finding of several identical somatic mutations in both components supports a clonal relationship between the neuroendocrine carcinoma and the adenocarcinoma. We suggest that a mutation in SMARCA4 could be responsible for the transformation of the adenocarcinoma component into the neuroendocrine phenotype. © 2014, International Institute of Anticancer Research. All rights reserved.


Wiedmann S.,University of Würzburg | Norrving B.,Lund University | Nowe T.,Charité - Medical University of Berlin | Abilleira S.,Stroke Programme Catalan Agency for Health Information | And 8 more authors.
Stroke | Year: 2012

Background and Purpose-: Quality indicators serve as standards of care by which performance of individual hospitals is measured. Although several audits for monitoring quality of stroke care have been established in Europe, there is currently no consensus on quality indicators for acute stroke care or for methodology for collecting information on these measures. Methods-: An up-to-date inventory on European stroke audits in place in 2006 was performed in the course of a project funded by the European Union (European Implementation Score Collaboration [EIS]). Two regional (Flanders, Belgium; Catalonia, Spain) and 4 national (Germany, Scotland, Sweden, England/Wales/Northern Ireland) stroke audits took part. Between November 2009 and July 2010, 2 standardized surveys and a series of interviews were performed to determine characteristics, Methods, and content of these quality initiatives. For quality purposes, all summarized information was validated by representatives of the respective audits. Results-: Overall, 123 quality indicators (91 process, 24 outcome, and 8 structural indicators) were identified. Anticoagulants in patients with atrial fibrillation and brain imaging were the only quality indicators used in all, whereas another 13 indicators were used in at least 2 of the quality initiatives. Substantial variations were found across the audits in terms of the development process of quality indicators, inclusion criteria, participation, population coverage, data documentation, follow-ups, benchmarking, and feedback of Results to participants. Conclusions-: There is a huge variety in measuring performance of acute stroke care in Europe, hampering valid comparisons of acute stroke care. Common standards for defining quality indicators and collecting information required for these measures should be defined in Europe. © 2011 American Heart Association, Inc.


Haydu J.E.,Columbia University | De Keersmaecker K.,Flemish Institute for Biotechnology | De Keersmaecker K.,Catholic University of Leuven | Duff M.K.,Columbia University | And 6 more authors.
Blood | Year: 2012

Oncogenic activating mutations in NOTCH1 occur in more than 50% of T-cell acute lymphoblastic leukemias (T-ALLs). In the present study, we describe a novel mechanism of NOTCH1 activation in T-ALL in which a deletion removing the 5′ portion of NOTCH1 abolishes the negative regulatory control of the extracellular domain and leads to constitutively active NOTCH1 signaling. Polypeptides translated from truncated transcripts encoded by the NOTCH1 deletion allele retain the transmembrane domain of the receptor and are constitutively cleaved by the γ-secretase complex, resulting in high levels of NOTCH1 signaling that can be effectively blocked by γ-secretase inhibitors. Our results expand the spectrum of oncogenic lesions activating NOTCH1 signaling in human T-ALL. © 2012 by The American Society of Hematology.


Vluymans S.,Ghent University | Vluymans S.,Flemish Institute for Biotechnology | Saeys Y.,Inflammation Research Center Flemish Institute for Biotechnology | Saeys Y.,Ghent University | And 3 more authors.
Fundamenta Informaticae | Year: 2015

Data used in machine learning applications is prone to contain both vague and incomplete information. Many authors have proposed to use fuzzy rough set theory in the development of new techniques tackling these characteristics. Fuzzy sets deal with vague data, while rough sets allow to model incomplete information. As such, the hybrid setting of the two paradigms is an ideal candidate tool to confront the separate challenges. In this paper, we present a thorough review on the use of fuzzy rough sets in machine learning applications. We recall their integration in preprocessing methods and consider learning algorithms in the supervised, unsupervised and semi-supervised domains and outline future challenges. Throughout the paper, we highlight the interaction between theoretical advances on fuzzy rough sets and practical machine learning tools that take advantage of them.


Willart M.A.M.,Ghent University | Poulliot P.,Ghent University | Lambrecht B.N.,Flemish Institute for Biotechnology | Lambrecht B.N.,Erasmus Medical Center | Kool M.,Erasmus Medical Center
Methods in Molecular Biology | Year: 2013

Sensitization of mice to real-life allergens or harmless antigen with the use of adjuvants will lead to the induction of DAMPs in the immune system. We have shown that the Th2-inducing adjuvant aluminum hydroxide or exposure of the airways to house dust mite leads to the release of DAMPs: uric acid, ATP, and IL-1. Exposure to DAMPs or PAMPs present in allergens or added to harmless allergens, such as the experimental allergen ovalbumin, induces several immune responses, including cellular influx and activation. Cellular influx can be analyzed by flow cytometry. Likewise, cellular activation can be assessed by measuring increased expression and release of chemokines and cytokines. These inflammatory mediators can be analyzed by ELISA or confocal microscopy. Here, we describe the protocols for these assessments and a protocol that takes advantage of bone marrow chimeric mice to further elucidate mechanism. © 2013 Springer Science+Business Media, LLC.


Menschaert G.,Ghent University | Van Criekinge W.,Ghent University | Notelaers T.,Catholic University of Leuven | Koch A.,Ghent University | And 5 more authors.
Molecular and Cellular Proteomics | Year: 2013

An increasing number of studies involve integrative analysis of gene and protein expression data, taking advantage of new technologies such as next-generation transcriptome sequencing and highly sensitive mass spectrometry (MS) instrumentation. Recently, a strategy, termed ribosome profiling (or RIBO-seq), based on deep sequencing of ribosome-protected mRNA fragments, indirectly monitoring protein synthesis, has been described. We devised a proteogenomic approach constructing a custom protein sequence search space, built from both Swiss-Prot- and RIBO-seq-derived translation products, applicable for MS/MS spectrum identification. To record the impact of using the constructed deep proteome database, we performed two alternative MS-based proteomic strategies as follows: (i) a regular shotgun proteomic and (ii) an N-terminal combined fractional diagonal chromatography (COFRADIC) approach. Although the former technique gives an overall assessment on the protein and peptide level, the latter technique, specifically enabling the isolation of N-terminal peptides, is very appropriate in validating the RIBO-seq-derived (alternative) translation initiation site profile. We demonstrate that this proteogenomic approach increases the overall protein identification rate 2.5% (e.g. new protein products, new protein splice variants, single nucleotide polymorphism variant proteins, and N-terminally extended forms of known proteins) as compared with only searching UniProtKB-SwissProt. Furthermore, using this custom database, identification of N-terminal COFRADIC data resulted in detection of 16 alternative start sites giving rise to N-terminally extended protein variants besides the identification of four translated upstream ORFs. Notably, the characterization of these new translation products revealed the use of multiple near-cognate (non-AUG) start codons. As deep sequencing techniques are becoming more standard, less expensive, and widespread, we anticipate that mRNA sequencing and especially custom-tailored RIBO-seq will become indispensable in the MS-based protein or peptide identification process. The underlying mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium with the dataset identifier PXD000124. © 2013 by The American Society for Biochemistry and Molecular Biology, Inc.


PubMed | Campus Management, Catholic University of Leuven, Flemish Institute for Biotechnology and CSIC - Doñana Biological Station
Type: Journal Article | Journal: FEMS microbiology ecology | Year: 2015

Floral nectars become easily colonized by microbes, most often species of the ascomycetous yeast genus Metschnikowia. Although it is known that nectar composition can vary tremendously among plant species, most probably corresponding to the nutritional requirements of their main pollinators, far less is known about how variation in nectar chemistry affects intraspecific variation in nectarivorous yeasts. Because variation in nectar traits probably affects growth and abundance of nectar yeasts, nectar yeasts can be expected to display large phenotypic variation in order to cope with varying nectar conditions. To test this hypothesis, we related variation in the phenotypic landscape of a vast collection of nectar-living yeast isolates from two Metschnikowia species (M. reukaufii and M. gruessii) to nectar chemical traits using non-linear redundancy analyses. Nectar yeasts were collected from 19 plant species from different plant families to include as much variation in nectar chemical traits as possible. As expected, nectar yeasts displayed large variation in phenotypic traits, particularly in traits related to growth performance in carbon sources and inhibitors, which was significantly related to the host plant from which they were isolated. Total sugar concentration and relative fructose content significantly explained the observed variation in the phenotypic profile of the investigated yeast species, indicating that sugar concentration and composition are the key traits that affect phenotypic variation in nectarivorous yeasts.


Coquet J.M.,Netherlands Cancer Institute | Coquet J.M.,Flemish Institute for Biotechnology | Middendorp S.,Netherlands Cancer Institute | Middendorp S.,University Utrecht | And 6 more authors.
Immunity | Year: 2013

T helper 17 (Th17) cells protect against infection but also promote inflammation and autoimmunity. Therefore, the factors that govern Th17 cell differentiation are of special interest. The CD27 and CD70 costimulatory pathway impeded Th17 effector cell differentiation and associated autoimmunity in a mouse model of multiple sclerosis. CD27 or CD70 deficiency exacerbated disease, whereas constitutive CD27 signaling strongly reduced disease incidence and severity. CD27 signaling did not impact master regulators of T helper cell lineage commitment but selectively repressed transcription of the key effector molecules interleukin-17 (IL-17) and the chemokine receptor CCR6 in differentiating Th17 cells. CD27 mediated this repression at least in part via the c-Jun N-terminal kinase (JNK) pathway that restrained IL-17 and CCR6 expression in differentiating Th17 cells. CD27 signaling also resulted in epigenetic silencing of the Il17a gene. Thus, CD27 costimulation via JNK signaling, transcriptional, and epigenetic effects suppresses Th17 effector cell function and associated pathological consequences. © 2013 Elsevier Inc.


Jiao Y.,University of Michigan | Darzi Y.,Flemish Institute for Biotechnology | Tawaratsumida K.,University of Michigan | Marchesan J.T.,University of Michigan | And 7 more authors.
Cell Host and Microbe | Year: 2013

Periodontitis is a common disease that is characterized by resorption of the alveolar bone and mediated by commensal bacteria that trigger host immune responses and bone destruction through unidentified mechanisms. We report that Nod1, an innate intracellular host receptor for bacterial peptidoglycan-related molecules, is critical for commensal-induced periodontitis in a mouse model. Mice lacking Nod1 exhibit reduced bone resorption as well as impaired recruitment of neutrophils to gingival tissues and osteoclasts to the alveolar bone, which mediate tissue and bone destruction. Further analysis showed that accumulation of a Nod1-stimulating commensal bacterium, NI1060, at gingival sites was sufficient to induce neutrophil recruitment and bone resorption. Genomic sequencing revealed that NI1060 is a mouse-specific bacterium that is related to bacteria associated with the development of aggressive periodontitis in humans. These findings provide insight into commensal-host interactions contributing to periodontitis and identify a potential target for preventing this common oral disease. © 2013 Elsevier Inc.

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