Gene expression analysis of the impact of TDP-43 knockout in human cells.
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA562297 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10045016_1.fastq.gz | Fastqsanger.gz | |||
| SRR10045016_2.fastq.gz | Fastqsanger.gz | |||
| SRR10045017_1.fastq.gz | Fastqsanger.gz | |||
| SRR10045017_2.fastq.gz | Fastqsanger.gz | |||
| SRR10045018_1.fastq.gz | Fastqsanger.gz |
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Project description:Purpose: The goal of this stuydy was to apply transcriptome profiling (RNA-seq) to human cells that either express or which lack the TDP-43 protein. Methods: mRNA profiles of TDP-43 KO HeLa cells and "rescued" TDP-43 KO cells wherein a wildtype TDP-43 transgene was re-expressed at endogenous levels were generated by deep sequencing, in triplicate, on Illumina’s HiSeq 2500 using 2x70bp paired-end reads, generating 104.4-128.2 million reads (52.2-64.1 million pairs) per sample. . The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat2 followed by Cufflinks Cuffmerge and Cuffdiff to define transcripts and establish their abundance and finally to perform differential gene expression analysis, using the assembled known plus novel transcripts . Results: Using an optimized data analysis workflow, we mapped approximately 50-60 million reads per sample to the human genome (build hg19) and identified transcripts whose abundance differed between the TDP-43 KO versus "rescued" conditions. Conclusions: Our study presents a detailed analysis of the impact of the knockout of TDP-43 on the transcriptome of a human cell line. The results reported here should provide a framework for defining transcripts whose abundnace and splicing are regulated by TDP-43.
2019-09-09 | GSE136366 | GEO
Project description:To investigate how translation changed as a function of TDP-43 CR loss, mass spectrometry (MS) based approach was performed to monitor the dynamics of TDP-43-associated protein complexes in response to CR deletion using TDP-43 knockout HEK293 cells expressing strep tagged wild type TDP-43 (TDP-43WT) or TDP-43ΔCR mutant.
2022-05-20 | PXD027494 | Pride
Project description:MicroRNAs (miRNAs) play important roles in a wide range of cellular processes. Aberrant regulation of miRNA genes contributes to human diseases, including cancer. The TAR DNA binding protein 43 (TDP-43), a DNA/RNA binding protein associated with neurodegeneration, is involved in miRNA biogenesis. Here, we systematically examined miRNAs whose expression levels are regulated by TDP-43 using RNA-Seq coupled with siRNA-mediated knockdown approach. TDP-43 knocking down affected the expression of a number of miRNAs. Alterations in isomiR patterns and miRNA arm selection after TDP-43 knockdown suggest a role of TDP-43 in miRNA editing. We examined correlation of selected TDP-43 associated miRNAs and their candidate target genes in human cancers. Our data reveal highly complex roles of TDP-43 in regulating different miRNAs and their target genes. Our results suggest that TDP-43 may promote migration of lung cancer cells by regulating miR-423-3p expression. On the other hand, TDP-43 increases miR-500a-3p expression and binds to the mature miR-500a-3p sequence. Low expression of miR-500a-3p was associated with poor survival of lung cancer patients, suggesting that TDP-43 may have a suppressive role in cancer by regulating miR-500a-3p. Our experiments reveal that cancer-associated genes LIF and PAPPA may be targets of miR-500a-3p. Together with other studies, our work suggests that TDP-43-regulated miRNAs may play multi-facet roles in the pathogenesis of cancer.
2016-08-02 | GSE85065 | GEO
Project description:MicroRNAs (miRNAs) play important roles in a wide range of cellular processes. Aberrant regulation of miRNA genes contributes to human diseases, including cancer. The TAR DNA binding protein 43 (TDP-43), a DNA/RNA binding protein associated with neurodegeneration, is involved in miRNA biogenesis. Here, we systematically examined miRNAs whose expression levels are regulated by TDP-43 using RNA-Seq coupled with siRNA-mediated knockdown approach. TDP-43 knocking down affected the expression of a number of miRNAs. Alterations in isomiR patterns and miRNA arm selection after TDP-43 knockdown suggest a role of TDP-43 in miRNA editing. We examined correlation of selected TDP-43 associated miRNAs and their candidate target genes in human cancers. Our data reveal highly complex roles of TDP-43 in regulating different miRNAs and their target genes. Our results suggest that TDP-43 may promote migration of lung cancer cells by regulating miR-423-3p expression. On the other hand, TDP-43 increases miR-500a-3p expression and binds to the mature miR-500a-3p sequence. Low expression of miR-500a-3p was associated with poor survival of lung cancer patients, suggesting that TDP-43 may have a suppressive role in cancer by regulating miR-500a-3p. Our experiments reveal that cancer-associated genes LIF and PAPPA may be targets of miR-500a-3p. Together with other studies, our work suggests that TDP-43-regulated miRNAs may play multi-facet roles in the pathogenesis of cancer. small RNA seq in SH-SY-5Y, SNB-19 and HT22 (TDP-43 siRNA VS Control siRNA)
2016-08-02 | E-GEOD-85065 | biostudies-arrayexpress
Project description:TDP-43 is an RNA/DNA-binding protein implicated in transcriptional repression and mRNA processing. Inclusions of TDP-43 are hallmarks of frontotemporal dementias and amyotrophic lateral sclerosis. Besides aggregation of TDP-43, loss of nuclear localization is observed in disease. To identify relevant targets of TDP-43, we performed an expression profiling study. Thereby, histone deacetylase 6 (HDAC6) downregulation was discovered upon TDP-43 silencing on mRNA and protein level in human embryonic kidney HEK293E and neuronal SH-SY5Y cells. This was accompanied by accumulation of the major HDAC6 substrate, acetyl-tubulin. Expression of wild-type but neither RNA-binding- nor nuclear-localization-deficient TDP-43 restored HDAC6 expression. Moreover, TDP-43 bound specifically to HDAC6 mRNA arguing for a direct functional interaction. Importantly, in vivo validation in TDP-43 knockout Drosophila melanogaster also showed HDAC6 mRNA decrease. HDAC6 is necessary for protein aggregate formation and degradation. Indeed, downregulation of HDAC6 reduced aggregate formation and increased cytotoxicity of expanded poly-glutamine ataxin-3 in TDP-43 silenced cells. This was completely restored by co-transfection with HDAC6. In conclusion, loss of functional TDP-43 causes HDAC6 downregulation and might thereby contribute to pathogenesis.
2009-10-20 | GSE18632 | GEO
Project description:The human Tar-DNA-binding protein TDP-43 is closely associated with ALS and other neurodegenerative disorders. TDP-43 contains two highly conserved RNA-binding motifs and possesses a variety of documented roles in RNA metabolism, including pre-RNA splicing and repression of transcription. We sought to measure the effect that knockout and over-expression of the fly orthologue of this protein, Tar-DNA-binding protein homolog (TBPH), has on the transcriptome of the central nervous system (CNS) of Drosophila melanogaster. To this end, we used massively parallel sequencing methods (RNA-seq) to transcriptionally profile the CNS in loss-of-function mutants and gain-of-function over-expression genotypes. We found that loss of TBPH resulted in widespread gene activation, much of which could be reversed by rescue of TBPH expression, suggesting that repression is one of the major roles of TBPH. Conversely, we found that over-expression of TBPH resulted largely in decreased gene expression. However, there was little overlap in the genes which were affected in these two genotypes, suggesting that the bulk of genes affected by TBPH loss-of-function and over-expression are different. We provide a comprehensive look at enriched gene ontologies in both cases, suggesting that TDP-43 plays a role in regulating basic processes in neurons. We also describe a number of genes whose splicing is likely to be altered in the absence of TDP-43. In this study we compare the effects of knockout of the TDP-43 ortholog (TBPH) in the fly nervous system with the effects of its overexpression. 2 treatment groups are presented. In the first, TDP-43 knockout (G2) is compared to control (A1) and rescue (G2; TDP-43-GAL4>UAS-TDP-43). In the second comparison, the motor neuron driver D42-GAL4 is used to overexpress TDP-43 in motor neurons, using LacZ as a control for overexpression of a foreign protein.
2012-06-30 | E-GEOD-31194 | biostudies-arrayexpress
Project description:The aim of this study is to understand the mechanisms of TDP-43 neurotoxicity. Here, we perform a RNA-Seq analysis in TDP-43 gain-of-fucntion (GOF) , TDP-43 loss-of-function and wild-type late pupae heads (73-90 hours APF) and perform TDP-43 GOF vs wild type and TDP-43 LOF vs wild-type differential expression analysis to show that both mechanisms presents defects in ecdysone receptor (ECR)-dependeint transcriptional program switching, and strongly deregulate expression from the neuronal microtubule associated protien Map205. RNA-seq was performed in two wild-type D.melanogaster biological replicates (Canton S, w1118 ), four biological replicates for TDP-43 (LOF) with two distinct genotypes (dTDP-43Δ142/Df(2R)106,dTDP-43Δ23/Δ142 ) and two TDP-43 GOF biological replicates (act5c>dTDP-43 ).
2013-01-22 | E-GEOD-42844 | biostudies-arrayexpress
Project description:The aim of this study is to understand the mechanisms of TDP-43 neurotoxicity. Here, we perform a RNA-Seq analysis in TDP-43 gain-of-fucntion (GOF) , TDP-43 loss-of-function and wild-type late pupae heads (73-90 hours APF) and perform TDP-43 GOF vs wild type and TDP-43 LOF vs wild-type differential expression analysis to show that both mechanisms presents defects in ecdysone receptor (ECR)-dependeint transcriptional program switching, and strongly deregulate expression from the neuronal microtubule associated protien Map205.
2013-01-22 | GSE42844 | GEO
Project description:TDP-43 is an important RNA binding protein. To better understand its binding targets in human neurons, we performed TDP-43 iCLIP on SHSY5Y cells.
2022-02-02 | E-MTAB-11243 | biostudies-arrayexpress
Project description:TDP-43 proteinopathies including frontotemporal lobar dementia (FTLD) and amyotrophic lateral sclerosis (ALS) are devastating neurodegenerative disorders characterized by aggregation and mislocalization of the nucleic-acid binding protein TDP-43 and subsequent neuronal dysfunction. Here, we developed an endogenous model of sporadic TDP-43 proteinopathy based on the principle that disease-associated TDP-43 acetylation at lysine 145 (K145) alters TDP-43 conformation, impairs its RNA-binding capacity, and induces downstream mis-regulation of target genes. Expression of aberrant acetylation-mimic TDP-43K145Q resulted in stress-induced phase-separated nuclear TDP-43 foci formation and loss-of-TDP-43-function in mouse primary neurons and human induced pluripotent stem cell (iPSC)-derived neurons. Aged mice harboring the single TDP-43K145Q mutation recapitulate several key hallmarks of neurodegenerative proteinopathies, including progressive TDP-43 phosphorylation and insolubility, cytoplasmic mis-localization, widespread transcriptomic and splicing alterations, and cognitive dysfunction. Our study supports a model in which aberrant TDP-43 acetylation drives neuronal dysfunction and cognitive decline through alternative splicing and transcription of genes important in synaptic plasticity and apoptosis, providing a new paradigm to interrogate FTLD disease mechanisms and uncover disease-modifying therapeutics.
2023-01-09 | GSE216294 | GEO