Single-cell human genetics: effects of structural variants and mutations during embryonic development at single cell resolution.

• Applicant: Professor Dr. Malte Spielmann
• Subject Area: Human Genetics
• Term: from 2019 to 2024
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 429814408

Rare genetic diseases are often severe multisystem disorders with a wide range of phenotypes and may vary widely among affected individuals ranging from relatively mild to severe. Diagnostic yields for rare pediatric genetic diseases are currently between 35 and 75%. Yet genotype-phenotype correlations are extremely difficult, since the severity of these disorders can differ even in individuals with mutations in the same gene. We hypothesize, that whole organism single cell profiling of patient specific mutations and structural variants during mouse embryogenesis can provide important new insights to understand phenotypic variability of rare multisystem disorders.A fundamental challenge to study in vivo embryogenesis, is the lack of current technologies with sufficient throughput and resolution to obtain a global view of the molecular states and trajectories of a rapidly diversifying and expanding number of cell types. To address these challenges, we will apply three main experimental approaches: AIM 1: We aim to investigate the pleiotropic effects of severe multisystem disorders during embryonic development at single cell level by analyzing mouse mutants harboring patient specific mutations. We will use the whole embryo sci-RNA-seq approach for phenotyping of Runx2 deficient mice, a model for cleidocranial dysplasia and a mouse models for Cornelia de Lange syndrome. We anticipate that the whole organism sci-RNA-seq approach will enable the discovery of subtle defects in the molecular programs or the relative proportions of specific cell types.AIM 2: We aim to study more complex genetic variants, e.g. microdeletion syndromes and trisomy 21 at single cell resolution. The specific challenge of these variants is that they include many genes and regulatory sequences, which in their unique combination contribute to the phenotype. We will study structural variants by analyzing the 16p11.2 microdeletion syndrome (16p11.2+/− mice) and a mouse models for human trisomy 21 (Hsa21 mice). Our data will advance our knowledge about SVs in human disease and establish single cell-RNA-seq as phenotyping tool for SVs in transgenic mice. AIM 3: We aim to investigate changes in chromatin accessibility and the non-coding regulatory landscape associated with congenital disease. We will use single cell ATAC-seq and create single cell atlas of chromatin accessibility during mouse organogenesis (E9.5-E13.5) that will serve as an important resource for the study of embryonic gene regulation. We will also analyze a mouse models for CdLS.The single cell approach is extremely ambitious and timely and has never been applied in the field of human genetics. We will generate an enormous amount of data that will be by itself a valuable resource worth publishing. We aim at nothing less than transforming complex processes in development biology into computational problems that can be investigated by algorithms rather than by wet lab-based assays.

• DFG Programme: Research Grants