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GSE122069

GSE GEO
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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)

SRA Experiments (10) and Runs (10)

Total: 9361 MB
SRX4965534 SRP167447 RNA-Seq SINGLE
GSM3454242: siControl 1; Homo sapiens; RNA-Seq
Sample: SRS4005024
BioProject: PRJNA503396
BioSample: SAMN10359264
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: SH-SY5Y cell line
treatment: siControl
Original files (1)
SH-SY5Y cell line
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR8144907 37518164 1896541486 898.05 SiC_1.fastq.bz2, SRR8144907, SRR8144907.sralite SRA
SRX4965535 SRP167447 RNA-Seq SINGLE
GSM3454243: siControl 2; Homo sapiens; RNA-Seq
Sample: SRS4005023
BioProject: PRJNA503396
BioSample: SAMN10359262
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: SH-SY5Y cell line
treatment: siControl
Original files (1)
SH-SY5Y cell line
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR8144908 54292655 2742080165 1045.09 SiC_2.fastq.bz2, SRR8144908, SRR8144908.sralite SRA
SRX4965536 SRP167447 RNA-Seq SINGLE
GSM3454244: siControl 3; Homo sapiens; RNA-Seq
Sample: SRS4005026
BioProject: PRJNA503396
BioSample: SAMN10359261
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: SH-SY5Y cell line
treatment: siControl
Original files (1)
SH-SY5Y cell line
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR8144909 40925555 2065748983 809.39 SiC_3.fastq.bz2, SRR8144909, SRR8144909.sralite SRA
SRX4965537 SRP167447 RNA-Seq SINGLE
GSM3454245: siTDP-43 1; Homo sapiens; RNA-Seq
Sample: SRS4005030
BioProject: PRJNA503396
BioSample: SAMN10359260
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: SH-SY5Y cell line
treatment: siTDP-43
Original files (1)
SH-SY5Y cell line
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR8144910 54264948 2743073476 1300.35 SiT_1.fastq.bz2, SRR8144910, SRR8144910.sralite SRA
SRX4965538 SRP167447 RNA-Seq SINGLE
GSM3454246: siTDP-43 2; Homo sapiens; RNA-Seq
Sample: SRS4005025
BioProject: PRJNA503396
BioSample: SAMN10359258
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: SH-SY5Y cell line
treatment: siTDP-43
Original files (1)
SH-SY5Y cell line
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR8144911 38499682 1944559431 746.03 SiT_2.fastq.bz2, SRR8144911, SRR8144911.sralite SRA
SRX4965539 SRP167447 RNA-Seq SINGLE
GSM3454247: siTDP-43 3; Homo sapiens; RNA-Seq
Sample: SRS4005027
BioProject: PRJNA503396
BioSample: SAMN10359255
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: SH-SY5Y cell line
treatment: siTDP-43
Original files (1)
SH-SY5Y cell line
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR8144912 66940547 3381030375 1287.02 SiT_3.fastq.bz2, SRR8144912, SRR8144912.sralite SRA
SRX4965540 SRP167447 RNA-Seq SINGLE
GSM3454248: TDP-43 wild type 79; Homo sapiens; RNA-Seq
Sample: SRS4005028
BioProject: PRJNA503396
BioSample: SAMN10359254
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: SH-SY5Y cell line
genotype/variation: wild type
Original files (1)
SH-SY5Y cell line
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR8144913 36442495 1842212645 755.76 79.fastq.bz2, SRR8144913, SRR8144913.sralite SRA
SRX4965541 SRP167447 RNA-Seq SINGLE
GSM3454249: TDP-43 wild type 80; Homo sapiens; RNA-Seq
Sample: SRS4005029
BioProject: PRJNA503396
BioSample: SAMN10359251
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: SH-SY5Y cell line
genotype/variation: wild type
Original files (1)
SH-SY5Y cell line
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR8144914 57874653 2925331756 1168.21 80.fastq.bz2, SRR8144914, SRR8144914.sralite SRA
SRX4965542 SRP167447 RNA-Seq SINGLE
GSM3454250: Mutant TDP-43 (N352S, homozygous) 81; Homo sapiens; RNA-Seq
Sample: SRS4005031
BioProject: PRJNA503396
BioSample: SAMN10359250
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: SH-SY5Y cell line
genotype/variation: Mutant TDP-43
Original files (1)
SH-SY5Y cell line
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR8144915 29845195 1508381294 627.97 81.fastq.bz2, SRR8144915, SRR8144915.sralite SRA
SRX4965543 SRP167447 RNA-Seq SINGLE
GSM3454251: Mutant TDP-43 (N352S, homozygous) 82; Homo sapiens; RNA-Seq
Sample: SRS4005032
BioProject: PRJNA503396
BioSample: SAMN10359248
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: SH-SY5Y cell line
genotype/variation: Mutant TDP-43
Original files (1)
SH-SY5Y cell line
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