Comparative RNAseq analysis for the study of motoneuron diseases in multi-omics approaches

Abstract Nearly half of patients with suspected monogenic Mendelian diseases still remain undiagnosed. The integration of genome sequencing and RNA sequencing can reveal the functional significance of rare changes. This is especially true for deep intronic non-coding variation that contributes to mis-splicing but is difficult to discern when analyzing whole genome data alone. However, this combined approach is challenged when studying motoneuron and other neurological diseases as obtaining affected tissue samples from living patients is typically not feasible. Here we explore the utility of typically available sources of material for RNAseq studies that can empower genome analysis. We found that fibroblasts cultured in vitro express 76.8%, 73.6%, and 81.2% of genes known to cause the monogenic diseases CMT, ataxia, and HSP, respectively. This outperformed other peripheral tissues such as whole blood and lymphocytes, thereby making fibroblasts a valuable tissue for studying motoneuron diseases. Only induced pluripotent stem cell (iPSC)-derived cortical neurons showed a higher number of expressed known disease genes; however, derived cortical neurons require significant resources and time. Finally, we analyzed RNA-seq data from fibroblasts of two HSP patients carrying a deep intronic splice disrupting variant in POLR3A, to evaluate the sensitivity and specificity of several alternative splicing detection tools for diagnostic purposes. Our results highlight the potential of fibroblast RNA-seq data for diagnosing and studying HSP and other motoneuron and neurological diseases using peripheral tissue.