Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Alzheimer’s, Parkinson’s disease and Amyotrophic Lateral Sclerosis gene expression patterns divergence reveals different grade of RNA metabolism involvement

ABSTRACT: Alzheimer’s disease (AD), Parkinson’s disease (PD) and Amyotrophic Lateral Sclerosis (ALS) are neurodegenerative disorders characterized by progressive degeneration of central or peripheral nervous system. A central role of RNA metabolism has emerged in these diseases, concerning mRNAs processing and non-coding RNAs biogenesis. We aimed to identify possible crossroads or deviations in the dysregulated pathways of AD, PD and ALS. We performed RNA-seq analysis to investigate the regulation of both coding and long non-coding RNAs (lncRNAs) in ALS, AD and PD patients and controls (CTRL) in Peripheral Blood Mononuclear Cells (PBMCs). A total of 293 differentially expressed (DE) lncRNAs and 87 mRNAs was found in ALS patients. In AD patients a total of 23 DE genes have emerged, 19 protein coding genes and 4 lncRNAs. By performing KEGG and GO analysis we found common affected pathways and biological processes in ALS and AD. In PD patients only 5 genes were found DE. Our data brought the light on the different importance of lncRNAs and mRNAs regulation in the principal neurodegenerative disorders, offering starting points for new investigations about pathogenic mechanism involved in them.

ORGANISM(S): Homo sapiens

PROVIDER: GSE161199 | GEO | 2020/12/21

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

A transcriptome analysis study on mRNA and long non-coding RNAs in patients with Parkinson’s disease

Project description:Parkinson’s disease (PD) is the second most common neurodegenerative disorder, affecting ~2–3% of people over 65 years of age. Recent studies have revealed that the molecular pathogenesis of PD involves a series of pathways and neurobiological processes, such as protein degradation, mitochondrial dysfunction, oxidative stress, autophagy, calcium homeostasis, axonal transport, and neuroinflammation, all suggesting that both the onset and course of PD is a complex multilevel and systematic process. Accumulating evidence demonstrates that long non-coding RNAs (lncRNAs) affect the pathogenesis of several diseases, such as cancers, immunological diseases, and neurodegenerative disorders, including Alzheimer’s disease and PD. Next generation sequencing provides a high-throughput method for exploring the diverse polyadenylated RNA populations. This approach allows accurate identification and quantitation of mRNAs and other non-coding RNAs, such as lncRNAs. The present study explored mRNAs and lncRNAs expression by using the next generation sequencing analysis (NGS) and the quantitative real-time PCR (qRT-PCR) assay for the confirmation of the NGS results, followed by functional analysis of the results.

2023-01-16 | E-MTAB-11326 | biostudies-arrayexpress

Long non-coding and coding RNAs characterization in Peripheral Blood Mononuclear Cells and Spinal Cord from Amyotrophic Lateral Sclerosis patients

Project description:Alteration in RNA metabolism, concerning both coding and long non-coding RNAs (lncRNAs), may play an important role in Amyotrophic Lateral Sclerosis (ALS) pathogenesis. In this work, we performed RNA-seq analysis to investigate, in Peripheral Blood Mononuclear Cells (PBMC) and spinal cord tissues, the regulation of non-coding and coding RNAs in Sporadic ALS patients (SALS), ALS mutated (FUS, TARDBP and SOD1) patients and matched controls. A total of 293 differentially expressed (DE) lncRNAs were found in SALS patients, as instead a limited amount of lncRNAs was found deregulated in mutated patients. Out of 87 mRNAs detected as differentially expressed in SALS patients, the 10 most differentially expressed were down-regulated and associated to transcription regulation, immunity and apoptosis pathways. 2 Taken together our data highlighted the importance, for the understanding of ALS disease, of extending the knowledge on transcriptome molecular alterations and on the significance in the disease of the classes of regulatory lncRNAs. Our data brought the light on the importance of lncRNAs and mRNAs regulation in central and peripheral systems, offering starting points for new investigations about pathogenic mechanism involved in ALS disease.

2018-04-22 | GSE106443 | GEO

Distinct Expression Profiles of long non-coding RNAs and messenger RNAs in circulating leukocytes of Parkinson’s disease

Project description:The molecular mechanism underlying Parkinson's disease (PD), an increasingly common neurodegenerative disease, remains unclear. Long non-coding RNA (lncRNA) plays essential roles in gene expression and human disease. We hypothesize that lncRNAs are involved in the pathogenesis of PD. We profiled the expression of lncRNA in circulating leukocytes of 5 PD patients and 5 healthy controls using microarray.

2019-12-04 | GSE133347 | GEO

Deshpande2019 - Random Forest model to predict long non-coding RNAs from coding RNAs in Zea Mays plant transcriptomic data

Project description:This is a Random Forest algorithm-based machine learning model to predict lncRNAs from coding mRNAs in plant transcriptomic data. The model assigns 1 for coding sequences and 2 for long non-coding sequences. The prediction is performed using a combination of Open Reading Frame (ORF) based, Sequence-based and Codon-bias features. Users need to download the curated ONNX model and also need to convert the sequences into feature matrix as mentioned in PLIT paper (Deshpande et al. 2019) to make predictions on sequences from Zea Mays sequence data.

2023-05-22 | BIOMD0000001067 | BioModels

One-shot analysis of translated mammalian lncRNAs with AHARIBO

Project description:A vast portion of the mammalian genome is transcribed as long non-coding RNAs (lncRNAs) acting in the cytoplasm with largely unknown functions. Surprisingly, lncRNAs have been shown to interact with ribosomes, encode uncharacterized proteins, or act as ribosome sponges. These functions still remain mostly undetected and understudied owing to the lack of efficient tools for genome-wide simultaneous identification of ribosome-associated lncRNAs and peptide-producing lncRNAs. Here we present AHARIBO, a method for the detection of lncRNAs either untranslated, but associated with ribosomes, or encoding small peptides. Using AHARIBO in mouse embryonic stem cells during neuronal differentiation, we isolated ribosome-protected RNA fragments, translated RNAs and corresponding de novo synthesized polypeptides. Besides identifying mRNAs under active translation and associated ribosomes, we found and distinguished lncRNAs acting as ribosome sponges or encoding micropeptides, laying the ground for a better functional understanding of hundreds lncRNAs.

2021-09-09 | PXD022679 | Pride

Comprehensive transcriptome profiling reveals multigene signatures in triple negative breast cancer

Project description:To develop and validate novel multigene signatures to facilitate individualized treatment of TNBC patients By integrating expression profiles of messenger RNAs (mRNAs) and long non-coding RNAs (lncRNAs). We analysed 165 TNBC samples and 33 paired normal breast tissues using transcriptome microarrays. Tumor-specific mRNAs and lncRNAs were identified and correlated with patientsâ?? recurrence-free survival (RFS). Using Cox regression model, we built two multigene signatures incorporating mRNAs and lncRNAs. The prognostic and predictive accuracy of the signatures were tested in a training set of 165 TNBC patients and validated in another 101 TNBC patients.

2016-01-04 | E-GEOD-76250 | biostudies-arrayexpress

Transcriptome-Wide Identification of Differentially Expressed Genes and Long Non-coding RNAs in Nitroglycerin Tolerant Rat Aorta

Project description:We investigated comprehensive transcriptomic change in rat aorta tolerant to nitroglycerin (GTN) with a focus on lncRNAs. We employed RNA sequencing (RNA-seq) technique and identified 22788 genes (RPKM > 0.1, 14720 protein coding and 4408 lncRNA). And 115 differentially expressed (DE) mRNAs (65 upregulated and 50 downregulated) and 104 DE lncRNAs (56 upregulated and 48 downregulated) were found in GTN-tolerant aortas. Many DE mRNAs and cis-target genes of DE lncRNAs have been implicated in regulation of blood pressure or cell contraction. Collectively, these results suggested that dysregulated mRNAs and lncRNAs contribute to the development of GTN tolerance and might be used as novel potential targets to prevent and reverse GTN tolerance.

2019-08-01 | GSE121924 | GEO

Expression profiles and potential functions of long non-coding RNAs and mRNAs in autoimmune pulmonary alveolar proteinosis patients

Project description:Autoimmune pulmonary alveolar proteinosis (APAP) is a rare lung disease which may be closely associated with autoantibody. However, there is little known about the function of long non-coding RNAs (lncRNAs) in APAP.To further investigate the role of lncRNAs in APAP, we screened the differential expression profiles of lncRNAs and mRNAs in peripheral blood samples between five APAP patients and five matched healthy controls. We analyzed the regulatory networks of lncRNA-mRNA and lncRNA-miRNA-mRNA via bioinformatics methods. This study identified differentially expressed (DE) lncRNAs and their potential corresponding mRNAs to provide a basis for the study of APAP pathogenesis.

2021-04-28 | GSE153957 | GEO

Gene expression analysis to identify long noncoding RNAs deregulated in Myc-driven B cell lymphoma

Project description:Myc is a well known transcription factor with important roles in cell cycle, apoptosis and cellular transformation. Long non-coding (lnc)RNAs have recently emerged as a important class of regulatory RNAs. Here, we show that lncRNAs are an extensive component of the Myc-regulated transcriptional program. Using the P493-6 inducible Myc model we demonstrate that both Myc-induced mRNAs and lncRNAs were significant enriched for Myc binding sites. In contrast to Myc-repressed mRNAs, Myc-repressed lncRNAs were significantly enriched for Myc binding sites. Subcellular localization analysis revealed that Myc-repressed lncRNAs and mRNAs are enriched in the nucleus while Myc-induced lncRNAs and mRNAs are enriched both in the cytoplasm and nucleus. Parallel analysis of differentially expressed lncRNAs and mRNAs identified 105 lncRNA-mRNA pairs that were in close vicinity, indicative for regulation in cis. To support the potential relevance of the Myc-regulated lncRNAs in cellular transformation, we analyzed their expression in primary Myc-high and Myc-low B-cell lymphomas. In total, 54% of the lncRNAs differentially expressed between the lymphoma subsets were identified as Myc-regulated in P493-6 cells. This study is the first to show that lncRNAs are an important factor within the Myc-regulated transcriptional program and indicates a marked difference between Myc-repressed lncRNAs and mRNAs. Expression of all known mRNAs and >10 000 lncRNAs was assessed in primary lymphoma tissue with high c-myc levels (Burkitt lymphoma; BL) and low c-myc levels (chronic lymphocytic leukemia; CLL)

2015-02-01 | E-GEOD-59479 | biostudies-arrayexpress

Identification of LncRNAs Differentially Expressed in the Serum of Alzheimer’s patients

Project description:Alzheimer’s disease (AD) is a common primary senile neurodegenerative disease which is the most common cause of dementia. The clinical manifestations are mainly progressive memory decline, cognitive dysfunction, behavioral abnormalities and personality disorders. Due to the unclear pathogenesis and the complexity of the pathogenesis, no AD drugs can reverse the disease process. Therefore, it is particularly important to reveal the underlying mechanism of AD. Many studies indicate that it is a multifactorial disease. However, the role of LncRNAs in the pathogenesis of AD remains unclear. In order to identify the transcriptional regulators of AD, we compared the expression of LncRNA in serum of AD patients and healthy volunteers by microarray analysis. This analysis revealed a set of LncRNAs specifically regulated in AD patients. These findings imply that lncRNA may play an important role in AD.

2021-08-28 | GSE182910 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data