iPSC CRISPR Facility

The iPSC CRISPR Facility is an expertise center intended to support, help, train and advise researchers with their respective iPSC and CRISPR-Cas9 experiments.  The facility collaborates with researchers (UMCG/RUG, non-profit and commercial) that see possibilities for iPSC and/or CRISPR-Cas9 in their research. The facility plans to generate iPSC from human somatic cells derived from multiple sources and provides full characterization of iPSC clones with the option to introduce genetic changes using CRISPR-Cas9 technology.

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[[Background iPSC and CRISPR-Cas9

Stem cells are unique because they can keep on dividing and are able to develop into any type of cell in the human body. Thereby, stem cells have the capacity to regenerate damaged tissues, making them very interesting from a therapeutic perspective. Stem cells are difficult to acquire, but recent technological advances have made it possible to reprogram already differentiated cells back to stem cells. These so called ‘induced pluripotent stem cells’ (iPSC) are an easy and limitless source of stem cells.

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Many human diseases are caused by alterations in the DNA. These mutations can either be inherited or acquired during life. Many disease-causing mutations have been identified over the past decade and techniques have been developed to quickly identify them in patients. Genome editing techniques including Clustered Regularly Interspaced Short Palindromic Repeats associated nucleases (CRISPR-Cas9) show that it is possible to revert disease mutations back to normal, thereby enabling the restoration of normal cell function. Performing genome editing on patient-derived iPSC may allow us to cure diseases in the future. Although these techniques hold enormous therapeutic promise, it is unclear if they are safe enough to be used on patients. The iPSC CRISPR facility will contribute to research aimed to increase our understanding of iPSC and CRISPR-Cas9 and its combined therapeutic potential.

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More information concerning stem cells can be found here (in Dutch): http://dsscr.nl/wp-content/uploads/2012/02/Handboek-voor-patienten.pdf

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[[Our Expertise

The Facility generates, characterizes and stores CRISPR-edited iPS cell lines. It also closely collaborates with a number of labs holding extensive experience with differentiating iPS cells to a wide variety of cell types. This combined expertise on iPSC and CRISPR allows the Facility to support researchers during any stage of their iPSC and/or CRISPR project, be it either through advice, training or experimental help. The Facility’s basic services include:

Generation of iPSC

  • Isolation of somatic cells from patient material
  • Reprogramming of somatic cells
  • Generation of iPS cells

Characterization of iPSC

  • pluripotent markers gene expression (qPCR or NGS), immunofluorescence
  • differentiation potential gene expression (qPCR or NGS), immunofluorescence
  • pluripotency potential teratome formation
  • karyotyping metaphase spread, single-cell DNA Seq

CRISPR Cas9-mediated genome editing

  • Gene knock-out
  • Gene tagging
  • Gene alterations
  • Gene regulation
  • Screen using human or mouse knock-out libraries
  • Visualization of genomic loci

CRISPR Cas9-mediated epigenome editing

  • Epigenetic writers and erasers for the regulation of gene expression (de Groote et al. NAR 2012, Cano-Rodriguez & Rots Curr Genet Med Rep 2016, Cano-Rodriguez et al. Nat Comm 2016)

Digital droplet PCR

  • Our platform is available for different applications (including CRISPR-Cas9, detection of rare mutations, copy-number variations, absolute quantification, etc.) for all researchers within the UMCG

CRISPR mouse transgenic facility

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Contact

If you are interested in making use of our expertise, please use the Request Form.

For questions, please contact:

Email:                    ips.crispr.facility@umcg.nl

Post address:       ERIBA, UMCG, Building 3226, PO Box 196, Internal Zip Code FA50, 9700 AD Groningen

Telephone:           +31 652724870

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[[The Team

The iPSC CRISPR team consists of a senior postdocs and two technicians.

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From left to right and top to bottom: Daniël Warmerdam, Mathilde Broekhuis, Stefan Juranek and Eslie Huizinga.

 

Ing. Mathilde Broekhuis

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m.j.c.broekhuis@umcg.nl

Mathilde has been trained as a technician in medical biochemistry at the Saxion Hogeschool in Enschede. After her studies she moved to Rotterdam to work in the lab of Rob Pieters at the department of Pediatric Oncology. She performed cytotoxicity assays and mutation detection on material from leukemia patients. In 2009, Mathilde moved to the lab of Gerald de Haan at the UMCG/RUG. She assisted in fundamental research on the hematopoietic system, performing lineage tracing and in vitro analysis. Lab management also became one of her interests, especially when the lab moved to the new ERIBA institute. Mathilde was the first team member of the new iPSC CRISPR facility that was started up at the end of 2015. As a senior technician she is involved in setting up a the facility lab and performing iPSC and CRISPR-mediated genome engineering.

Ing. Eslie Huizinga

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g.c.huizinga@umcg.nl

Eslie graduated as a biomedical research technician at the Hanze Hogeschool in Groningen in 2016. She did her graduation project at the Pediatric Oncology department of Eveline de Bont in the UMCG. During this intership she assisted Walderik Zomerman with his work on the role of the CREB protein in medulloblastoma. After her studies she joined the iPSC CRISPR facility as a junior technician, to expand her lab skills in iPSC and CRISPR-CAS9 technology.]]

 

Dr. Arun Thiruvalluvan

a.thiruvalluvan@umcg.nl

During his PhD, He examined the potential use of human ES/iPSCs derived cells as a tool for stem cell-based therapy and disease modeling. He addressed myelin-restorative strategies by grafting human iPSC-derived oligodendrocytes in animal models for MS (cuprizone and EAE). Using a similar technology with forced transcription factor expression, he studied the transdifferentiation of astrocytes into oligodendrocytes as an alternative source for cell-based remyelination therapy. Moreover, he established MS patient-derived iPSC cell lines that may serve as disease modeling tools to study intrinsic mechanisms underlying MS pathogenesis. Besides that, he used iPS cells of patients with the genetic neurological disorders SCA-3 (Spinocerebellar ataxia) to obtained detailed insights into the pathogenic mechanisms underlying nerve cell degeneration in SCA3.

 

Dr. René Wardenaar

r.wardenaar@umcg.nl

René Wardenaar obtained his PhD in 2016 from the University of Groningen. His thesis described the analysis of sequencing data (whole-genome and bisulfite sequencing) and tiling array data (MeDIP-chip) generated by several studies that are focused on quantifying the contribution of DNA methylation to heritable phenotypic variation in the model plant Arabidopsis thaliana. Part of his thesis got published  in Science in 2014, in which he, together with colleagues and collaborators, described how differentially methylated regions (DMRs) can contribute to phenotypic variation independently from sequence variation and act as bona fide epigenetic quantitative trait loci. Besides these plant-related studies he also participated in other projects that for example were focused on the role of DNA methylation in cervical cancer and the extent of structural variation in the Dutch population. He has a broad interest in biology and joined the iPSC – CRISPR facility in July 2018 where he is supporting the team with the analysis of various types of data.

 

 

 

 

 

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