Single cell sequencing of human nucleus pulposus
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE153066 | GEO | 2023/12/31
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: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: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: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:Intervertebral disc degeneration is the main cause of low back pain and the mechanism of which is far from fully revealed. Although multiple factors are related to the intervertebral disc degeneration, inflammation and matrix metabolism dysregulation are the two key factors that play an important role in degeneration. Here, we found that inflammation-related factor CHI3L1 is highly regulated in the nucleus pulposus during degeneration in both RNA and protein level. Immunohistochemical analysis show that the expression of CHI3L1 are NP tissue specific, and increased significantly in the degenerated nucleus pulposus cells. The mechanism of CHI3L1 is thus studied in this experiment.
2020-02-11 | GSE135219 | 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: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:Nucleus pulposus stem cells is the endogenous stem cell in nucleus pulposus tissues(NPMSCs). The senescene of NPMSCs will cause its malfunction and further induce intervertebral disc degeneration.The expression of specific sets of genes will altered during aging. Thus, identify these key regulater genes is important. We used microarrays to detail the global programme of gene expression underlying NPMSCs aging and identified distinct classes of up and down-regulated genes during this process
2019-08-19 | GSE126883 | 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.
2015-06-19 | GSE59485 | GEO
Project description:Transcriptomic analysis of nucleus pulposus (NP) tissues from intervertebral discs of 14- and 24-month-old mice with the conditional postnatal overexpression of HIF-2α. Hypoxia-inducible factors (HIFs) are essential for the homeostasis of the hypoxic tissues, and therefore, increased activity of the transcription factor HIF-2α is shown to contribute to the pathogenesis of mild disc degeneration in the spine. We examined the transcriptomic profiles of nucleus pulposus cells in control and K19-HIF-2α-dPA overexpression mice using microarrays.
2024-03-27 | GSE249908 | GEO