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GSE122069

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Premature polyadenylation-mediated loss of stathmin-2 is a hallmark of TDP-43-dependent neurodegeneration

Organism: Homo sapiens
Platform: GPL20301
Samples: 10
Experiment Types:
Expression profiling by high throughput sequencing
Submitted: Nov 01 2018
Last Updated: Mar 21 2019
Status: Public on Jan 01 2019
Contact: Don,W,Cleveland (Ludwig Institute for Cancer Research)

Relations

BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA503396 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP167447

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
Processing steps for GSE122069
  1. 50bp single-end FASTQ files were obtained using the Illumina demultiplexing pipeline.
  2. 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)

GSE122069_RSEM.gene.TPM.txt.gz Download
GEO Samples (10)

Dataset Citations (1)

Potentially Related Publications (1)

This accession was text-mined from the PMC full text of these publications. It may be referenced for comparison or reused from another study rather than generated for them.

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