MicroRNAs expression profiling of human nucleus pulposus cells: control vs. degeneration
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE19943 | GEO | 2012/01/01
SECONDARY ACCESSION(S): PRJNA120173
REPOSITORIES: GEO
Similar Datasets
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: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: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
Project description:Nucleus pulposus cells (NPCs) were used to examine the effect of LINC02569, a novel lncRNA. In particular, its effect in intervertebral disc degeneration was determined. Treatment of LINC02569 siRNA (si-02569) was to be compared with negative control siRNA (si-NC).
2022-02-08 | GSE185668 | GEO
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:Background: The nucleus pulposus is a constituent structure of the human intervertebral disc, and its degeneration can cause Intervertebral disc degeneration (IDD). However the cellular molecular mechanisms involved remain elusive. Methods: Through bioinformatics analysis, the single-cell transcriptome sequencing expression profiles of human normal nucleus pulposus cells (NNP) and human degenerative nucleus pulposus cells (DNP) were compared to clarify the transcriptome differential expression profiles of human normal and human degenerative nucleus pulposus cells. The single-cell sequencing results of the two samples were analyzed using bioinformatics methods to compare the differences in histiocytosis between human normal nucleus pulposus and human degenerated nucleus pulposus, map the histiocytes of NNP and DNP, perform cell differentiation trajectories for the cell populations of interest and predict cell function, and explore their heterogeneity by pathway analysis and Gene ontology analysis. Results: Nine cell types were identified, which were Chondrocyte1, Chondrocyte2, Chondrocyte3, Chondrocyte4, Chondrocyte5, Endothelial, Macrophage, Neutrophil, and T cells. Analysis of the proportion of chondrocytes in different tissues revealed that chondrocyte 1 accounted for a higher proportion of normal nucleus pulposus cells and highly expressed COL2A1 compared with degenerated nucleus pulposus cells; chondrocyte 2, chondrocyte 3, chondrocyte 4, and chondrocyte 5 accounted for a higher proportion of degenerated nucleus pulposus cells compared with normal nucleus pulposus cells. Among them, chondrocyte 2 was an inhibitory calcified chondrocyte with high expression of MGP, Chondrocytes 3 were fibrochondrocytes with high expression of COL1A1, Chondrocytes 4 are chondrocytes that highly express pain inflammatory genes such as PTGES, Chondrocytes 5 were calcified chondrocytes with high expression of FN1. (Chondrocytes 4 and chondrocytes 5 were found for the first time in a study of single-cell transcriptome sequencing of disc tissue.) Cell trajectory analysis revealed that chondrocyte 1 was at the beginning of the trajectory and chondrocyte 3 was at the end of the trajectory, while chondrocyte 5 appeared first in the trajectory relative to chondrocyte 2 and chondrocyte 4. Conclusion: After functional identification of the specifically expressed genes in five chondrocytes, it was found that chondrocyte 1 was a chondrocyte with high expression of COL2A1, COL9A2, COL11A2, and CHRDL2 in a high proportion of normal nucleus pulposus cells, and chondrocyte 3 was a fibrochondrocyte with high expression of COL1A1, COL6A3, COL1A2, COL3A1, AQP1, and COL15A1 in an increased proportion during nucleus pulposus cell degeneration. Through cell trajectory analysis, it was found that chondrocytes 5 specifically expressing FN1, SESN2, and GDF15 may be the key cells leading to degeneration of nucleus pulposus cells. Chondrocytes 2 expressing MGP, MT1G, and GPX3 may play a role in reversing calcification and degeneration, and chondrocytes 4 expressing PTGES, TREM1, and TIMP1 may play a role in disc degeneration pain and inflammation.
2022-12-11 | GSE205535 | GEO
Project description:Elucidating how cell populations promote onset and progression of intervertebral disc degeneration (IDD) has the potential to enable more precise therapeutic targeting of cells and mechanisms. Single cell RNA-sequencing (scRNA-seq) was performed on surgically separated annulus fibrosus (AF) (19,978; 26,983 cells) and nucleus pulposus (NP) (20,884; 24,489 cells) from healthy and diseased human intervertebral discs (IVD). In both tissue types, we observed depletion of cell subsets involved in maintenance of healthy IVD, specifically the immature cell subsets – fibroblast progenitors and stem cells – indicative of an impairment of normal tissue self-renewal. We also identified tissue-specific changes. In NP, several fibrotic populations were increased in degenerated IVD, indicating tissue-remodeling. In degenerated AF, we identified a novel disease-associated subset, which is a stem cell-derived abnormally differentiated chondrocytic population and expresses disease-promoting genes. It was associated with pathogenic biological processes and the main gene regulatory networks includedthrombospondinsignaling and FOXO1 transcription factor. Our data reveal new insights of both shared and tissue-specific changes in specific cell populations in AF and NP during IVD degeneration. These identified mechanisms and molecules are novel and more precise targets for IDD prevention and treatment.
2024-04-05 | GSE230808 | GEO
Project description:Intervertebral disc degeneration (IDD) leads to low back pain and disability globally. The pathophysiology of IDD is not entirely understood. There is increasing evidence that long noncoding RNAs (lncRNAs) play a key regulatory role in a wide range of biological processes. The purpose of this study was to comprehensively lncRNA and mRNA expression profiles of human intervertebral disc (IVD) tissues, specifically nucleus pulpous (NP) tissues, with early and advanced stages of disc degeneration. The overview of lncRNA and mRNA expression profiles in the current study revealed that differentially expressed lncRNAs and mRNAs were identified that have been reported to be relevant to IDD. Importantly, differentially expressed lncRNAs and mRNAs that regulate the major signaling pathways, such as NF-κB, MAPK, and Wnt signaling, that are well known to be responsible for the pathogenesis of IDD.
2023-02-09 | GSE186542 | GEO
Project description:Intervertebral disc degeneration (IVDD) is a main cause of degenerative disc disease, which results in substantial pain among patients. However, the mechanism of degeneration remains unclear. Thus far, basic research on human IVDD has focused on only a limited number of proteins and has not been conducted from a holistic perspective. In this study, we used tandem mass tag (TMT) labeling combined with liquid chromatography-tandem mass spectrometry (LC-MS/MS) to perform differential proteomic analysis on fetal and geriatric lumbar disc nucleus pulposus tissue. These data indicate that differential proteomics analysis may be an important method for elucidation of the pathophysiological process and molecular biological mechanism of human IVDD from a holistic perspective. The findings in this study will aid in screening of new biomarkers for early diagnosis and targeted treatment of IVDD.
2020-05-02 | PXD015000 | iProX
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