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Genome-wide maps of chromatin state in pluripotent and lineage-committed cells

ABSTRACT: The objective of this study was to compare the expression of the transcriptome in healthy and degenerative intervertebral discs. According to the standard of Pfirrmann Grading, the patients with Pfirrmann Grade III and above were divided into the degeneration group and the rest were the control group. During the operation, the nucleus pulposus tissue of patients were collected and sequenced in Illumina HiSeq 4000. Sequencing results were further calculated using Cufflinks, Deseq and Clusterprofiler.

ORGANISM(S): Homo sapiens

PROVIDER: GSE176205 | GEO | 2022/05/01

REPOSITORIES: GEO

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An Organ Culture System to Model Early Degenerative Changes of the Intervertebral Disc: II Profiling Global Gene Expression Changes

Project description:To mimic a degenerative insult, rat intervertebral discs were cultured in the presence of TNF-alpha, IL-1beta and serum limiting conditions. Gene expression analysis was performed using a microarray to identify differential gene expression between experimental and control groups. The discs were collected and the annulus fibrosus (AF) was separated from the nucleus pulposus (NP). Total RNA from NP was used for RNA extraction and hybridization on Affymetrix microarrays: Control group - Ctr-1, Ctr-2, Ctr-3, Ctr-4 and Experimental group-Exp-1, Exp-2, Exp-3, Exp-4.

2012-11-29 | E-GEOD-42611 | biostudies-arrayexpress

Revisiting the microRNA expression profiling of human intervertebral disc degeneration (IDD)

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.

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Sox9 Deletion Causes Severe Intervertebral Disc Degeneration Characterized by Apoptosis, Matrix Remodeling, and Compartment-Specific Transcriptomic Changes

Project description:Transcriptomic analysis of nucleus pulposus (NP) and annulus fibrosus (AF) tissues from intervertebral discs of 3-month-old mice with the conditional postnatal deletion of Sox9. The transcription factor Sox9 is essential for the maintenance and health of the intervertebral disc of mice. We examined the transcriptomic profiles of nucleus pulposus and annulus fibrosus cells in control and Sox9 conditional knock-out mice using microarrays.

2023-05-19 | GSE150850 | GEO

Loss of function mutation in progressive ankylosis (Ank) gene causes aberrant mineralization and acquisition of osteoblast-like-phenotype by annulus fibrosus cells in the intervertebral disc

Project description:Transcriptomic analysis of nucleus pulposus (NP) and annulus fibrosus (AF) tissues from intervertebral discs of 3-month-old mice with loss of function mutation of Ank gene. Regulator of extracellular inorganic pyrophosphate, Ank is essential for preventing ectopic mineralization in the extracellular matrices, maintaining the health of the intervertebral disc of mice. We examined the transcriptomic profiles of nucleus pulposus and annulus fibrosus cells in control and Ank mutant mice using microarrays.

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Tagln+ progenitors contribute to the development and maintenance of nucleus pulposus

Project description:Failure of intervertebral disc components, e.g. the nucleus pulposus causes intervertebral disc disease and associated low-back pain. Despite the high prevalence of disc disease, the changes in intervertebral disc cells and their regenerative potential with ageing and degeneration are not fully elucidated. Understanding the cell lineage, cell differentiation and maintenance of nucleus pulposus may have therapeutic application for the regeneration of degenerative disc, with significant impact for healthy ageing. Here we found that TAGLN expressing cells are present in human healthy nucleus pulposus, but diminish in degenerative disc. By lineage analyses in mice, we found cells in the nucleus pulposus are derived from a peripherally located population of notochord-derived Tagln expressing cells (PeriNP cells). The PeriNP cells are proliferative and can differentiate into the inner part of the nucleus pulposus. The Tagln+ cells and descendants diminish during aging and puncture induced disc degeneration. The maintenance and differentiation of PeriNP cells is partially regulated by Smad4 dependent signaling. Removal of Smad4 by nucleus pulposus specific Cre (Foxa2mNE-Cre), results in decreased Tagln+ cells and abnormal disc morphology, leading to disc degeneration. Our findings propose that the PeriNP Tagln expressing cells are a pool of notochord-derived progenitors that are important for maintenance of the nucleus pulposus and provide insights for regenerative therapy against intervertebral disc degeneration.

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Gene expression profile at single cell level of nucleus pulposus cells (NPCs) from the nucleus pulposus (NP) tissue in the mild degenerative intervertebral discs (MDD) and server degenerative intervertebral discs(SDD).

Project description:Gene expression profile at single cell level of nucleus pulposus cells (NPCs) from the nucleus pulposus (NP) tissue in the mild degenerative intervertebral discs (MDD) and server degenerative intervertebral discs(SDD).

| PRJNA1025305 | ENA

Homo sapiens

Project description:Expression data between human degenerative and non-degenerative intervertebral discs

| PRJNA149897 | ENA

The expression profiling of circular RNAs (circRNA) in human intervertebral disc degeneration (IDD)

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

Gene Expression Profiling Identifies Interferon Signalling Molecules and IGFBP3 in Human Degenerative Annulus Fibrosus

Project description:Low back pain is a major cause of disability especially for people between 20 and 50 years of age. As a costly healthcare problem, it imposes a serious socio-economic burden. Current surgical therapies have considerable drawbacks and fail to replace the normal disc in facilitating spinal movements and absorbing load. Therefore, the focus of regenerative medicine is on identifying biomarkers and signalling pathways to improve our understanding about the cascades of disc degeneration and allow for the design of specific therapies. We hypothesized that comparing microarray profiles from degenerative and non-degenerative discs will lead to the identification of dysregulated signalling and pathophysiological targets. Microarray data sets were generated from human annulus fibrosus cells and analysed using IPA ingenuity pathway analysis system. Gene expression values were validated by qRT-PCR, and respective proteins were identified by immunohistochemistry. Microarray analysis revealed 17 dysregulated molecular markers and various dysregulated cellular functions, including cell proliferation and inflammatory response, in the human degenerative annulus fibrosus. The most significant canonical pathway induced in degenerative annulus fibrosus was found to be the interferon signalling pathway. In conclusion, this study indicates interferon-alpha signalling pathway activation with IFIT3 and IGFBP3 up-regulation which may affect cellular function in human degenerative disc. 48 samples of intervertebral disc tissue - annulus fibrosus and nucleus pulposus - displaying varying degrees (grades) of degeneration

2015-10-23 | E-GEOD-70362 | biostudies-arrayexpress

Single-Cell RNA-Sequencing Atlas of Bovine Caudal Intervertebral Discs: Discovery of Heterogeneous Cell Populations with Distinct Roles in Homeostasis

Project description:We investigated the heterogeneous cell populations composing Bovine Intervertebral Discs (IVDs) through single cell RNA sequencing technologies. The assay sequenced over 14,000 cells composing 5 bovine discs from 3 unique bovine tails. Through both established and custom analysis pipelines, we characterize cell heterogeneity between populations of Nucleus Pulposus and Annulus Fibrosus cells. We further characterize populations of Endothelial, Muscle, Immune, and Notochord.

2021-10-07 | GSE179714 | GEO

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