Cell catalogue of genetic developmental disorders

Researchers often need many years to gain new insights into congenital genetic defects and the resulting malformations and disorders. Using single-cell sequencing, the Lübeck geneticist Malte Spielmann, Professor of Human Genetics at the University of Lübeck and Director of the Institute of Human Genetics at the University Medical Centre Schleswig-Holstein, Campus Lübeck and Kiel, together with an international research team, has succeeded in identifying the effects of specific mutations at molecular and cellular level in a single experiment involving more than 1.5 million cells. The resulting cell catalogue includes data on mutations and their effects on development at an unprecedented breadth and resolution.

As genetic disorders often occur during early pregnancy, they cannot be analysed in human embryos or cell cultures. Mouse models are often used in research for this purpose. Thanks to the development of modern technologies for the targeted modification of genetic material, such as CRISPR/Cas9, genetically manipulated mice, so-called "knockout" mice, can be produced much faster and with greater accuracy. However, current technologies for the analysis and characterisation of embryonic malformations operate at a very low throughput, are extremely labour-intensive and it often takes several years to study a single knockout mouse. Methods with the sensitivity and throughput required to analyse complex organ systems such as a developing brain are still lacking.

The aim of the new study was therefore to use single-cell RNA sequencing to establish an alternative method for analysing embryonic malformations in the mouse model. An international research team led by Professor Malte Spielmann from the University of Lübeck and the University Medical Centre Schleswig-Holstein in Germany investigated the gene expression of over 100 mouse embryos with 25 different genetic alterations in a single large experiment. A study on this scale would have taken countless years using conventional methods. The resulting single-cell atlas of fetal gene expression enables to research and identify different cell types responsible for embryonic malformations.

Prof Spielmann compares the promise of the technology to the effect of the Hubble Space Telescope. "Single cell methods - you can't overestimate their importance for understanding developmental biology," he says. "They really give us a picture that we've never seen before. I am convinced that this new approach will allow us to find even the smallest cellular changes that were previously overlooked, which will help us to better understand the development of embryonic malformations and thus identify potential targets for future therapies."

To analyse the data, the authors developed new computer algorithms allowing to reconstruct the information about each individual cell on the computer. They not only succeeded in grouping the cells according to type and subtype, but also in tracing their developmental pathways and detecting minimal cellular differences and changes. Using this method, the scientists identified 77 main cell types and around 650 cell subtypes. Another major advantage of this new approach is the significantly reduced number of animals used for this analysis, as only a single experiment was carried out and all further analyses were performed in silico, i.e. on the computer.