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cBiT: A transcriptomics database for innovative biomaterial engineering KU Leuven

Dennie GAJ Hebels, Aurélie Carlier, Maarten LJ Coonen, Daniel H Theunissen, Jan de Boer
Creating biomaterials that are suited for clinical application is still hampered by a lack of understanding of the interaction between a cell and the biomaterial surface it grows on. This surface communication can strongly impact cellular behavior, which in turn affects the chances of a successful interaction between a material and the host tissue. Transcriptomics data have previously been linked to measurements of biomaterial properties in ...

Transcriptomics data of a human in vitro model of non-alcoholic steatohepatitis exposed to elafibranor Vrije Universiteit Brussel

Joost Boeckmans, Karolien Buyl, Alessandra Natale, Valerie Vandenbempt, Steven Branson, Veerle Rita J De Boe, Vera Rogiers, Joery De Kock, Robim Marcelino Rodrigues, Tamara Vanhaecke, et al.

The present dataset contains the transcriptomic characterization of a novel in vitro model of non-alcoholic steatohepatitis (NASH) as well as its transcriptomics read-outs for the evaluation of elafibranor, a potential anti-NASH compound. We report whole genome microarray data (Affymetrix HG U133 plus 2.0) of human multipotent stem cell-derived hepatic cells (hSKP-HPC) exposed to mediators of NASH. These cells were exposed to lipogenic ...

Spatial Transcriptomics and In Situ Sequencing to Study Alzheimer's Disease KU Leuven

Wei-Ting Chen, Ashley Lu, Katleen Craessaerts, Benjamin Pavie, Carlo Sala Frigerio, Nikky Corthout, Xiaoyan Qian, Jana Lalakova, Malte Kuhnemund, Iryna Voytyuk, et al.
Although complex inflammatory-like alterations are observed around the amyloid plaques of Alzheimer's disease (AD), little is known about the molecular changes and cellular interactions that characterize this response. We investigate here, in an AD mouse model, the transcriptional changes occurring in tissue domains in a 100-μm diameter around amyloid plaques using spatial transcriptomics. We demonstrate early alterations in a gene co-expression ...

Benchmarking of cell type deconvolution pipelines for transcriptomics data Universiteit Gent

Francisco Avila Cobos, José Alquicira-Hernandez, Joseph E. Powell, Pieter Mestdagh, Katleen De Preter
Many computational methods have been developed to infer cell type proportions from bulk transcriptomics data. However, an evaluation of the impact of data transformation, pre-processing, marker selection, cell type composition and choice of methodology on the deconvolution results is still lacking. Using five single-cell RNA-sequencing (scRNA-seq) datasets, we generate pseudo-bulk mixtures to evaluate the combined impact of these factors. Both ...

Diagnosing enterovirus meningitis via blood transcriptomics UZBrussel

Esther Bartholomeus, Nicolas De Neuter, Annelies Lemay, Luc Pattyn, David Tuerlinckx, David Weynants, Koen Van Lede, Gerlant Dirk Z van Berlaer, Dominique Bulckaert, Tine Boiy, et al.

BACKGROUND: Meningitis can be caused by several viruses and bacteria. Identifying the causative pathogen as quickly as possible is crucial to initiate the most optimal therapy, as acute bacterial meningitis is associated with a significant morbidity and mortality. Bacterial meningitis requires antibiotics, as opposed to enteroviral meningitis, which only requires supportive therapy. Clinical presentation is usually not sufficient to ...

Catalyzing Transcriptomics Research in Cardiovascular Disease: The CardioRNA COST Action CA17129 KU Leuven

Clarissa Pedrosa da Costa Gomes, Bence Agg, Andrejaana Andova, Serdal Arslan, Andrew Baker, Monika Bartekova, Dimitris Beis, Fay Betsou, Stephanie Bezzina Wettinger, Branko Bugarski, et al.
Cardiovascular disease (CVD) remains the leading cause of death worldwide and, despite continuous advances, better diagnostic and prognostic tools, as well as therapy, are needed. The human transcriptome, which is the set of all RNA produced in a cell, is much more complex than previously thought and the lack of dialogue between researchers and industrials and consensus on guidelines to generate data make it harder to compare and reproduce ...

Transcriptomics analysis reveals new insights in E171-induced molecular alterations in a mouse model of colon cancer KU Leuven

Heloise Proquin, Marlon J Jetten, Marloes Jonkhout, Luis Guillermo Garduno-Balderas, Jacob J Briede, Theo M de Kok, Henk van Loveren, Yolanda I Chirino
Titanium dioxide as a food additive (E171) has been demonstrated to facilitate growth of chemically induced colorectal tumours in vivo and induce transcriptomic changes suggestive of an immune system impairment and cancer development. The present study aimed to investigate the molecular mechanisms behind the tumour stimulatory effects of E171 in combination with azoxymethane (AOM)/dextran sodium sulphate (DSS) and compare these results to a ...

Understanding Alzheimer disease at the interface between genetics and transcriptomics Universiteit Antwerpen

Johannes Maria Verheijen, Kristel Sleegers
Over 25 genes are known to affect the risk of developing Alzheimer disease (AD), the most common neurodegenerative dementia. However, mechanistic insights and improved disease management remains limited, due to difficulties in determining the functional consequences of genetic associations. Transcriptomics is increasingly being used to corroborate or enhance interpretation of genetic discoveries. These approaches, which include second and third ...

Research into the respiratory immunodisturbing mechanisms of chemical allergens by means of in vitro test systems and transcriptomics Universiteit Gent

Sandra Verstraelen
Chemical-induced respiratory allergy poses significant challenges for the toxicologist and regulator, not least because there are, as yet, no validated or widely accepted methods available for the identification of chemicals that have the potential to cause respiratory sensitization. This may be attributable to the fact that there remains uncertainty about the complete mechanisms through which respiratory sensitization to chemicals can be ...

Heterologous oligonucleotide microarrays for transcriptomics in a non-model species: a proof-of-concept study of drought stress in Musa KU Leuven

Mark Davey, Neil S Graham, Bart Vanholme, Rony Swennen, Sean T May, Johan Keulemans
BACKGROUND: 'Systems-wide' approaches such as microarray RNA-profiling are ideally suited to the study of the complex overlapping responses of plants to biotic and abiotic stresses. However, commercial microarrays are only available for a limited number of plant species and development costs are so substantial as to be prohibitive for most research groups. Here we evaluate the use of cross-hybridisation to Affymetrix oligonucleotide GeneChip(R) ...