Projects in complex genetics

• Role of celiac disease-associated genes predicted to play a role in intestinal epithelial barrier function, using a 3D CaCo2 culture model (spheroids). The genes of interest have been knocked down by short hairpin delivery.
  Maria Zorro and Luz Maria Medrano in collaboration with Sven van Ijzendoorn (PI) and Lucja Larosz (Dept of Cell Biology, UMCG)

• Investigating potential use of circulating miRNAs as biomarkers for celiac disease. We are profiling circulating miRNAs by next generation sequencing in plasma samples from celiac disease patients before and after they started treatment (gluten-free diet).
  Ineke Tan and Yang Li in collaboration with the PreventCD consortium and Rodrigo Coutinho de Almeida (University of Paraná, Brazil)

• Study of circulating miRNAs and of small and large RNA transcriptomes derived from biopsies of ~35 celiac disease patients and ~10 controls by next generation sequencing.
  Ineke Tan and Yang Li in collaboration with Donatella Barisani (University of Milano-Bicocca, Italy) and Rodrigo Coutinho de Almeida (University of Paraná, Brazil)

• Designing a test to monitor progression in multiple sclerosis (MS). We are profiling circulating miRNAs (next generation sequencing) in the plasma or cerebro­spinal fluid of patients with Relapsing Remitting MS or Secondary Progressive MS.
  Yang Li in collaboration with Jan Meilof (Dept of Neurology, UMCG) and Anna Stachurska (Poland)

• Study into effects of genetics, TCR-usage and patient's age on the transcriptome (determined by next generation sequencing) of stimulated gluten-specific T cell clones in time.
  Zuzanna Borek and Yang Li in collaboration with Frits Koning and Jeroen van Bergen (Leiden University Medical Center)
• Study into effects of celiac disease-associated SNPs on enhancer usage and gene expression in stimulated gluten-specific T cell clones. We are performing genotyping, DNase hypersensitive site mapping, RNAseq and proSeq (precision run-on sequencing).
  Zuzanna Borek, Iris Jonkers and Yang Li in collaboration with Ludvig Sollid and Shuo-Wang Qiao (University of Oslo) and Henk Stunnenberg and Mena Matarese (Radboud Institute for Molecular Life Sciences)

• An analysis of next generation sequencing data to understand the transcriptome of intraepithelial lymphocytes known to be the effector T cells in celiac disease.
  Yang Li and Raul Aguirre in collaboration with Bana Jabri and Toufic Mayassi (University of Chicago)

• CeDNN - the collection of blood, stool, urine and exhaled breath samples, buccal swabs, and general and intestinal health questionnaires from 500 celiac disease patients, plus 1000 of their relatives and 500 partners, and from 500 IBS patients. The samples are collected and processed to enable genotyping, transcriptomics, epigenetics, metabolomics, and microbiome research.
  Ineke Tan, Rutger Modderman, Mathieu Platteel and Astrid Maatman in collaboration with Rinse Weersma and Marijn Visschedijk (Dept of Gastroenterology, UMCG)

• Pathway analysis approaches and eQTL analyses are being applied to next generation sequencing data to predict disease mechanisms. The starting points for these analyses are disease-associated SNPs (found by GWAS or ImmunoChip analysis) and their coding and non-coding genes. The results of these studies are being used to design in vitro experiments.
  Vinod Kumar and Lude Franke

• In the wet lab, we are studying the role of various genes (identified in the above studies) in the immune system, with a focus on lncRNAs. After in silico prioritization, lentiviral short hairpin delivery or CRISPR/CAS9 techniques are used to introduce mutations or to achieve complete knockout of candidates in immune cell line models, including gluten-specific T cell clones and intraepithelial lymphocytes obtained from intestinal biopsies of celiac disease patients.