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| Status |
Public on Sep 04, 2020 |
| Title |
Transcriptome Alterations in Myotonic Dystrophy Frontal Cortex |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Myotonic dystrophy is caused by expanded CTG/CCTG microsatellite repeats, leading to multi-systemic symptoms in skeletal muscle, heart, gastrointestinal, endocrine, and central nervous systems (CNS), among others. For many patients, CNS issues can be as or more debilitating than muscle symptoms; they include hypersomnolence, executive dysfunction, white matter atrophy, and neurofibrillary tangles. Although transcriptomes from DM1 skeletal muscle have provided useful insights into pathomechanisms and biomarkers, similarly extensive studies have not yet been performed in the CNS. To elucidate underlying causes of CNS dysfunction in patients, we have generated and analyzed RNA-seq transcriptomes from the frontal cortex of 21 DM1 patients, 4 DM2 patients, and 8 unaffected controls. One hundred and thirty high confidence splicing changes were identified, many occurring exclusively in the CNS and not in the periphery. Mis-spliced exons were found in neurotransmitter receptors, ion channels, and synaptic scaffolds, and we identified an alternative exon in GRIP1 that modulates association with kinesins. Splicing changes exhibited a gradient of severity correlating with CTG repeat length, as measured by optical mapping of individual DNA molecules. All individuals studied, including those with modest splicing defects, showed a subset of alleles with repeats longer than 1000 CTGs. Analyses of gene expression changes showed up-regulation of genes transcribed in microglia and endothelial cells, suggesting neuroinflammation, and down-regulation of genes transcribed in neurons. Gene expression changes for RNAs encoding proteins detectable in CSF were also found to correlate with mis-splicing, with implications for CNS biomarkers of disease severity. These findings provide a framework for future mechanistic and therapeutic studies of CNS issues in DM.
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| Overall design |
We used Illumina RNA-sequencing across a cohort of frozen post-mortem autopsy tissue across 33 individuals to do comparative analysis.
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| Contributor(s) |
Otero BA, Poukalov K, Hildebrandt RP, Thornton CA, Jinnai K, Fujimara H, Kimura T, Hagerman KA, Sampson JB, Day JW, Wang ET |
| Citation(s) |
33472074 |
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| Submission date |
Sep 03, 2020 |
| Last update date |
Sep 01, 2021 |
| Contact name |
Eric T Wang |
| E-mail(s) |
eric.t.wang@ufl.edu
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| Phone |
3522737601
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| Organization name |
University of Florida
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| Department |
Molecular Genetics and Microbiology
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| Lab |
Wang Lab
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| Street address |
2033 Mowry Road
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| City |
Gainesville |
| State/province |
Florida |
| ZIP/Postal code |
32610 |
| Country |
USA |
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| Platforms (1) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
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| Samples (33)
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| Relations |
| BioProject |
PRJNA661286 |
| SRA |
SRP279982 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE157428_DM1expression_TS5.txt.gz |
3.0 Mb |
(ftp)(http) |
TXT |
| GSE157428_DM1psitable_TS2.txt.gz |
4.2 Mb |
(ftp)(http) |
TXT |
| GSE157428_DM2expression_TS6.txt.gz |
1.4 Mb |
(ftp)(http) |
TXT |
| GSE157428_DM2psitable_TS4.txt.gz |
3.0 Mb |
(ftp)(http) |
TXT |
| GSE157428_Supplemental_TS1.txt.gz |
1.1 Kb |
(ftp)(http) |
TXT |
| GSE157428_Supplemental_TS3.txt.gz |
8.7 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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