Proteomic analyses reveal that loss of TDP-43 affects RNA processing and intracellular transport

Štalekar, Maja; Yin, Xiaoke; Rebolj, K.; Darovic, Simona; Troakes, Claire; Mayr, Manuel; Shaw, Christopher E.; Rogelj, Boris

doi:10.1016/j.neuroscience.2015.02.046

Cited by 53 publications

(63 citation statements)

References 73 publications

(81 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Consistent with this possibility, a recent proteomic study of TDP-43 depletion in human SH-SY5Y cells [63] that protein levels were changed for 3 of the 95 human cryptic exon containing genes. Two, HUWE1 and GOLGB1 had protein levels that were 8 and 31% of the control cells respectively whereas the third, HNRNPH3 was found to be 7-fold increased under TDP-43 depletion.…”

Section: Discussionmentioning

confidence: 66%

See 1 more Smart Citation

Quantitative analysis of cryptic splicing associated with TDP-43 depletion

Humphrey

Emmett

Fratta³

et al. 2017

BMC Med Genomics

View full text Add to dashboard Cite

BackgroundReliable exon recognition is key to the splicing of pre-mRNAs into mature mRNAs. TDP-43 is an RNA-binding protein whose nuclear loss and cytoplasmic aggregation are a hallmark pathology in amyotrophic lateral sclerosis and frontotemporal dementia (ALS/FTD). TDP-43 depletion causes the aberrant inclusion of cryptic exons into a range of transcripts, but their extent, relevance to disease pathogenesis and whether they are caused by other RNA-binding proteins implicated in ALS/FTD are unknown.MethodsWe developed an analysis pipeline to discover and quantify cryptic exon inclusion and applied it to publicly available human and murine RNA-sequencing data.ResultsWe detected widespread cryptic splicing in TDP-43 depletion datasets but almost none in another ALS/FTD-linked protein FUS. Sequence motif and iCLIP analysis of cryptic exons demonstrated that they are bound by TDP-43. Unlike the cryptic exons seen in hnRNP C depletion, those repressed by TDP-43 cannot be linked to transposable elements. Cryptic exons are poorly conserved and inclusion overwhelmingly leads to nonsense-mediated decay of the host transcript, with reduced transcript levels observed in differential expression analysis. RNA-protein interaction data on 73 different RNA-binding proteins showed that, in addition to TDP-43, 7 specifically bind TDP-43 linked cryptic exons. This suggests that TDP-43 competes with other splicing factors for binding to cryptic exons and can repress cryptic exon inclusion.ConclusionsOur quantitative analysis pipeline confirms the presence of cryptic exons during the depletion of TDP-43 but not FUS providing new insight into to RNA-processing dysfunction as a cause or consequence in ALS/FTD.Electronic supplementary materialThe online version of this article (doi:10.1186/s12920-017-0274-1) contains supplementary material, which is available to authorized users.

show abstract

Section: Discussionmentioning

confidence: 66%

“…In addition, IGF2BP1 has been reported as binding to TDP-43 in HEK293T and HeLa cell extracts [57, 58], whereas SRSF7 was reported as binding to TDP-43 in mouse N2A cells [56]. None of the observed proteins have been reported to change their protein level in response to TDP-43 depletion [63]. …”

Section: Discussionmentioning

confidence: 99%

Quantitative analysis of cryptic splicing associated with TDP-43 depletion

Humphrey

Emmett

Fratta³

et al. 2017

BMC Med Genomics

View full text Add to dashboard Cite

show abstract

“…Transportin 1 does not directly bind to TDP-43 [45] but TDP-43 aggregates sequester Transportin 1 in the cytoplasm of cortical neurons contributing to nucleo-cytoplasmic transport defects [13]. It has also been suggested that depletion of TDP-43 results in elevated levels of Transportin 1 [63]. Thus, our results suggest that nucleo-cytoplasmic transport is an important contributing factor in CSMN degeneration due to TDP-43 dysregulation.…”

Section: Discussionmentioning

confidence: 81%

Mitochondria, ER, and nuclear membrane defects reveal early mechanisms for upper motor neuron vulnerability with respect to TDP-43 pathology

et al. 2018

View full text Add to dashboard Cite

Insoluble aggregates containing TDP-43 are widely observed in the diseased brain, and defined as “TDP-43 pathology” in a spectrum of neurodegenerative diseases, such as amyotrophic lateral sclerosis (ALS), Alzheimer’s disease and ALS with frontotemporal dementia. Here we report that Betz cells of patients with TDP-43 pathology display a distinct set of intracellular defects especially at the site of nuclear membrane, mitochondria and endoplasmic reticulum (ER). Numerous TDP-43 mouse models have been generated to discern the cellular and molecular basis of the disease, but mechanisms of neuronal vulnerability remain unknown. In an effort to define the underlying causes of corticospinal motor neuron (CSMN) degeneration, we generated and characterized a novel CSMN reporter line with TDP-43 pathology, the prp-TDP-43A315T-UeGFP mice. We find that TDP-43 pathology related intracellular problems emerge very early in the disease. The Betz cells in humans and CSMN in mice both have impaired mitochondria, and display nuclear membrane and ER defects with respect to TDP-43 pathology.

show abstract

“…Recently, novel hypotheses have emerged about how loss of nuclear TDP-43 function may lead to neuronal dysfunction and degeneration. In mouse embryonic stem cell, HeLa cell, and conditional TDP-43 knockout mouse models, TDP-43 mutations, depletion, or sequestration into inclusions lead to aberrant splicing [3, 38, 56, 75] and altered expression of numerous proteins [57, 70], including those involved in nucleocytoplasmic transport, RNA processing, and DNA repair. Loss of nuclear TDP-43 results in, for example, incorporation of cryptic exons into mRNAs [33, 38, 74, 75]; often such exons introduce frameshifts or premature stop codons that lead the transcript to undergo nonsense mediated decay.…”

Section: Discussionmentioning

confidence: 99%

Neurons selectively targeted in frontotemporal dementia reveal early stage TDP-43 pathobiology

et al. 2018

View full text Add to dashboard Cite

TAR-DNA binding protein 43 (TDP-43) aggregation is the most common pathological hallmark in frontotemporal dementia (FTD) and characterizes nearly all patients with motor neuron disease (MND). The earliest stages of TDP-43 pathobiology are not well characterized, and whether neurodegeneration results from TDP-43 loss-of-function or aggregation remains unclear. In the behavioral variant of FTD (bvFTD), patients undergo selective dropout of von Economo neurons (VENs) and fork cells within the frontoinsular (FI) and anterior cingulate cortices. Here, we examined TDP-43 pathobiology within these vulnerable neurons in the FI across a clinical spectrum including 17 patients with sporadic bvFTD, MND, or both. In an exploratory analysis based on our initial observations, we further assessed 10 patients with C9orf72-associated bvFTD/MND. VENs and fork cells showed early, disproportionate TDP-43 aggregation that correlated with anatomical and clinical severity, including loss of emotional empathy. The presence of a TDP-43 inclusion was associated with striking nuclear and somatodendritic atrophy. An intriguing minority of neurons lacked detectable nuclear TDP-43 despite the apparent absence of a cytoplasmic TDP-43 inclusion. These cells showed neuronal atrophy comparable to inclusion-bearing neurons, suggesting that loss of nuclear TDP-43 function promotes neurodegeneration, even when TDP-43 aggregation is inconspicuous or absent.

show abstract

Proteomic analyses reveal that loss of TDP-43 affects RNA processing and intracellular transport

Cited by 53 publications

References 73 publications

Quantitative analysis of cryptic splicing associated with TDP-43 depletion

Quantitative analysis of cryptic splicing associated with TDP-43 depletion

Mitochondria, ER, and nuclear membrane defects reveal early mechanisms for upper motor neuron vulnerability with respect to TDP-43 pathology

Neurons selectively targeted in frontotemporal dementia reveal early stage TDP-43 pathobiology

Contact Info

Product

Resources

About