Intersect-RNA-seq reveals disease-specific mis-splicing

Correction of mis-splicing events is a growing therapeutic approach for neurological diseases such as spinal muscular atrophy or neuronal ceroid lipofuscinosis 7, which are caused by splicing-affecting mutations. Mis-spliced effector genes that do not harbour mutations are also good candidate therapeutic targets in diseases with more complex aetiologies such as cancer, autism, muscular dystrophies or neurodegenerative diseases. Next-generation RNA sequencing (RNA-seq) has boosted investigation of global mis-splicing in diseased tissue to identify such key pathogenic mis-spliced genes. Nevertheless, while analysis of tumour or dystrophic muscle biopsies can be informative on early stage pathogenic mis-splicing, for neurodegenerative diseases, these analyses are intrinsically hampered by neuronal loss and neuroinflammation in post-mortem brains.

To infer splicing alterations relevant to Huntington’s disease pathogenesis, researchers at the Severo Ochoa Molecular Biology Center performed intersect-RNA-seq analyses of human post-mortem striatal tissue and of an early symptomatic mouse model in which neuronal loss and gliosis are not yet present. Together with a human/mouse parallel motif scan analysis, this approach allowed them to identify the shared mis-splicing signature triggered by the Huntington’s disease-causing mutation in both species and to infer upstream deregulated splicing factors. Moreover, the researchers identified a plethora of downstream neurodegeneration-linked mis-spliced effector genes that—together with the deregulated splicing factors—become new possible therapeutic targets. In summary, here the investigators report pathogenic global mis-splicing in Huntington’s disease striatum captured by their new intersect-RNA-seq approach that can be readily applied to other neurodegenerative diseases for which bona fide animal models are available.

Workflow of the intersect-RNA-seq approach

Steps for human/mouse intersect-RNA-seq analysis of neurodegenerative disease-specific mis-splicing and identification of underlying altered splicing factors (SF) and pathogenic effectors. AS = alternative splicing; HD = Huntington’s disease; WB = western blot.