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MECP2-related pathways are dysregulated in a cortical organoid model of Myotonic dystrophy [bulk RNA-Seq]

ABSTRACT: Myotonic dystrophy type 1 (DM1) is a multisystem, autosomal-dominant inherited disorder caused by CTG microsatellite repeat expansions (MREs) in the 3’ untranslated region of the dystrophia myotonica-protein kinase (DMPK) gene. Despite its prominence as the most common adult-onset muscular dystrophy, patients with congenital to juvenile-onset forms of DM1 can present with debilitating neurocognitive symptoms along the autism spectrum, characteristic of possible in utero cortical defects. However, the molecular mechanism by which CTG MREs lead to these developmental central nervous system (CNS) manifestations is unknown. Here, we showed that CUG foci discovered early in maturation of three-dimensional cortical organoids from DM1 patient-derived induced pluripotent stem cells, cause hyperphosphorylation of CUGBP Elav-Like Family Member 2 (CELF2 ) protein. Integrative single-cell RNA-seq and enhanced crosslinking and immunoprecipitation (eCLIP ) analysis revealed reduced CELF2 protein-RNA substrate interactions resulting in mis-regulation of genes critical for excitatory synaptic signaling in glutamatergic neurons, including key components of the Methyl-CpG binding protein 2 (MECP2) pathway. Comparisons to MECP2(-/-) cortical organoids revealed convergent molecular and cellular defects such as glutamate toxicity and neuronal loss. Our findings provide evidence suggesting that early-onset DM1 might involve neurodevelopmental disorder-associated pathways and identify N-Methyl-D-aspartic acid (NMDA ) antagonists as potential treatment avenues for neuronal defects in DM1. To determine if CUG expansions in DMPK alter cellular RNA composition during differentiation, we performed transcriptomic analyses using RNA-seq at four consecutive developmental stages, ranging from iPSCs to 6-month-old cortical organoids from two independent differentiations. mine We then performed gene expression profiling analysis using data obtained from RNA-seq of 4 different time points.

ORGANISM(S): Homo sapiens

PROVIDER: GSE201897 | GEO | 2022/06/30

REPOSITORIES: GEO

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Project description:Myotonic dystrophy type 1 (DM1) is a multisystem, autosomal-dominant inherited disorder caused by CTG microsatellite repeat expansions (MREs) in the 3’ untranslated region of the dystrophia myotonica-protein kinase (DMPK) gene. Despite its prominence as the most common adult-onset muscular dystrophy, patients with congenital to juvenile-onset forms of DM1 can present with debilitating neurocognitive symptoms along the autism spectrum, characteristic of possible in utero cortical defects. However, the molecular mechanism by which CTG MREs lead to these developmental central nervous system (CNS) manifestations is unknown. Here, we showed that CUG foci discovered early in maturation of three-dimensional cortical organoids from DM1 patient-derived induced pluripotent stem cells, cause hyperphosphorylation of CUGBP Elav-Like Family Member 2 (CELF2 ) protein. Integrative single-cell RNA-seq and enhanced crosslinking and immunoprecipitation (eCLIP ) analysis revealed reduced CELF2 protein-RNA substrate interactions resulting in mis-regulation of genes critical for excitatory synaptic signaling in glutamatergic neurons, including key components of the Methyl-CpG binding protein 2 (MECP2) pathway. Comparisons to MECP2(-/-) cortical organoids revealed convergent molecular and cellular defects such as glutamate toxicity and neuronal loss. Our findings provide evidence suggesting that early-onset DM1 might involve neurodevelopmental disorder-associated pathways and identify N-Methyl-D-aspartic acid (NMDA ) antagonists as potential treatment avenues for neuronal defects in DM1. To evaluate if the post-translational modification of CELF2 impacts its RNA targets, we generated transcriptome-wide eCLIP maps of CELF2 protein-RNA interactions in mature, 6-month-old control and DM1 cortical organoids. All CELF2 eCLIP libraries per organoid line were performed in biologically independent duplicates, with each replicate experiment consisting of a CELF2 (IP) and a paired size-matched input (SMInput) library . We used CLIPper to identify clusters of reads representing regions in the transcriptome significantly associated with CELF2 binding in both neurotypical lines and compared them to DM1 cortical organoids with 600 and 1200 CUG repeats.

Project description:Myotonic dystrophy type 1 is a dominantly inherited multisystemic disease caused by CTG tandem repeat expansions in the DMPK 3' untranslated region. These expanded repeats are transcribed and produce toxic CUG RNAs that sequester and inhibit activities of the MBNL family of developmental RNA processing factors. Although myotonic dystrophy is classified as a muscular dystrophy, the brain is also severely affected by an unusual cohort of symptoms, including hypersomnia, executive dysfunction, as well as early onsets of tau/MAPT pathology and cerebral atrophy. To address the molecular and cellular events that lead to these pathological outcomes, we recently generated a mouse Dmpk CTG expansion knockin model and identified choroid plexus epithelial cells as particularly affected by the expression of toxic CUG expansion RNAs. To determine if toxic CUG RNAs perturb choroid plexus functions, alternative splicing analysis was performed on lateral and hindbrain choroid plexi from Dmpk CTG knockin mice. Choroid plexus transcriptome-wide changes were evaluated in Mbnl2 knockout mice, a developmental-onset model of myotonic dystrophy brain dysfunction. To determine if transcriptome changes also occurred in the human disease, we obtained post-mortem choroid plexus for RNA-seq from donors without neurologically unaffected (two females, three males; ages 50-70) and myotonic dystrophy type 1 donors (one female, three males; ages 50-70). To test that choroid plexus transcriptome alterations resulted in altered CSF composition, we obtained CSF via lumbar puncture from patients with myotonic dystrophy type 1 (five females, five males; ages 35-55) and non-myotonic dystrophy patients (three females, four males; ages 26-51) and Western blot and osmolarity analyses were used to test CSF alterations predicted by choroid plexus transcriptome analysis. We determined that CUG RNA induced toxicity was more robust in the lateral choroid plexus of Dmpk CTG knockin mice due to comparatively higher Dmpk and lower Mbnl RNA levels. Impaired transitions to adult splicing patterns during choroid plexus development were identified in Mbnl2 knockout mice, including mis-splicing previously found in Dmpk CTG knockin mice. Whole transcriptome analysis of myotonic dystrophy type 1 choroid plexus revealed disease-associated RNA expression and mis-splicing events. Based on these RNA changes, predicted alterations in ion homeostasis, secretory output, and CSF composition were confirmed by analysis of myotonic dystrophy type 1 CSF. Our results implicate choroid plexus spliceopathy and concomitant alterations in CSF homeostasis as an unappreciated contributor to myotonic dystrophy type 1 CNS pathogenesis.

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MECP2-related pathways are dysregulated in a cortical organoid model of Myotonic dystrophy [bulk RNA-Seq]

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