GSE122069
GSE GEOPremature polyadenylation-mediated loss of stathmin-2 is a hallmark of TDP-43-dependent neurodegeneration
Relations
Summary
Amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) are associated with loss of nuclear TDP-43. Here we identify that TDP-43 regulates expression of the neuronal growth-associated factor stathmin-2. Lowered TDP-43 levels, which reduce its binding to sites within the first intron of stathmin-2 pre-mRNA, uncover a cryptic polyadenylation site whose utilization produces a truncated, non-functional mRNA. Reduced stathmin-2 expression is found in neurons trans-differentiated from patient fibroblasts expressing an ALS-causing TDP-43 mutation, in motor cortex and spinal motor neurons from sporadic ALS patients and familial ALS patients with expansion in C9orf72, and in induced pluripotent stem cell (iPSC)-derived motor neurons depleted of TDP-43. Remarkably, while reduction in TDP-43 is shown to inhibit axonal regeneration of iPSC-derived motor neurons, rescue of stathmin-2 expression restores axonal regenerative capacity. Thus, premature polyadenylation-mediated reduction in stathmin-2 is a hallmark of ALS/FTD that functionally links reduced nuclear TDP-43 function to enhanced neuronal vulnerability.
Overall Design
Analysis of gene expression changes linked to TDP-43 loss by siRNA (n=3 biological replicates each conditon) or linked to mutant TDP-43 expression by genome editing in SH-SY5Y cells (n=2 biological replicates each condition).
Analysis (2 steps)
View Data Processing- 50bp single-end FASTQ files were obtained using the Illumina demultiplexing pipeline.
- STAR (Dobin et al., 2013) and RSEM (Li and Dewey, 2011) were used to align the reads to the human reference sequence HG38 and to calculate the raw counts and transcripts per million (TPM) values for genes, respectively
Supplementary Files (1)
GEO Samples (10)
Dataset Citations (1)
SRA Experiments (10) and Runs (10)
Total: 9361 MBSample attributes
Original files (1)
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR8144907 | 37518164 | 1896541486 | 898.05 | SiC_1.fastq.bz2, SRR8144907, SRR8144907.sralite | SRA |
Sample attributes
Original files (1)
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR8144908 | 54292655 | 2742080165 | 1045.09 | SiC_2.fastq.bz2, SRR8144908, SRR8144908.sralite | SRA |
Sample attributes
Original files (1)
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR8144909 | 40925555 | 2065748983 | 809.39 | SiC_3.fastq.bz2, SRR8144909, SRR8144909.sralite | SRA |
Sample attributes
Original files (1)
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR8144910 | 54264948 | 2743073476 | 1300.35 | SiT_1.fastq.bz2, SRR8144910, SRR8144910.sralite | SRA |
Sample attributes
Original files (1)
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR8144911 | 38499682 | 1944559431 | 746.03 | SiT_2.fastq.bz2, SRR8144911, SRR8144911.sralite | SRA |
Sample attributes
Original files (1)
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR8144912 | 66940547 | 3381030375 | 1287.02 | SiT_3.fastq.bz2, SRR8144912, SRR8144912.sralite | SRA |
Sample attributes
Original files (1)
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR8144913 | 36442495 | 1842212645 | 755.76 | 79.fastq.bz2, SRR8144913, SRR8144913.sralite | SRA |
Sample attributes
Original files (1)
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR8144914 | 57874653 | 2925331756 | 1168.21 | 80.fastq.bz2, SRR8144914, SRR8144914.sralite | SRA |
Sample attributes
Original files (1)
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR8144915 | 29845195 | 1508381294 | 627.97 | 81.fastq.bz2, SRR8144915, SRR8144915.sralite | SRA |
Sample attributes
Original files (1)
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR8144916 | 34286894 | 1731619903 | 723.03 | 82.fastq.bz2, SRR8144916, SRR8144916.sralite | SRA |
Linked Publications (1)
Data Files (10)
| Accession | File Name | Stored Type | Output Type | Mapping Assembly | Size | Download | |
|---|---|---|---|---|---|---|---|
| — | 79.fastq.bz2 | RNA-Seq | 755.8 MB | link | |||
| — | 80.fastq.bz2 | RNA-Seq | 1.1 GB | link | |||
| — | 81.fastq.bz2 | RNA-Seq | 628.0 MB | link | |||
| — | 82.fastq.bz2 | RNA-Seq | 723.0 MB | link | |||
| — | SiC_1.fastq.bz2 | RNA-Seq | 898.0 MB | link | |||
| — | SiC_2.fastq.bz2 | RNA-Seq | 1.0 GB | link | |||
| — | SiC_3.fastq.bz2 | RNA-Seq | 809.4 MB | link | |||
| — | SiT_1.fastq.bz2 | RNA-Seq | 1.3 GB | link | |||
| — | SiT_2.fastq.bz2 | RNA-Seq | 746.0 MB | link | |||
| — | SiT_3.fastq.bz2 | RNA-Seq | 1.3 GB | link |