A panel of TDP-43-regulated splicing events verify loss of TDP-43 function in amyotrophic lateral sclerosis brain tissue
biorxiv(2023)
摘要
TDP-43 dysfunction is a molecular hallmark of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). A major hypothesis of TDP-43 dysfunction in disease is the loss of normal nuclear function, resulting in impaired RNA regulation and the emergence of cryptic exons. Cryptic exons and exon changes are emerging as promising markers of lost TDP-43 function in addition to revealing biological pathways involved in neurodegeneration in ALS/FTD. In this brief report, we identified markers of TDP-43 loss of function by depleting TARDBP from post-mortem human brain pericytes, a manipulable in vitro primary human brain cell model, and identifying differential exon usage events with bulk RNA-sequencing analysis. We present these data in an interactive database ( ) together with seven other TDP-43-depletion datasets we meta-analysed previously, for user analysis of differential expression and splicing signatures. Differential exon usage events that were validated by qPCR were then compiled into a ‘differential exon usage panel’ with other well-established TDP-43 loss-of-function exon markers. This differential exon usage panel was investigated in ALS and control motor cortex tissue to verify whether, and to what extent, TDP-43 loss of function occurs in ALS. We find that profiles of TDP-43-regulated cryptic exons and changed exon usage discriminate ALS brain tissue from controls, verifying TDP-43 loss of function as a pathomechanism in ALS. We propose that TDP-43-regulated splicing markers with most predictive value for therapeutic intervention will be those based on splicing events that occur both in tissues/biofluids amenable to sampling, and in brain tissue susceptible to disease.
### Competing Interest Statement
The authors have declared no competing interest.
* ALS
: Amyotrophic lateral sclerosis
BBB
: Blood-brain barrier
BSCB
: Blood-spinal cord barrier
cDNA
: Complementary DNA
Ct
: Cycle number threshold
DEU
: Differential exon usage
FTD
: Frontotemporal dementia
LOF
: Loss of function
log2FC
: Log2 fold change
MC
: Motor cortex
mRNA
: Messenger RNA
MTG
: Middle temporal gyrus
PBS
: Phosphate-buffered saline
PCA
: Principal component analysis
qPCR
: Quantitative polymerase chain reaction
RIN
: RNA integrity number
RRM
: RNA recognition motif
Scr
: Scrambled siRNA
SD
: Standard deviation
siRNA
: Small interfering RNA
siTDP
: siRNA against TARDBP
SNP
: Single nucleotide polymorphism
TDP-43
: TAR DNA binding protein of 43 kDa
UTR
: Untranslated region
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