MiR-seq analysis of nucleus pulposus tissues from compression-induced intervertebral disc degeneration rats
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ABSTRACT:
ORGANISM(S): Rattus norvegicus
PROVIDER: GSE230509 | GEO | 2024/06/20
REPOSITORIES: GEO
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Project description:Abnormal mechanical load is a main risk factor of intervertebral disc degeneration (IDD), and cellular senescence is a pathological change in IDD. Additionally, extracellular matrix (ECM) stiffness promotes human nucleus pulposus cells (hNPCs) senescence. However, the molecular mechanism underlying mechano-induced cellular senescence and IDD progression is not yet fully elucidated. First, we demonstrated that mechano-stress promoted hNPCs senescence via NF-κB signaling. Subsequently, we identified periostin as the main mechano-responsive molecule in hNPCs through unbiased sequencing, which was transcriptionally upregulated by NF-κB p65; moreover, secreted periostin by senescent hNPCs further promoted senescence and upregulated the catabolic process in hNPCs through activating NF-κB, forming a positive loop. Both Postn (encoding periostin) knockdown via siRNA and periostin inactivation via neutralizing antibodies alleviated IDD and NPCs senescence. Furthermore, we found that mechano-stress initiated the positive feedback of NF-κB and periostin via PIEZO1. PIEZO1 activation by Yoda1 induced severe IDD in rat tails without compression, and Postn knockdown alleviated the Yoda1-induced IDD in vivo. Here, we reported for the first time that self-amplifying loop of NF-κB and periostin initiated via PIEZO1 under mechano-stress accelerated NPCs senescence, leading to IDD. Furthermore, periostin neutralizing antibodies, which may serve as potential therapeutic agents for IDD, interrupted this loop.
2022-06-06 | GSE185728 | GEO
Project description:miR-seq analysis of nucleus pulposus tissues from compression-induced intervertebral disc degeneration rats
| PRJNA961676 | ENA
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: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:Understanding the molecular mechanisms regulating the maintenance and destruction of intervertebral disc may lead to the development of new therapies for intervertebral disc degeneration (IDD). Here we present evidence from miRNA microarray analyses of clinical data sets along with in vitro and in vivo experiments that miR-141 is a key regulator of IDD. Gain- and loss-of-function studies show that miR-141 drives IDD by inducing nucleus pulposus (NP) apoptosis. Furthermore, miR-141 KO in mice attenuated spontaneous and surgically induced IDD. Mechanistically, miR-141 promotes IDD development by targeting and depleting SIRT1, a negative regulator of NF-κB pathway. Therapeutically, upregulation or downregulation of miR-141 by nanoparticle delivery in IDD model aggravated or alleviated experimental IDD, respectively. Our findings reveal a novel mechanism by which miR-141, in part, promotes IDD progression by interacting with SIRT1/NF-κB pathway. Blockade of miR-141 in vivo may serve as a potential therapeutic approach in the treatment of IDD.
2018-12-11 | GSE116726 | GEO
Project description:ABSTRACT:
Intervertebral disc degeneration (IDD) arises from an intricate imbalance between the anabolic and catabolic processes governing the extracellular matrix (ECM) within the disc. Biochemical processes are complex, redundant and feedback-looped, and improved integration of knowledge is needed. To addess this, a literature-based regulatory network model (RNM) for nucleus pulposus cells (NPC) is proposed, representing the normal state of the intervertebral disc (IVD), in which proteins are represented by nodes that interact among each other through activation and/or inhibition edges. This model includes 32 different proteins and 150 edges by incorporating critical biochemical interactions in IVD regulation, tested in vivo or vitro in humans’ and animals’ NPC, alongside non tissue specific protein-protein interactions. We used the network to calculate the dynamic regulation of each node through a semi-quantitative method. The basal steady state successfully represented the activity of a normal NPC, and the model was assessed through the published literature, by replicating two independent experimental studies in human normal NPC. Pro-catabolic or pro-anabolic shifts of the network activated by nodal perturbations could be predicted. Sensitivity analysis underscores the significant influence of transforming growth factor beta (TGF-β) and interleukin-1 receptor antagonist (IL-1Ra) on the regulation of structural proteins and degrading enzymes within the system. Given the ongoing challenge of elucidating the mechanisms driving ECM degradation in IDD, this unique IVD RNM holds promise as a tool for exploring and predicting IDD progression, shedding light on IVD phenotypes and guiding experimental research efforts.
2024-11-04 | MODEL2407080001 | BioModels
Project description:In addition to the well-known short noncoding RNAs as miRNAs, increasing evidence suggests that long noncoding RNAs (lncRNAs) act as key regulators in a wide aspect of biologic processes. Dysregulated expression of lncRNAs has been demonstrated being implicated in a variety of human diseases. However, there is relative paucity of information regarding the role of lncRNAs in intervertebral disc degeneration (IDD) hitherto. We have addressed the expression profiles of miRNAs in IDD previously. To determine whether lncRNAs is differentially expressed in IDD, we employed a lncRNA-mRNA microarray analysis of human nucleus pulposus (five degenerative as IDD and five normal specimens as control). With abundant probes accounting for 33,045 lncRNAs and 30,215 coding transcripts in our microarray, microarray data profiling indicated that 18995 lncRNAs and 14635 mRNAs were detected in all samples with 2309 lncRNAs and 3017 mRNAs differentially expressed in degenerated samples. Amongst them, 164 lncRNAs (97 up and 67 down) and 265 mRNAs were highly differentially expressed with an absolute fold change greater than ten. The upregulated mRNAs included the extracellular matrix components as COL1A2, LUM, FN1ACAN, DCN and ITFG2. 1100 lncRNAs and 1379 mRNAs were altered in the same direction in at least 4 of the 5 degenerative samples with fold change greater than 2 respectively. Three lncRNAs were chosen for the real-time quantitative PCR (qRT-PCR) analysis. qRT-PCR results showed a high consistency with the microarray data. In this study, to explore the potential involvement of lncRNAs in IDD, we conducted lncRNA and mRNA profiling in 5 human control nucleus pulposus tissue and 5 degenerative nucleus pulposus tissue by microarray.Biological replicates: 5 control, 5 degenerated, independently harvested.
2014-11-17 | E-GEOD-56081 | 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:Dysregulation of microRNAs (miRNAs) plays a critical role in the development of intervertebral disc degeneration (IDD). In this study, we present evidence from in vitro and in vivo research to elucidate the mechanism underlying the role of miR-760 in IDD. miRNA microarray and quantitative reverse transcription-polymerase chain reaction were used to determine the miRNA profiles in patients with IDD. Functional analysis was performed to evaluate the role of miR-760 in the pathogenesis of IDD. Luciferase reporter and western blotting assays were used to confirm the miRNA targets. The expression of miR-760 was significantly decreased in degenerative nucleus pulposus (NP) cells and negatively correlated with disc degeneration grade. Functional assays demonstrated that miR-760 delivery significantly increased NP cell proliferation and promoted the expression of collagen II and aggrecan. Moreover, MyD88 was identified as a target gene of miR-760. miR-760 effectively suppressed MyD88 expression by interacting with the 3′-untranslated region, which was abolished by miR-760 binding site mutations. An in vivo experiment using an IDD mouse model showed that the upregulation of miR-760 could effectively suspend IDD. Therefore, miR-760 was found to play an important role in IDD and can be used as a promising therapeutic target for the treatment of patients with IDD.
2022-03-17 | E-MTAB-11554 | 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