Bulk RNA-seq of human nucleusus pulposus from disc-degenerated patients
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA831444 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR18906889_1.fastq.gz | Fastqsanger.gz | |||
| SRR18906889_2.fastq.gz | Fastqsanger.gz | |||
| SRR18906890_1.fastq.gz | Fastqsanger.gz | |||
| SRR18906890_2.fastq.gz | Fastqsanger.gz | |||
| SRR18906891_1.fastq.gz | Fastqsanger.gz |
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Project description:Failure of the nucleus pulposus (NP) causes intervertebral disc (IVD) disease and associated low-back pain, which are highly prevalent among the aged populations. Molecular and cellular changes underpinning the structural failures in age-associated IVD diseases (IDDs) remain poorly elucidated. Here, we first identified that TAGLN, which encodes the cytoskeleton regulator transgelin, was transcribed in healthy NPs of both human and mouse, but diminished with ageing. Immunostaining showed that TAGLN were expressed on the peripheral of mouse NP (periNP). Lineage analyses in Tagln-CreERT2 mice showed that NP cells were derived from Tagln+ cells in the periNP. The PeriNP cells were proliferative and can differentiate into the inner NP (innerNP). These Tagln+ cells and their descendants diminish with ageing or puncture-induced degeneration. Single-cell transcriptomics from neonatal and adult Tagln-CreERT2 IVDs confirmed that Tagln descendants uniquely populate the NP, wherein four sub-populations were identified: chondrocyte-like, Cd228+, Tagln+ and Car3+. Immunostaining confirmed Car3 expressed in innerNP. Computational analysis indicated the lineage trajectory from Tagln+ to Car3+ sub-population, along with the involvement of Fos/Jun/TGFβ cascades and partial epithelial-to-mesenchymal transition process. Removal of TGFβ mediator Smad4 by notochord specific Foxa2mNE-Cre resulted in decreased Tagln+ cells and abnormal disc morphology, resembling disc degeneration. Our study generates a single-cell transcriptomic atlas for healthy IVD, identifies Tagln+ PeriNP cells as a progenitor pool crucial for the IVD homeostasis, and provides potential targets for regenerative cell therapy against IVD degeneration.
2024-05-14 | GSE201396 | GEO
Project description:In order to discover the cell type in nucleus pulposus and find the cell type specific genetic change during intervertebral disc degeneration, we applied single cell RNA sequencing of nucleus pulposus tissue from degenerated and non-degenerated disc.
2023-12-31 | GSE153066 | GEO
Project description:MicroRNAs expression profiling of human nucleus pulposus cells derived from patients with disc degeneration in comparison with those derived from patients with scoliosis as control. Two-condition experiment: control nucleus pulposus cells vs. degenerative nucleus pulposus cells. Biological replicates: 3 control, 3 degenerated, independently harvested. Four replicates per array. The supplementary file 'GSE19943_fold_pvalue.txt' contains fold-changes and p-values.
2012-01-01 | E-GEOD-19943 | biostudies-arrayexpress
Project description:MicroRNA expression profiling of human nucleus pulposus derived from patients with IDD in comparison with those derived from cadaveric disc as normal control. We have identified the expression profiles of miRNAs in IDD using scoliotic nucleus pulposus as controls (GSE19943). It is noteworthy that scoliotic discs are not strictly normal discs. Therefore, the microRNA expression profiles were revisited using normal discs as control. Two-condition experiment: control nucleus pulposus vs. degenerative nucleus pulposus. Biological replicates: 5 control, 5 degenerated, independently harvested (the same samples as in GSE56081). Four replicates per array.
2016-06-30 | E-GEOD-63492 | biostudies-arrayexpress
Project description:Assessment of the putative differential gene expression profiles in high osmolality-treated bovine nucleus pulposus intervertebral disc cells for a short (5 h) and a long (24 h) time period. Identification of novel genes up- or down-regulated as an early or a late response to hyperosmotic stress. A 5 and 24 h-hyperosmotic treatment of nucleus pulposus cells led to transcriptional changes in >100 and 200 genes, respectively. Nucleus pulposus intervertebral disc cells were exposed to hyperosmotic stress for 5 and 24 h before RNA extraction and transcriptomics analysis. Three biological replicates were tested for each condition. Selected genes found to be differentially expressed were validated by RT-qPCR. Functional experiments were performed in order to assess the role of specific proteins encoded by genes found to be up-regulated in the osmo-reguatory response of intervertebral disc cells.
2015-06-19 | E-GEOD-59485 | biostudies-arrayexpress
Project description:Circular RNA expression profiling of human nucleus pulposus derived from patients with IDD in comparison with those derived from cadaveric disc as normal control. We have identified the expression profiles of miRNAs (GSE63492), lncRNAs, mRNAs (GSE56081) in IDD using 5 normal discs as control and 5 IDD discs. Accumulating evidence indicates that circRNAs are key regulators of gene expression by interacting with miRNAs. circRNA is a novel type of RNA that, unlike linear RNA, forms a covalently closed continuous loop, and is highly represented in the eukaryotic transcriptome. Two-condition experiment: control nucleus pulposus vs. degenerative nucleus pulposus. Biological replicates: 5 control, 5 degenerated, independently harvested (the same samples as GSE56081 and GSE63492). Four replicates per array.
2016-08-04 | E-GEOD-67566 | biostudies-arrayexpress
Project description:Assessment of the putative differential gene expression profiles in high osmolality-treated bovine nucleus pulposus intervertebral disc cells for a short (5 h) and a long (24 h) time period. Identification of novel genes up- or down-regulated as an early or a late response to hyperosmotic stress. A 5 and 24 h-hyperosmotic treatment of nucleus pulposus cells led to transcriptional changes in >100 and 200 genes, respectively.
2015-06-19 | GSE59485 | GEO
Project description:Background: Low back pain is a leading cause of disability worldwide and is frequently attributed to intervertebral disc (IVD) degeneration. Though the contributions of the adjacent cartilage endplates (CEP) to IVD degeneration are well documented, the phenotype and functions of the resident CEP cells are critically understudied. To better characterize CEP cell phenotype and possible mechanisms of CEP degeneration, bulk and single-cell RNA-Sequencing of non-degenerated and degenerated CEP cells were performed. Methods: Human lumbar CEP cells from degenerated (Thompson Grade ≥ 4) and non-degenerated (Thompson Grade ≤ 2) discs were expanded for bulk (N=4 non-degenerated, N=4 degenerated) and single-cell (N=1 non-degenerated, N=1 degenerated) RNA-Sequencing. Genes identified from bulk RNA-Sequencing were categorized by function and their expression in non-degenerated and degenerated CEP cells were compared. A PubMed literature review was also performed to determine which genes were previously identified and studied in the CEP, IVD, and other cartilaginous tissues. For single-cell RNA-Sequencing, different cell clusters were resolved using unsupervised clustering and functional annotation. Differential gene expression analysis and Gene Ontology, respectively, were used to compare gene expression and functional enrichment between cell clusters, as well as between non-degenerated and degenerated CEP samples. Results: Bulk RNA-Sequencing revealed 38 genes were significantly upregulated and 15 genes were significantly downregulated in degenerated CEP cells relative to non-degenerated cells (|Fold change| ≥ 1.5). Of these, only 2 genes were previously studied in CEP cells and 31 were previously studied in the IVD and other cartilaginous tissues. Single-cell RNA-Sequencing revealed 11 unique cell clusters, including multiple chondrocyte and progenitor subpopulations with distinct gene expression and functional profiles. Analysis of genes in the bulk RNA-Sequencing dataset showed that progenitor cell clusters from both samples were enriched in “non-degenerated” genes, but not “degenerated” genes. For both bulk- and single-cell analyses, gene expression and pathway enrichment analyses highlighted several pathways that may regulate CEP degeneration, including transcriptional regulation, translational regulation, intracellular transport, and mitochondrial dysfunction. Conclusions: This thorough analysis using RNA-Sequencing methods highlighted numerous differences between non-degenerated and degenerated CEP cells, the phenotypic heterogeneity of CEP cells, and several pathways of interest that may be relevant in CEP degeneration.
2024-01-10 | GSE242040 | GEO
Project description:Background: Low back pain is a leading cause of disability worldwide and is frequently attributed to intervertebral disc (IVD) degeneration. Though the contributions of the adjacent cartilage endplates (CEP) to IVD degeneration are well documented, the phenotype and functions of the resident CEP cells are critically understudied. To better characterize CEP cell phenotype and possible mechanisms of CEP degeneration, bulk and single-cell RNA-Sequencing of non-degenerated and degenerated CEP cells were performed. Methods: Human lumbar CEP cells from degenerated (Thompson Grade ≥ 4) and non-degenerated (Thompson Grade ≤ 2) discs were expanded for bulk (N=4 non-degenerated, N=4 degenerated) and single-cell (N=1 non-degenerated, N=1 degenerated) RNA-Sequencing. Genes identified from bulk RNA-Sequencing were categorized by function and their expression in non-degenerated and degenerated CEP cells were compared. A PubMed literature review was also performed to determine which genes were previously identified and studied in the CEP, IVD, and other cartilaginous tissues. For single-cell RNA-Sequencing, different cell clusters were resolved using unsupervised clustering and functional annotation. Differential gene expression analysis and Gene Ontology, respectively, were used to compare gene expression and functional enrichment between cell clusters, as well as between non-degenerated and degenerated CEP samples. Results: Bulk RNA-Sequencing revealed 38 genes were significantly upregulated and 15 genes were significantly downregulated in degenerated CEP cells relative to non-degenerated cells (|Fold change| ≥ 1.5). Of these, only 2 genes were previously studied in CEP cells and 31 were previously studied in the IVD and other cartilaginous tissues. Single-cell RNA-Sequencing revealed 11 unique cell clusters, including multiple chondrocyte and progenitor subpopulations with distinct gene expression and functional profiles. Analysis of genes in the bulk RNA-Sequencing dataset showed that progenitor cell clusters from both samples were enriched in “non-degenerated” genes, but not “degenerated” genes. For both bulk- and single-cell analyses, gene expression and pathway enrichment analyses highlighted several pathways that may regulate CEP degeneration, including transcriptional regulation, translational regulation, intracellular transport, and mitochondrial dysfunction. Conclusions: This thorough analysis using RNA-Sequencing methods highlighted numerous differences between non-degenerated and degenerated CEP cells, the phenotypic heterogeneity of CEP cells, and several pathways of interest that may be relevant in CEP degeneration.
2024-01-10 | GSE242443 | GEO
Project description:It is well documented that low back pain is a common condition and the leading cause of disability globally. A widely recognised contributor to low back pain is intervertebral disc degeneration (IVDD), which is the major cause of a series of degenerative disc diseases. Recently, it has been reported that circRNAs are involved in the development of IVDD. However, the mechanisms by which m6A modifies circRNA in nucleus pulposus cells remain poorly understood. Here, we aim to identify differentially expressed m6A circRNAs in degenerative nucleus pulposus cells and figure out how the circRNAs regulate IVDD progression and the m6A methylation functions.
2023-08-21 | GSE199993 | GEO