Integrated transcriptome and proteome analyses identify novel regulatory network of nucleus pulposus cells in intervertebral disc degeneration

A diagnostic signatures for intervertebral disc degeneration using TNFAIP6 and COL6A2 based on single-cell RNA-seq and bulk RNA-seq analyses

OBJECTIVES

Intervertebral disc degeneration (IVDD) is a prevalent degenerative condition associated with a high incidence rate of low back pain and disability. This study aimed to identify potential biomarkers and signaling pathways associated with IVDD.

METHODS

Biomarkers were discerned through bulk-RNA and single-cell RNA sequencing (scRNA-Seq) investigations of IVDD cases from the Gene Expression Omnibus (GEO) database. Following this, two central genes were identified. Furthermore, gene set enrichment analysis (GSEA) and receiver operating characteristic (ROC) curve analysis were conducted. The transcriptional factor (TF) derived from nucleus pulposus (NP) cells was examined through the DoRothEA R package. RT-qPCR and IHC techniques were employed to confirm the expression of the two hub genes and their associated genes in tissue samples.

RESULTS

The proteins Tumor necrosis factor-inducible gene 6 protein (TNFAIP6) and collagen VI-α2 (COL6A2) were frequently analyzed using a combination of DEGs from datasets GSE70362, GSE124272, and scRNA-seq. Examination of gene expression across multiple datasets indicated significant differences in TNFAIP6 and COL6A2 levels in IVDD compared to control or normal groups (p < 0.05). These two central genes demonstrated strong diagnostic utility in the training cohort and reliable predictive value in the validation datasets. Our study verified the potential role of ZEB2 as a TF in regulating two key genes associated with IVDD. Furthermore, qPCR and IHC confirmed elevated expression levels of the hub genes and transcription factor.

CONCLUSION

We identified biomarkers, specifically TNFAIP6 and COL6A2, that have the potential to predict disease activity and aid in the diagnosis of IVDD.

Engineering extracellular matrix-based hydrogels for intervertebral disc regeneration

Lower back pain (LBP) is a major health concern, especially in older adults. A key aetiological factor is intervertebral disc (IVD) degeneration. It is mediated by dysregulation of extracellular matrix (ECM) and inflammation. In recent years, regenerative therapies have garnered attention for their potential to restore disc function by addressing the underlying biological alterations within the IVD. This review focuses on the comprehensive understanding of the anatomy and physiology of the IVD, highlighting its life cycle from embryonic development, and maturation to degenerative phenotype. We describe current treatments for managing LBP caused by IVD degeneration. This review emphasizes on the recent advancements in hydrogel engineering, highlighting natural, synthetic, and composite hydrogels and their application in ECM-targeted regenerative therapy for IVD degeneration. By exploring innovations in hydrogel technology, including improvements in crosslinking techniques and controlled degradation rates-we discuss how these materials could enhance IVD regeneration and potentially be used for the management of LBP. With their enhanced biomimicry, hydrogel-based ECM mimics offer a promising pathway for developing effective, durable therapies that address the root causes of disc degeneration, providing new hope for individuals living with chronic LBP.

Exploring the molecular mechanisms underlying intervertebral disc degeneration by analysing multiple datasets

The purpose of this study was to explore the genetic characteristics and immune cell infiltration related to intervertebral disc degeneration through multidataset analysis, predict potential therapeutic drugs, and provide a theoretical basis for clinical treatment. The gene expression profile data of the GSE70362, GSE186542, and GSE245147 datasets were downloaded from the Gene Expression Omnibus (GEO) database, and the hub genes were identified through differentially expressed gene analysis, Gene Ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) functional annotation and Mendelian randomization analysis were performed. Hub genes and immune cells were identified. Infiltration status was determined through GSEA and GSVA to clarify the specific signalling pathways associated with key genes and explore the potential molecular mechanisms by which key genes affect disease progression. The key genes were reversely predicted using miRNA grid construction and transcription factor regulation, and genes related to disease regulation were obtained from the GeneCards database. Finally, the differentially expressed genes were used for drug prediction through the Connectivity Map database to identify potential drugs for the treatment of intervertebral disc degeneration. The feasibility of the predicted drugs was tested by molecular docking technology. Real-time quantitative PCR was used to confirm the expression of key genes in the tissue samples.A total of 126 differentially expressed genes were identified in the GEO database, and 4 differentially expressed hub genes (COL6A2, DCXR, GLRX, and PDGFRB) were identified through bioinformatics methods. Immune infiltration analysis revealed that NK cells, macrophages, and eosinophils were activated during IVDD, whereas mast cells and T cells were suppressed. GO and KEGG analyses revealed that key genes are involved in the development of this disease through signalling pathways such as the glycolysis pathway, the oxidative phosphorylation pathway, the cholesterol regulatory pathway, and the haem metabolism pathway. Analysis of the constructed miRNA grid revealed that key genes are jointly regulated by multiple transcription factors, among which the most important motif is cisbp_M5578. Disease regulation-related genes were obtained through the GeneCards database, analysis of the correlation with key genes was performed, and the expression levels of the two mRNA and miRNA were significantly correlated. Finally, drug prediction performed through the Connectivity Map database revealed that drugs such as Abt-751, LY-2183240, podophyllotoxin, and vindesine can alleviate or even reverse the disease state. Finally, we collected 10 IVDD and 10 healthy disc tissue samples, and the RT‒qPCR results were consistent with the bioinformatics results. We identified COL6A2, DCXR, GLRX, and PDGFRB as key genes involved in IVDD. In addition, drugs such as Abt-751 are expected to control and reverse the progression of the disease. In the future, these key genes and predicted drugs may provide new directions for further mechanistic studies as well as new therapies for IVDD patients.

Nucleus pulposus cell network modelling in the intervertebral disc

Intervertebral disc degeneration (IDD) results from an imbalance between anabolic and catabolic processes in the extracellular matrix (ECM). Due to complex biochemical interactions, a comprehensive understanding is needed. This study presents a regulatory network model (RNM) for nucleus pulposus cells (NPC), representing normal intervertebral disc (IVD) conditions. The RNM includes 33 proteins, and 153 interactions based on literature, incorporating key NPC regulatory mechanisms. A semi-quantitative approach calculates the basal steady state, accurately reflecting normal NPC activity. Model validation through published studies replicated pro-catabolic and pro-anabolic shifts, emphasizing the roles of transforming growth factor beta (TGF-β) and interleukin-1 receptor antagonist (IL-1Ra) in ECM regulation. This IVD RNM is a valuable tool for predicting IDD progression, offering insights into ECM degradation mechanisms and guiding experimental research on IVD health and degeneration.

Research progress on the regulation of bone marrow stem cells by noncoding RNAs in adolescent idiopathic scoliosis

Adolescent idiopathic scoliosis (AIS) is a common spinal deformity in young women, but its pathogenesis remains unclear. The primary pathogenic factors contributing to its development include genetics, abnormal bone metabolism, and endocrine factors. Bone marrow stem cells (BMSCs) play a crucial role in the pathogenesis of AIS by regulating its occurrence and progression. Noncoding RNAs (ncRNAs) are also involved in the pathogenesis of AIS, and their role in regulating BMSCs in patients with AIS requires further evaluation. In this review, we discuss the relevant literature regarding the osteogenic, chondrogenic, and lipogenic differentiation of BMSCs. The corresponding mechanisms of ncRNA-mediated BMSC regulation in patients with AIS, recent advancements in AIS and ncRNA research, and the importance of ncRNA translation profiling and multiomics are highlighted.

Single-cell transcriptomics reveals heterogeneity and intercellular crosstalk in human intervertebral disc degeneration

The complexity of the human intervertebral disc (IVD) has hindered the elucidation of the microenvironment and mechanisms underlying IVD degeneration (IVDD). Here we determined the landscapes of nucleus pulposus (NP), annulus fibrosus (AF), and immunocytes in human IVD by scRNA-seq. Six NP subclusters and seven AF subclusters were identified, whose functional differences and distribution during different stages of degeneration (Pfirrmann I-V) were investigated. We found MCAM⁺ progenitor in AF, as well as CD24⁺ progenitor and MKI67⁺ progenitor in NP, forming a lineage trajectory from CD24⁺/MKI67⁺ progenitors to EffectorNP_⅓ during IVDD. There is a significant increase in monocyte/macrophage (Mφ) in degenerated IVDs (p = 0.044), with Mφ-SPP1 exclusively found in IVDD but not healthy IVDs. Further analyses of the intercellular crosstalk network revealed interactions between major subpopulations and changes in the microenvironment during IVDD. Our results elucidated the unique characteristics of IVDD, thereby shedding light on therapeutic strategies.

Immuno-Modulatory Effects of Intervertebral Disc Cells

Low back pain is a highly prevalent, chronic, and costly medical condition predominantly triggered by intervertebral disc degeneration (IDD). IDD is often caused by structural and biochemical changes in intervertebral discs (IVD) that prompt a pathologic shift from an anabolic to catabolic state, affecting extracellular matrix (ECM) production, enzyme generation, cytokine and chemokine production, neurotrophic and angiogenic factor production. The IVD is an immune-privileged organ. However, during degeneration immune cells and inflammatory factors can infiltrate through defects in the cartilage endplate and annulus fibrosus fissures, further accelerating the catabolic environment. Remarkably, though, catabolic ECM disruption also occurs in the absence of immune cell infiltration, largely due to native disc cell production of catabolic enzymes and cytokines. An unbalanced metabolism could be induced by many different factors, including a harsh microenvironment, biomechanical cues, genetics, and infection. The complex, multifactorial nature of IDD brings the challenge of identifying key factors which initiate the degenerative cascade, eventually leading to back pain. These factors are often investigated through methods including animal models, 3D cell culture, bioreactors, and computational models. However, the crosstalk between the IVD, immune system, and shifted metabolism is frequently misconstrued, often with the assumption that the presence of cytokines and chemokines is synonymous to inflammation or an immune response, which is not true for the intact disc. Therefore, this review will tackle immunomodulatory and IVD cell roles in IDD, clarifying the differences between cellular involvements and implications for therapeutic development and assessing models used to explore inflammatory or catabolic IVD environments.

Identification of Core Genes and Screening of Potential Targets in Intervertebral Disc Degeneration Using Integrated Bioinformatics Analysis

Background: Intervertebral disc degeneration (IDD), characterized by diverse pathological changes, causes low back pain (LBP). However, prophylactic and delaying treatments for IDD are limited. The aim of our study was to investigate the gene network and biomarkers of IDD and suggest potential therapeutic targets.

Methods: Differentially expressed genes (DEGs) associated with IDD were identified by analyzing the mRNA, miRNA, and lncRNA expression profiles of IDD cases from the Gene Expression Omnibus (GEO). The protein–protein interaction (PPI) network, Gene Ontology (GO) enrichment, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis as well as miRNA–lncRNA–mRNA networks were conducted. Moreover, we obtained 71 hub genes and performed a comprehensive analysis including GO, KEGG, gene set enrichment analysis (GSEA), gene set variation analysis (GSVA), Disease Ontology (DO), methylation analysis, receiver operating characteristic (ROC) curve analysis, immune infiltration analysis, and potential drug identification. We finally used qRT-PCR to verify 13 significant DEGs in normal and degenerative nucleus pulposus cells (NPCs).

Results: We identified 305 DEGs closely related to IDD. The GO and KEGG analyses indicated that changes in IDD are significantly associated with enrichment of the inflammatory and immune response. GSEA analysis suggested that cell activation involved in the inflammatory immune response amide biosynthetic process was the key for the development of IDD. The GSVA suggested that DNA repair, oxidative phosphorylation, peroxisome, IL-6-JAK-STAT3 signaling, and apoptosis were crucial in the development of IDD. Among the 71 hub genes, the methylation levels of 11 genes were increased in IDD. A total of twenty genes showed a high functional similarity and diagnostic value in IDD. The result of the immune cell infiltration analysis indicated that seven genes were closely related to active natural killer cells. The most relevant targeted hub genes for potential drug or molecular compounds were MET and PIK3CD. Also, qRT-PCR results showed that ARHGAP27, C15orf39, DEPDC1, DHRSX, MGAM, SLC11A1, SMC4, and LINC00887 were significantly downregulated in degenerative NPCs; H19, LINC00685, mir-185-5p, and mir-4306 were upregulated in degenerative NPCs; and the expression level of mir-663a did not change significantly in normal and degenerative NPCs.

Conclusion: Our findings may provide new insights into the functional characteristics and mechanism of IDD and aid the development of IDD therapeutics.

PERK signaling activation restores nucleus pulposus degeneration by activating autophagy under hypoxia environment

OBJECTIVES

Intervertebral disc (IVD) degeneration is an important disease with no efficient biological therapy identified. Autophagy, a wildly known therapeutic target for human disease, has been demonstrated to be activated under hypoxia, with underlying mechanism remains elusive. Thus, this study aims to specify the role of autophagy in IVD degeneration, the regulating mechanism of hypoxia-inducing autophagy, and the therapeutic value of autophagy for IVD degeneration.

METHODS

RNA-seq was used to screen the primary pathway affected in NP cells under hypoxia, the specific link between hypoxia and autophagy were investigated using ChIP-seq and dual luciferase reporter assay. Conditional ATG7 knockout mice (ATG7^-/-) were constructed for assessing the effect of autophagy on IVD degeneration, and puncture induced mice model of IVD degeneration were used for intradiscal injection to evaluate the therapeutic value of autophagy.

RESULTS

We demonstrated that hypoxia induces autophagy by transcriptional activation of autophagic gene LC3B and ATG7, which is controlled by PERK signaling. Then, we observed that inhibiting autophagy or PERK signaling leads to impaired NP cell viability and function, furthermore, using ATG7 knockout (ATG7^-/-) mice, we identified the protective role of autophagy in IVD. Furthermore, we found that intradiscal injection of PERK signaling agonist, CCT020312, significantly restores the degeneration level of needle punctured mice IVD.

CONCLUSION

We showed that the activation of PERK signaling upon hypoxia serves as a vital mechanism to induce autophagy and identified the therapeutic value of PERK signaling agonist for IVD degeneration treatment.