Identification of common pathway and hub genes in the degeneration of both annulus fibrosus and nucleus pulposus in intervertebral disc

Beta-defensin 1 knockdown ameliorates the characteristics of intervertebral disc degeneration by altering nucleus pulposus and annulus fibrosus cell phenotypes via suppression of the extracellular signal-regulated kinase signaling pathway

OBJECTIVE

Beta-defensin 1 (DEFB1), is a member of the defensin family involved in inflammation, cell apoptosis and senescence. We hypothesized that DEFB1 is essential for intervertebral disc (IVD) homeostasis. Our objective was to elucidate the roles of DEFB1 in IVD degeneration (IDD).

DESIGN

DEFB1 expression in human degenerated and non-degenerated IVD tissues was measured. In the rat coccygeal IDD model, morphological changes and extracellular signal-regulated kinase 1/2 (ERK1/2) expression were assessed following DEFB1 knockdown lentivirus injection into rat tail discs. In vitro, DEFB1 knockdown or DEFB1-overexpressing plasmid was transfected into nucleus pulposus (NP) and annulus fibrosus (AF) cells. Under interleukin (IL)-1β stimulation, protein expression, cytokine levels, cell viability, cell senescence, cell apoptosis and cell cycle were evaluated.

RESULTS

IDD tissue from human and rat models exhibited higher DEFB1 levels compared to non-degenerated IVD samples. DEFB1 knockdown ameliorated histopathological changes and reduced inflammation in rat IVD tissues. Under IL-1β stimulation, DEFB1 knockdown increased cell viability (NP cells mean difference 0.28 [95% CI: 0.21, 0.35], AF cells 0.24 [0.20, 0.29]), and decreased cell senescence (-11.78 [-13.73, -9.83], -11.88 [-13.89, -9.87]), cell apoptosis (-9.15 [-11.20, -7.11], -7.40 [-9.36, -5.44]), and G1-phase arrest (-16.74 [-19.87, -13.61], -18.70 [-22.13, -15. 27]) in NP and AF cells. Conversely, DEFB1 overexpression had the opposite effects. DEFB1 knockdown reduced ERK1/2 phosphorylation in vivo and in vitro. The ERK antagonist ameliorated DEFB1 overexpression-induced changes in cellular phenotype.

CONCLUSIONS

DEFB1 knockdown ameliorated IDD features, potentially by regulating ERK signaling in NP and AF cells. Targeting DEFB1 could be a promising therapeutic strategy for IDD.

Combined single-cell RNA sequencing and mendelian randomization to identify biomarkers associated with necrotic apoptosis in intervertebral disc degeneration

BACKGROUND

Intervertebral disc degeneration (IDD) is associated with back pain; back pain is a world-wide contributor to poor quality of life, while necroptosis has the characteristics of necroptosis and apoptosis, however, its role in IDD is still unclear. Therefore, the aim of this study was to identify biomarkers associated with necroptosis in IDD.

PURPOSE

To explore biomarkers associated with necroptosis in IDD, reveal the pathogenesis of IDD, as well as provide new directions for the diagnosis and treatment of this disease.

STUDY DESIGN/SETTINGS

Retrospective cohort study. Our study employs scRNA-seq coupled with MR analysis to investigate the causal relationship between necroptosis and IDD, laying a foundational groundwork for unveiling the intricate pathogenic mechanisms of this condition.

METHODS

Data quality control and normalisation was executed in single-cell dataset, GSE205535. Then, different cell types were obtained by cell annotation through marker genes. Subsequently, chi-square test was employed to assess the distribution difference of different cell types between IDD and control to screen key cells. AUCell was applied to calculate necroptosis-related genes (NRGs) scores of all cell types, further key cells were divided into high and low NRGs groups according to the median AUC scores of different cell types. Afterwards, the differentially expressed genes (DEGs) within the 2 score groups were screened. Then, the genes that had causal relationship with IDD were selected as biomarkers by univariate and multivariate Mendelian randomization (MR) analysis. Finally, the expression of biomarkers in different cell types and pseudo-time analysis was analyzed separately.

RESULTS

In GSE205535, 16 different cell populations identified by UMAP cluster analysis were further annotated to 8 cell types using maker genes. Afterwards, 53 DEGs were screened between the high and low NRGs groups. In addition, 9 genes with causal relationship with IDD were obtained by univariate MR analysis, further multivariate MR analysis proved that NT5E and TMEM158 had a direct causal relationship with IDD, which were used as biomarkers in this study. This study not only found that the expression levels of NT5E and TMEM158 were higher in IDD group, but also found that fibrochondrocytes and inflammatory chondrocytes were the key cells of NT5E and TMEM158, respectively. In the end, the biomarkers had the same expression trend in the quasi-time series, and both of them from high to low and then increased.

CONCLUSIONS

NT5E and TMEM158, as biomarkers of necroptotic apoptotic IDD, were causally associated with IDD.

CLINICAL SIGNIFICANCE

The understanding of chondrocytes as key cells provides new perspectives for deeper elucidation of the pathogenesis of IDD, improved diagnostic methods, and the development of more effective treatments. These findings are expected to provide a more accurate and personalised approach to clinical diagnosis and treatment, thereby improving the prognosis and quality of life of patients with IDD.

A novel multi-omics approach for identifying key genes in intervertebral disc degeneration

Many different cell types and complex molecular pathways are involved in intervertebral disc degeneration (IDD). We used a multi-omics approach combining single-cell RNA sequencing (scRNA-seq), differential gene expression analysis, and Mendelian randomization (MR) to clarify the underlying genetic architecture of IDD. We identified 1,164 differentially expressed genes (DEGs) across four important cell types associated with IDD using publicly available single-cell datasets. A thorough gene network analysis identified 122 genes that may be connected to programmed cell death (PCD), a crucial route in the etiology of IDD. SLC40A1, PTGS2, and GABARAPL1 have been identified as noteworthy regulatory genes that may impede the advancement of IDD. Furthermore, distinct cellular subpopulations and dynamic gene expression patterns were revealed by functional enrichment analysis and pseudo-temporal ordering of chondrocytes. Our results highlight the therapeutic potential of GABARAPL1, PTGS2, and SLC40A1 targeting in the treatment of IDD.

The Sanbi Decoction alleviates intervertebral disc degeneration in rats through intestinal flora and serum metabolic homeostasis modulation

BACKGROUND

Intervertebral disc degeneration (IVDD) is an essential cause of low back pain (LBP), the incidence of which has risen in recent years and is progressively younger, but treatment options are limited, placing a serious economic burden on society. Sanbi decoction (SBD) is an important classical formula for the treatment of IVDD, which can significantly improve patients' symptoms and is a promising alternative therapy.

PURPOSE

The aim of this study is to investigate the safety and efficacy of SBD in the treatment of IVDD and to explore the underlying mechanisms by using an integrated analytical approach of microbiomics and serum metabolomics, as well as by using molecular biology.

METHODS

A rat IVDD puncture model was established and treated by gavage with different concentrations of SBD, and clean faeces, serum, liver, kidney, and intervertebral disc (IVD) were collected after 4 weeks. We assessed the safety by liver and kidney weighing, functional tests and tissue staining, the expression of tumor necrosis factor-alpha (TNF-ɑ), interleukin 1β (IL-1β) and interleukin 6 (IL-6) inflammatory factors in serum was detected by ELISA kits, and X-ray test, magnetic resonance imaging (MRI) examination, immunohistochemistry (IHC), western blotting (WB), hematoxylin-eosin (HE) staining and safranin O-fast green (SO/FG) staining were used to assess the efficacy. Finally, we performed 16S rRNA sequencing analysis on the faeces of different groups and untargeted metabolomics on serum and analyzed the association between them.

RESULTS

SBD can effectively reduce the inflammatory response, regulate the metabolic balance of extracellular matrix (ECM), improve symptoms, and restore IVD function. In addition, SBD can significantly improve the diversity of intestinal flora and maintain the balance. At the phylum level, SBD greatly increased the relative abundance of Patescibacteria and Actinobacteriota and decreased the relative abundance of Bacteroidota. At the genus level, SBD significantly increased the relative abundance of Clostridia_UCG-014, Enterorhabdus, and Adlercreutzia, and decreased the relative abundance of Ruminococcaceae_UCG-005 (p < 0.05). Untargeted metabolomics indicated that SBD significantly improved serum metabolites and altered serum expression of 4alpha-phorbol 12,13-didecanoate (4alphaPDD), euscaphic acid (EA), alpha-muricholic acid (α-MCA), 5-hydroxyindoleacetic acid (5-HIAA), and kynurenine (Kyn) (p < 0.05), and the metabolic pathways were mainly lipid metabolism and amino acid metabolism.

CONCLUSIONS

This study demonstrated that SBD can extensively regulate intestinal flora and serum metabolic homeostasis to reduce inflammatory response, inhibit the degradation of ECM, restore IVD height and water content to achieve apparent therapeutic effect for IVDD.