04 March 2020, Cambridge – Induced pluripotent stem cells (iPSCs) are suitable for discovering the genes that underlie complex and also rare genetic diseases. Scientists from the German Cancer Research Center (DKFZ) and the European Molecular Biology Laboratory (EMBL), together with international partners, have studied genotype–phenotype relationships in iPSCs using data from approximately 1,000 donors.

Tens of thousands of tiny genetic variations (SNPs, single-nucleotide polymorphisms) have been identified in the human genome that are associated with specific diseases. Many of these genetic variants are not located in the protein-coding regions of genes, but affect regulatory sections. Therefore, scientists are trying to find out if and in which tissues these variants can be linked to changes in the activity of specific genes.

Together with scientists from Stanford University and additional international cooperation partners, Oliver Stegle’s team has compiled sequence and transcriptome data on iPSCs from around 1,000 donors. The researchers use these data to identify correlations between individual genetic variants and altered expression patterns in stem cells. The results have now been published in the journal Nature Genetics.

Linking genetic variants to diseases

For more than 67% of all genes active in iPSCs, the researchers found differential expression patterns depending on genetic variants. Many of these associations are novel and have not been described in somatic cell types before. For over 4,000 of these associations, it was possible to link the genetic variants responsible for the altered expression patterns to specific diseases. These included, for example, variants associated with coronary heart disease, lipid metabolism disorders, or hereditary cancers.

Stegle and colleagues also investigated whether iPSCs are suitable for identifying the causative genes of rare genetic diseases. They used iPSC lines from 65 patients with various rare diseases, whose causal gene variants were already known through previous analyses. In the transcriptome data of these iPSC lines, the scientists searched for particularly conspicuous outliers in the expression data. These analyses reliably led them to trace the genetic basis of the disease.

“Such screenings were previously impossible because there were simply no sufficiently large reference collections of iPSC transcriptomes,” explains Marc Jan Bonder, Postdoctoral Fellow at EMBL. “We were surprised to find such a large number of disease-associated genetic variants that are already visible in the expression pattern at the earliest time point of cell differentiation, represented by the iPSCs.”

Genetic variants across neuronal differentiation

In a companion paper published in the same issue of Nature Genetics, Stegle and colleagues from EMBL’s European Bioinformatics Institute (EMBL-EBI), the Wellcome Sanger Institute and Open Targets used more than 200 iPSC lines to investigate how genetic variants affect differentiation into neuronal cells.

“The study demonstrates the power of combining single cell sequencing with iPSC technologies to dissect the effect of genetic variants in cell types that would otherwise be inaccessible,” says Oliver Stegle, division head at DKFZ and a Group Leader at EMBL.

The scientists performed single cell RNA sequencing at different time points of neuronal cell differentiation. This allowed them to analyse how genetic variants affect expression patterns in different cellular states, including different neuronal cell types.

“Carrying out single cell sequencing on neuronal cell types such as the ones we looked at has proven to be technically very tricky in the past” says John Marioni, Head of Research at EMBL-EBI. “Combining single cell sequencing with iPSC technologies in this way has made it possible to get a better understanding of the genetic variants present across dopaminergic neuron differentiation.”

This press release was originally published by DKFZ.

 

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