Huntington’s disease-specific mis-splicing unveils key effector genes and altered splicing factors

Abstract

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. Non-mutation harboring mis-spliced effector genes are also good candidate therapeutic targets in diseases with more complex etiologies 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 (HD) pathogenesis, here we 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 us to identify the shared mis-splicing signature triggered by the HD-causing mutation in both species and to infer upstream deregulated splicing factors. Moreover, we 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 we report pathogenic global mis-splicing in HD striatum captured by our new intersect-RNA-seq approach that can be readily applied to other neurodegenerative diseases for which bona fide animal models are available.

Deregulation of ncRNA in Neurodegenerative Disease: Focus on circRNA, lncRNA and miRNA in Amyotrophic Lateral Sclerosis

“…In human cells, about 90-95% of genes are subjected to alternative splicing. Genetic mutations affecting such process can lead to the formation of abnormal transcripts or proteins with altered stability and function (Scotti and Swanson, 2016a;Elorza et al, 2021). In fact, several studies have established that missplicing is involved in various diseases such as cancer, muscular dystrophy, neurodegenerative diseases Ule and Blencowe, 2019;Srebrow and Kornblihtt, 2006;Scotti and Swanson, 2016b;Nik and Bowman, 2019. NDs encompass a broad range of neurological disorders characterized by a progressive loss of neurons in specific areas of the brain or spinal cord.…”

“…In general, ncRNAs have been described as significant players in biological regulatory networks that, in turn, affect different protein effectors involved in the response to specific biological stimuli or in determining the future of the cell ( Wang et al, 2019 ). Alternative RNA splicing is a biochemical process in which introns are removed and remaining exons are bound, creating thereby different transcription isoforms of individual genes in order to increase the molecular diversity ( Scotti and Swanson, 2016a ; Bagyinszky et al, 2020 ; Elorza et al, 2021 ). In human cells, about 90–95% of genes are subjected to alternative splicing.…”

Do Fragile X Syndrome and Other Intellectual Disorders Converge at Aberrant Pre-mRNA Splicing?

“…Detailed molecular analysis of targets of translational de-repression in FXS led to the finding that a chromatin modifier, SETD2 (SET domain containing methyltransferase protein), is altered, resulting in downstream alterations in the chromatin landscape and genome-wide aberrant alternative splicing of mRNAs (5). Aberrant alternative splicing has previously been studied in complex NDDs such as ASD (6)(7)(8) and other psychiatric illnesses with a neurodevelopmental trajectory including Schizophrenia (8,9), Bipolar Disorder (8, 9), Huntington's (10), and recently in monogenic IDs such as FXS (5), PTEN (11), and RTT (12-14) (Table 1).…”

“…Alternative splicing is detected in all metazoans and is closely correlated with organismal complexity (25). Furthermore, alternative splicing patterns are tissue-and celltype-specific (10,26), and in vertebrates, mainly contribute to the development and function of the central nervous system. Some neuronal genes such as Neurexins, n-Cadherins, and calciumactivated potassium channels can produce hundreds of mRNA isoforms resulting in a functionally diverse protein arsenal for efficient neuron functioning.…”

Dysregulated Spliceosome Gene Expression May Be a Common Process in Brains of Neurological and Psychiatric Disorders

“…Six associated pathways were over-represented in all 6 disorders, including the major and the minor mRNA splicing pathways and RNA metabolism. Therefore, we found that aberrations in the mRNA splicing process may be a common trajectory to many complex brain disorders involving the spliceosome complex.Recently, AS dysregulation was reported in AD, where several mis-splicing events in the brain have been associated with amyloid burden and neuro brillary [21], ASD, SCZ [28][29][30][31], and Huntington's disease [32,33], furthermore, emerging splicing therapeutics are promising therapeutic approaches in aberrant/deregulated AS [34][35][36][37][38], and clinical trials are currently underway for spinal muscular atrophy (https://clinicaltrials.gov/ct2/show/NCT04240314).We hypothesize that the excessive splicing changes observed in brain conditions may be related to changes in their regulators, spliceosome-related genes (SGs). Therefore, this study aims at identifying SG expression changes in multiple brain disorders using postmortem brain transcriptome data.…”