- Research
- Open access
- Published:
Diagnostic model based on key autophagy-related genes in intervertebral disc degeneration
BMC Musculoskeletal Disorders volume 24, Article number: 927 (2023)
Abstract
Background
Current research on autophagy is mainly focused on intervertebral disc tissues and cells, while there is few on human peripheral blood sample. therefore, this study constructed a diagnostic model to identify autophagy-related markers of intervertebral disc degeneration (IVDD).
Methods
GSE150408 and GSE124272 datasets were acquired from the Gene Expression Omnibus database, and differential expression analysis was performed. The IVDD-autophagy genes were obtained using Weighted Gene Coexpression Network Analysis, and a diagnostic model was constructed and validated, followed by Gene Set Variation Analysis (GSVA) and Gene Set Enrichment Analysis (GSEA). Meanwhile, miRNA–gene and transcription factor–gene interaction networks were constructed. In addition, drug-gene interactions and target genes of methylprednisolone and glucosamine were analyzed.
Results
A total of 1,776 differentially expressed genes were identified between IVDD and control samples, and the composition of the four immune cell types was significantly different between the IVDD and control samples. The Meturquoise and Mebrown modules were significantly related to immune cells, with significant differences between the control and IVDD samples. A diagnostic model was constructed using five key IVDD-autophagy genes. The area under the curve values of the model in the training and validation datasets were 0.907 and 0.984, respectively. The enrichment scores of the two pathways were significantly different between the IVDD and healthy groups. Eight pathways in the IVDD and healthy groups had significant differences. A total of 16 miRNAs and 3 transcription factors were predicted to be of great value. In total, 84 significantly related drugs were screened for five key IVDD-autophagy genes in the diagnostic model, and three common autophagy-related target genes of methylprednisolone and glucosamine were predicted.
Conclusion
This study constructs a reliable autophagy-related diagnostic model that is strongly related to the immune microenvironment of IVD. Autophagy-related genes, including PHF23, RAB24, STAT3, TOMM5, and DNAJB9, may participate in IVDD pathogenesis. In addition, methylprednisolone and glucosamine may exert therapeutic effects on IVDD by targeting CTSD, VEGFA, and BAX genes through apoptosis, as well as the sphingolipid and AGE-RAGE signaling pathways in diabetic complications.
Highlights
The autophagy-related diagnostic model closely associated with immunity was constructed based on five key autophagy-related genes in IVDD patients’ peripheral blood sample, which could diagnose of IVDD.
Methylprednisolone and glucosamine, empirical used clinical therapeutic drugs for IVDD, might exert therapeutic effect by targeting CTSD, VEGFA, and BAX through apoptosis, sphingolipid signaling pathway, and AGE-RAGE signaling pathway in diabetic complications.
This study provides new insights for the diagnosis and therapy of IVDD.
Background
The intervertebral disc (IVD), a soft tissue structure connects the upper and lower vertebral bodies, is composed of the nucleus pulposus, annulus fibrosus, and cartilage endplate [1, 2]. The functions of IVD include buffering pressure and maintaining stability, physiological curvature, and flexibility of the spine [2]. IVD degeneration (IVDD), a common chronic degenerative disease, is the leading cause of low back pain and seriously affects the health and quality of life of the aged [3, 4]. It is suggested that the prevalence rate of IVDD among middle-aged and older people can be above 90%; however, with the acceleration of population aging and changes in work and lifestyle, the incidence rate has been increasing annually, showing an increasing trend in the youth [5, 6]. The etiology of IVDD is far from being understood, however, there is consensus that not a single factor can be held responsible for the complex phenomenon of disc degeneration. Rather a multitude of exogenous and endogenous factors might influence the progress of degenerative changes of the discs. Insufficient nutritional supply of the disc is thought to be a primarily problem contributing to disc degeneration, while genetic predisposition also has a major impact on IVDD. Polymorphisms affect genes that are involved in the maintenance of integrity or functionality of the disc matrix, suggesting that the genetic background plays a major role in the integrity of a healthy disc [7]. Currently, many methods are used in the treatment of IVDD, including drug therapy, surgical treatment, and physical therapy; however, they only perform lenitive function and finally remove the disc [8,9,10]. Therefore, given the high incidence of IVDD and aggravation of the disease, there is an urgent need to identify effective diagnostic and treatment measures for patients.
Autophagy refers to a dynamic process of highly conserved intracellular and lysosome-dependent degradation [11, 12]. While intracellular autophagy remains at a relatively low level under normal circumstances, autophagy levels can be upregulated under the action of some drugs or environmental stress, such as amino acid depletion, oxidative stress, and hypoxia [13, 14]. Therefore, autophagy disorders are associated with various diseases, including cancers, cardiovascular diseases, and chronic infectious diseases [15,16,17]. In recent years, autophagy has been demonstrated to play a pivotal role in the process of IVDD [18, 19], and the regulation of autophagy could protect against and postpone the progress of IVDD [20, 21]. However, the key autophagy-related genes and molecular mechanisms involved in IVDD remain enigmatic.
Currently, the early diagnosis of IVDD relies on time-consuming MRI scans, and the research on autophagy is mainly focused on IVD tissues and cells rather than human peripheral blood samples [19]. However, identifying key autophagy-related genes for IVDD could facilitate its early diagnosis, and the peripheral blood offers great advantage in view of the convenience of sampling. Fortunately, several studies have shown that the utilization of gene expression profiles and machine learning can serve to identify novel biomarkers in IVDD [22, 23]. Thus, this study aimed to identify autophagy-related markers and molecular mechanisms involved in IVDD and construct a diagnostic model based on human peripheral blood samples. This study provides novel and unique insights into IVDD treatments and therapeutic strategies. Figure 1 shows a schematic representation of the study design.
Materials and methods
Data collection and processing
Autophagy-related genes were acquired from the Human Autophagy Database and references (PMID32065482 [24] and PMID33392087 [25]), and overlapping genes were deleted. Two datasets related to IVDD, GSE150408 and GSE124272, were obtained from the Gene Expression Omnibus (GEO) database [26]. To ensure the accuracy of the results, GSE150408 with a relatively large sample size (containing 17 control samples and 17 IVDD samples) was used as a training dataset for diagnostic model construction, while GSE124272 (containing eight control samples and eight IVDD samples) was used as the validation dataset. The gene expression matrix probe value was used to log2 standardize the data quality control stage of the model, and the annotation file “GPL21185” provided internally by GEO was utilized to convert the probe to Gene Symbol for gene annotation. The average value was selected as the expression value when several probes matched a single-gene symbol.
Differentially expressed genes (DEGs) between IVDD and control samples
The “limma” package [27] in R software was used to screen the DEGs between IVDD and control samples with threshold of P < 0.05. The screened DEGs were intersected with autophagy-related genes to obtain autophagy-DEGs.
Immune infiltration analysis
The fraction of 22 immune cell infiltrations between IVDD and control samples was explored using CIBERSORT [28], and the difference in the fraction of 22 immune cell infiltrations between IVDD and control samples was compared using the Mann–Whitney U test with a cut-off value of P < 0.05.
Weighted gene coexpression Network Analysis (WGCNA)
To explore the correlation between the DEGs and immune cells, WGCNA was performed. First, genes were screened using the “WGCNA” package (v 1.71) [29] to control the quality of gene expression values, mainly based on the top 75% genes with a median absolute deviation > 0.01. Then hclust clustering of sample populations was carried out using the “sampleTree” function. Then the coexpression network of all DEGs between IVDD and control samples was constructed, and the “pickSoftThreshold” function in “WGCNA” package was employed both to obtain the optimum “power” value (R-square > 0.85) and built the coexpression network (maxBlockSize = 5000). The edge properties of undirected networks were calculated as follows: \({Abs\left(Cor\right(genex,geney\left)\right)}^{power}\). The edge properties of a directed network were calculated as follows: \({(1+\frac{Cor(genex,geney)}{2})}^{power}\). The formula for calculating the edge properties of the sign hybrid was: \(Cor{(genex,geney)^{power}}ifCor > 0\,else\,0\). The “plotDendroAndColors” was used to draw the hierarchical clustering of gene modules. Then Spearman correlation was performed between gene modules and immune cells to identify significant differences between control and IVDD samples at a threshold P < 0.05 and |Coeff| > 0.2 to consider the modules as IVDD-related modules.
Diagnostic model construction
The genes in the IVDD-related modules were intersected with autophagy-related genes to obtain IVDD-autophagy genes. Then, the key IVDD-autophagy genes were acquired using the least absolute shrinkage and selection operator (LASSO) regression. Considering the two-classification characteristics of case control studies, the study used the “glmnet” function to set family = “binary” for fitting, and the feature of the model was calculated using the following formula: \({feature}_{sample}=\sum _{1}^{n}{Coef}_{i}*{x}_{i}\) (where feature represents the feature value of the sample in the model; Coefi represents the regression coefficient of the gene in LASSO regression; and xi represents the gene expression). The samples were categorized into IVDD and healthy groups based on the median cut-off value of the featuresample. The “roc” function in pROC package was utilized to calculate the area under the curve (AUC) value to analyze the prediction performance. The GSE124272 dataset was used to validate the proposed model.
Gene Set Variation Analysis (GSVA) and Gene Set Enrichment Analysis (GSEA)
Seventeen immune-related pathways were obtained from the ImmPort database, and GSVA analysis was performed. In addition, using the hallmark gene sets, the GSEA and GSVA were conducted. In addition, to investigate the potential mechanism of genes in the diagnostic model, enrichment analysis was performed using the clusterProfiler package [30] with a threshold of P < 0.05 and enrichment factor > 1.5.
Construction of miRNA-gene, transcription factor (TF)-gene interaction networks
The MiWalk database was used to screen for common miRNAs of genes in the diagnostic model, Jaspar database [31] was used to predict the TF of genes in the diagnostic model, and miRNA/TF-target gene networks were constructed using Cytoscape software.
Drug-gene interaction
The genes in the diagnostic model served as promising targets for searching for drugs in the CLUE website with a threshold of P < 0.05 and z-score > 2. Then, the STITCH database was used to construct a drug-gene interaction network with the parameter of the minimum required interaction score: medium confidence (0.400).
Target genes of methylprednisolone and glucosamine
Methylprednisolone and glucosamine are the empirical used clinical therapeutic drugs for IVDD. To explore the autophagy-related target genes of methylprednisolone and glucosamine, their target genes were predicted in Comparative Toxicogenomics Database (CTD) and then intersected with autophagy-related genes/DEGs, followed by enrichment analysis.
Results
DEGs in control and IVDD samples
In total, 1,776 DEGs were screened between the control and IVDD samples (Fig. 2A), and 739 autophagy-related genes were identified. Then, the 1,776 DEGs were intersected with the 739 autophagy-related genes, and 63 autophagy-DEGs were obtained (Fig. 2B and C).
Immune cells infiltration between control and IVDD samples
The fraction of 22 immune cell infiltrates between IVDD and control samples were explored, and the fraction of neutrophils was found to be higher in IVDD samples than in control samples (Fig. 3A). In addition, as shown in Fig. 3B, activated dendritic cells, plasma cells, neutrophils, and gamma delta T cells differed significantly between the control and IVDD samples (P < 0.05).
Construction of coexpression network and diagnostic model
In total, 1,332 genes were screened to build the coexpression network, and the value of “power” (power = 4) when the R-square value reached 0.85 was selected (Fig. 4A). Three modules were obtained, including Meturquoise, Meblue, and Mebrown (Fig. 4B). Meturquoise and Mebrown modules were significantly related to immune cells with significant differences between control and IVDD samples and were considered as IVDD-related modules (Fig. 4C). The Meturquoise genes (164 genes) and Mebrown (78 genes) modules intersected with the 739 autophagy-related genes to obtain 11 genes, which were considered as IVDD-autophagy genes (Fig. 4D). Based on the 11 IVDD-autophagy genes, 5 key IVDD-autophagy genes were obtained using LASSO regression to construct the diagnostic model (Fig. 5A), including PHF23, RAB24, STAT3, TOMM5, and DNAJB9 (Fig. 5B); and the AUC values of the model in the training and validation datasets were 0.907 and 0.984, respectively (Fig. 5C and D).
GSVA and GSEA
GSVA results showed that the enrichment scores of the two pathways showed significant differences between the IVDD and healthy groups, including interferon and chemokine receptors (Fig. 6A). The correlation analysis results showed that the five gene expressions of the five genes in the diagnostic model were significantly related with interferon and chemokine receptors, among which RAB24 was the most significantly related with interferon receptor (Fig. 6B).
As shown in Fig. 7A, eight pathways showed significant differences between IVDD and healthy groups. The correlation analysis results showed that the five gene expressions of the five genes in the diagnostic model was significantly related to the GSVA score of the eight pathways; among which, RAB24 showed the most significant relation with the hallmark complement (Fig. 7B). Five genes in the diagnostic model showed significant enrichment in radial glial cell differentiation, regulation of autophagy, regulation of autophagosome maturation, and negative regulation of the endoplasmic reticulum unfolded protein response (Fig. 7C).
MiRNA-gene, TF-gene interaction networks
In total, 16 common miRNAs of five key IVDD-autophagy genes in the diagnostic model were screened in the MiWalk database, and three TFs of five key IVDD-autophagy genes in the diagnostic model were predicted in the Jaspar database. Then, the miRNA-gene and TF-gene interaction networks were constructed using Cytoscape software (Fig. 8A and B).
Drug-gene interaction and target genes of methylprednisolone and glucosamine
The CLUE website was used to search for drugs related to the five key IVDD-autophagy genes, and 84 significantly related drugs were screened (z-score > 2, P < 0.05). STAT3 was significantly associated with niclosamide, sorafenib, and gemcitabine (median confidence = 0.400, Fig. 8C). The CTD database was used to predict the target genes of methylprednisolone and glucosamine, which intersected with the 63 autophagy-DEGs, and three common autophagy-related target genes of methylprednisolone and glucosamine were obtained (Fig. 9A). The enrichment analysis of these three autophagy-related target genes of methylprednisolone and glucosamine showed that they were significantly enriched in apoptosis, sphingolipid signaling pathway, AGE-RAGE signaling pathway in diabetic complications, and EGFR tyrosine kinase inhibitor resistance (Fig. 9B). Moreover, the predicted target genes of methylprednisolone and glucosamine intersected with 1,776 DEGs, and 7 target DEGs of methylprednisolone and glucosamine were obtained (Fig. 9C). Enrichment analysis showed that the seven target DEGs of methylprednisolone and glucosamine were involved in the sphingolipid signaling pathway, human papillomavirus infection, pancreatic cancer, and tuberculosis (Fig. 9D).
Discussion
In this study, a diagnostic model was constructed based on five key autophagy-related genes: PHF23, RAB24, STAT3, TOMM5, and DNAJB9. PHF23 was recently identified as an autophagy inhibitor, and a previous study demonstrated that PHF23 inhibition has therapeutic potential in degenerative joint diseases [32]. Hai et al. indicated that RAB24 might participate in the development of IVDD by triggering numerous immune-associated pathways [33]. Suzuki et al. found that the IL-6/JAK/STAT3 pathway is involved in the pathogenesis of IVDD [34]. TOMM5 and DNAJB9 have been reported to be involved in the development of cancer, type 2 diabetes mellitus, and obesity [35,36,37,38,39]; however, few studies of TOMM5 and DNAJB9 on IVDD have been reported. Therefore, the functions of TOMM5 and DNAJB9 in IVDD should be studied further. In addition, receiver operating characteristic curve was constructed to estimate the predictive ability of the diagnostic model, and AUC values of the model in the training and validation datasets were 0.907 and 0.984, respectively. These indicate that the performance of the diagnostic model is credible. Moreover, enrichment analysis showed that the five key IVDD-autophagy genes in the diagnostic model were significantly enriched in radial glial cell differentiation, regulation of autophagy, and regulation of autophagosome maturation. Published studies have confirmed that autophagy markers exist in IVD tissue, and in vitro, disc cells regulate autophagy in response to cellular stressors [19]. Thus, these five key IVDD-autophagy genes may play a role in IVDD through these biological processes.
Currently, some miRNAs are known to be involved in various pathological processes of IVDD [40, 41]. Zhao et al. showed that miR-19b-3p relieves IVDD by modulating the PTEN/PI3K/Akt/mTOR signaling pathway [42]. Gao et al. found that N6-methyladenosine-induced miR-143-3p promotes IVDD by regulating SOX5 [43]. Wang et al. reported that miRNA-140-3p alleviates IVDD via the KLF5/N-cadherin/MDM2/Slug axis [44]. Thus, in this study, the common miRNAs of five key autophagy-related genes in the diagnostic model were screened, and 16 common miRNAs were identified, including has-miR-8085, has-miR-198, has-miR-6865-5p, and has-miR-6879-5p. Besides, three TFs of the five key IVDD-autophagy genes in the diagnostic model were predicted, including MA0098.1. ETS1, MA1536.1.NR2C2, and MA0719.1.RHOXF1. Thus, it is suggested that these 16 miRNAs and 3 TFs may be involved in the pathogenesis of IVDD by targeting the five key autophagy-related genes.
In total, 84 significantly related drugs of the five key IVDD-autophagy genes were screened. In addition, STAT3 expression was significantly associated with niclosamide, sorafenib, and gemcitabine. A previous study has reported that inflammation is an important factor in the onset and progression of disc degeneration [45]. Li et al. revealed that sorafenib restrains lipopolysaccharide/endotoxin-induced inflammation by regulating Lyn-MAPK-NF-kB/AP-1 pathway and TLR4 expression [46]. Therefore, these 84 drugs can be used as therapeutic agents for IVDD. It has also been reported that methylprednisolone and glucosamine used in the treatment can significantly alleviate lower back and leg pain caused by IVDD and improve spinal cord function [47, 48]. Thus, the target genes of methylprednisolone and glucosamine were predicted to intersect with the 63 autophagy-DEGs, and three common autophagy-related target genes of methylprednisolone and glucosamine were identified, including CTSD, VEGFA, and BAX. Teixeira et al. indicated that CTSD modulates the formation of the terminal complement complex in cultured human disc tissues [49]. Feng et al. suggested that Bushen Huoxue decoction intervenes in IVDD through VEGF-A [50]. Feng et al. showed that high glucose induces the ChREBP/p300 transcriptional complex to activate the proapoptotic genes, PUMA and BAX, to contribute to IVDD [51]. Moreover, enrichment analysis showed that these three common autophagy-related target genes of methylprednisolone and glucosamine were significantly involved in apoptosis, sphingolipid signaling, and AGE-RAGE signaling in diabetic complications. Dysregulation of apoptosis has been reported to be involved in the development of degenerative diseases, such as osteoarthritis [52]. Numerous studies have shown that inflammation alters the microenvironment of nucleus pulposus cells, induces apoptosis, and ultimately leads to IVDD [45, 53]. Excessive sphingolipid synthesis can cause degenerative diseases, such as childhood amyotrophic lateral sclerosis [54]. Xia et al. used transcriptome sequencing to identify new therapeutic targets for IVDD and found that DEGs, between the IVDD and non-IVDD groups, were enriched in the AGE-RAGE signaling pathway in diabetic complications [55]. These results support those of the present study, suggesting that methylprednisolone and glucosamine might exert therapeutic effects in IVDD by targeting CTSD, VEGFA, and BAX through apoptosis, sphingolipid signaling pathway, and AGE-RAGE signaling pathway in diabetic complications. However, further in-depth studies are required to confirm these findings.
Nevertheless, this study had some limitations. First, the data were downloaded from public databases; other large-sample datasets are required to validate the results of this study. Second, the five key IVDD-autophagy genes, potential drugs, and target genes, and the molecular mechanisms of methylprednisolone and glucosamine identified in this study should be examined further in other cohorts and in vivo and in vitro experiments. Third, CIBERSORT algorithm was the only one used to estimate the fractions of immune cells infiltration between IVDD and control samples; therefore, flow cytometry should be performed to further validate the reliability of the results.
Conclusion
In summary, this study developed a reliable autophagy-related diagnostic model that is strongly related to the immune microenvironment of IVD and offers insights into latent therapeutic targets for patients with IVDD. Autophagy-related genes, containing PHF23, RAB24, STAT3, TOMM5, and DNAJB9, may participate in pathogenesis of IVDD. In addition, methylprednisolone and glucosamine may exert therapeutic effects on IVDD by targeting CTSD, VEGFA, and BAX through apoptosis, sphingolipid signaling pathway, AGE-RAGE signaling pathway in diabetic complications.
Data Availability
This study analyses publicly available datasets. These data can be found at GSE150408 and GSE124272 (https://www.ncbi.nlm.nih.gov/geo/). All data generated in this study is available from the corresponding author upon reasonable request.
References
Urban JP, Winlove CP. Pathophysiology of the intervertebral disc and the challenges for MRI. J Magn Reson Imaging: JMRI. 2007;25(2):419–32.
Humzah MD, Soames RW. Human intervertebral disc: structure and function. Anat Rec. 1988;220(4):337–56.
Adams MA, Roughley PJ. What is intervertebral disc degeneration, and what causes it? Spine 2006, 31(18):2151–61.
Fraser RD, Osti OL, Vernon-Roberts B. Intervertebral disc degeneration. Eur Spine Journal: Official Publication Eur Spine Soc Eur Spinal Deformity Soc Eur Sect Cerv Spine Res Soc. 1993;1(4):205–13.
Cheung KM, Karppinen J, Chan D, Ho DW, Song YQ, Sham P, Cheah KS, Leong JC, Luk KD. Prevalence and pattern of lumbar magnetic resonance imaging changes in a population study of one thousand forty-three individuals. Spine. 2009;34(9):934–40.
Stolworthy DK, Bowden AE, Roeder BL, Robinson TF, Holland JG, Christensen SL, Beatty AM, Bridgewater LC, Eggett DL, Wendel JD, et al. MRI evaluation of spontaneous intervertebral disc degeneration in the alpaca cervical spine. J Orthop Research: Official Publication Orthop Res Soc. 2015;33(12):1776–83.
Hanaei S, Abdollahzade S, Khoshnevisan A, Kepler CK, Rezaei N. Genetic aspects of intervertebral disc degeneration. Rev Neurosci. 2015;26(5):581–606.
Sharifi S, Bulstra SK, Grijpma DW, Kuijer R. Treatment of the degenerated intervertebral disc; closure, repair and regeneration of the annulus fibrosus. J Tissue Eng Regen Med. 2015;9(10):1120–32.
Steele J, Bruce-Low S, Smith D, Osborne N, Thorkeldsen A. Can specific loading through exercise impart healing or regeneration of the intervertebral disc? The Spine Journal: Official Journal of the North American Spine Society. 2015;15(10):2117–21.
Chen BL, Guo JB, Zhang HW, Zhang YJ, Zhu Y, Zhang J, Hu HY, Zheng YL, Wang XQ. Surgical versus non-operative treatment for lumbar disc herniation: a systematic review and meta-analysis. Clin Rehabil. 2018;32(2):146–60.
Kim KH, Lee MS. Autophagy–a key player in cellular and body metabolism. Nat Reviews Endocrinol. 2014;10(6):322–37.
Glick D, Barth S, Macleod KF. Autophagy: cellular and molecular mechanisms. J Pathol. 2010;221(1):3–12.
Filomeni G, De Zio D, Cecconi F. Oxidative stress and autophagy: the clash between damage and metabolic needs. Cell Death Differ. 2015;22(3):377–88.
Monaci S, Coppola F, Rossi D, Giuntini G, Filippi I, Marotta G, Sozzani S, Carraro F, Naldini A. Hypoxia Induces Autophagy in Human Dendritic Cells: Involvement of Class III PI3K/Vps34. Cells 2022, 11(10).
Onorati AV, Dyczynski M, Ojha R, Amaravadi RK. Targeting autophagy in cancer. Cancer. 2018;124(16):3307–18.
Klionsky DJ, Petroni G, Amaravadi RK, Baehrecke EH, Ballabio A, Boya P, Bravo-San Pedro JM, Cadwell K, Cecconi F, Choi AMK, et al. Autophagy in major human diseases. EMBO J. 2021;40(19):e108863.
Mizushima N, Levine B. Autophagy in Human Diseases. N Engl J Med. 2020;383(16):1564–76.
Zhang TW, Li ZF, Dong J, Jiang LB. The circadian rhythm in intervertebral disc degeneration: an autophagy connection. Exp Mol Med. 2020;52(1):31–40.
Kritschil R, Scott M, Sowa G, Vo N. Role of autophagy in intervertebral disc degeneration. J Cell Physiol. 2022;237(2):1266–84.
Gong CY, Zhang HH. Autophagy as a potential therapeutic target in intervertebral disc degeneration. Life Sci. 2021;273:119266.
Bahar ME, Hwang JS, Ahmed M, Lai TH, Pham TM, Elashkar O, Akter KM, Kim DH, Yang J, Kim DR. Targeting Autophagy for Developing New Therapeutic Strategy in Intervertebral Disc Degeneration. Antioxidants (Basel, Switzerland) 2022, 11(8).
Ma X, Su J, Wang B, Jin X. Identification of Characteristic Genes in Whole Blood of Intervertebral Disc Degeneration Patients by Weighted Gene Coexpression Network Analysis (WGCNA). Comput Math Methods Med 2022, 2022:6609901.
Yang Z, Yuan ZZ, Ma XL. Identification of a potential novel biomarker in intervertebral disk degeneration by bioinformatics analysis and experimental validation. Front Immunol. 2023;14:1136727.
Wang Y, Zhao W, Xiao Z, Guan G, Liu X, Zhuang M. A risk signature with four autophagy-related genes for predicting survival of glioblastoma multiforme. J Cell Mol Med. 2020;24(7):3807–21.
Fang Q, Chen H. Development of a Novel Autophagy-Related prognostic signature and Nomogram for Hepatocellular Carcinoma. Front Oncol. 2020;10:591356.
Clough E, Barrett T. The Gene expression Omnibus Database. Methods in Molecular Biology (Clifton NJ). 2016;1418:93–110.
Ritchie ME, Phipson B, Wu D, Hu Y, Law CW, Shi W, Smyth GK. Limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 2015;43(7):e47.
Chen B, Khodadoust MS, Liu CL, Newman AM, Alizadeh AA. Profiling Tumor infiltrating Immune cells with CIBERSORT. Methods in Molecular Biology (Clifton NJ). 2018;1711:243–59.
Langfelder P, Horvath S. WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics. 2008;9:559.
Yu G, Wang LG, Han Y, He QY. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS. 2012;16(5):284–7.
Castro-Mondragon JA, Riudavets-Puig R, Rauluseviciute I, Lemma RB, Turchi L, Blanc-Mathieu R, Lucas J, Boddie P, Khan A et al. Manosalva Pérez N : JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles. Nucleic acids research 2022, 50(D1):D165-d173.
Sun K, Jing X, Guo J, Yao X, Guo F. Mitophagy in degenerative joint diseases. Autophagy. 2021;17(9):2082–92.
Hai B, Song Q, Du C, Mao T, Jia F, Liu Y, Pan X, Zhu B, Liu X. Comprehensive bioinformatics analyses reveal immune genes responsible for altered immune microenvironment in intervertebral disc degeneration. Mol Genet Genomics: MGG. 2022;297(5):1229–42.
Suzuki S, Fujita N, Fujii T, Watanabe K, Yagi M, Tsuji T, Ishii K, Miyamoto T, Horiuchi K, Nakamura M, et al. Potential involvement of the IL-6/JAK/STAT3 pathway in the pathogenesis of intervertebral disc degeneration. Spine. 2017;42(14):E817–e824.
Chen J, Meng Y, Zhou J, Zhuo M, Ling F, Zhang Y, Du H, Wang X. Identifying candidate genes for type 2 diabetes Mellitus and obesity through gene expression profiling in multiple tissues or cells. J Diabetes Res. 2013;2013:970435.
Xu W, Zhao D, Huang X, Zhang M, Yin M, Liu L, Wu H, Weng Z, Xu C. The prognostic value and clinical significance of mitophagy-related genes in hepatocellular carcinoma. Front Genet. 2022;13:917584.
Cheng Y, Liu J, Fan H, Liu K, Zou H, You Z. Integrative analyses of a mitophagy-related gene signature for predicting prognosis in patients with uveal melanoma. Front Genet. 2022;13:1050341.
Kim HY, Kim YM, Hong S. DNAJB9 suppresses the metastasis of triple-negative breast cancer by promoting FBXO45-mediated degradation of ZEB1. Cell Death Dis. 2021;12(5):461.
Sun F, Liao Y, Qu X, Xiao X, Hou S, Chen Z, Huang H, Li P, Fu S. Hepatic DNAJB9 drives anabolic biasing to reduce steatosis and obesity. Cell Rep. 2020;30(6):1835–1847e1839.
Cazzanelli P, Wuertz-Kozak K. MicroRNAs in intervertebral disc degeneration, apoptosis, inflammation, and mechanobiology. Int J Mol Sci 2020, 21(10).
Yang F, Wang J, Chen Z, Yang Y, Zhang W, Guo S, Yang Q. Role of microRNAs in intervertebral disc degeneration (review). Experimental and Therapeutic Medicine. 2021;22(2):860.
Zhao Y, Li A. miR-19b-3p relieves intervertebral disc degeneration through modulating PTEN/PI3K/Akt/mTOR signaling pathway. Aging. 2021;13(18):22459–73.
Gao D, Hu B, Ding B, Zhao Q, Zhang Y, Xiao L. N6-Methyladenosine-induced mir-143-3p promotes intervertebral disc degeneration by regulating SOX5. Bone. 2022;163:116503.
Wang Z, Zhang S, Zhao Y, Qu Z, Zhuang X, Song Q, Leng J, Liu Y. MicroRNA-140-3p alleviates intervertebral disc degeneration via KLF5/N-cadherin/MDM2/Slug axis. RNA Biol. 2021;18(12):2247–60.
Lyu FJ, Cui H, Pan H, Mc Cheung K, Cao X, Iatridis JC, Zheng Z. Painful intervertebral disc degeneration and inflammation: from laboratory evidence to clinical interventions. Bone Res. 2021;9(1):7.
Li X, Xu M, Shen J, Li Y, Lin S, Zhu M, Pang Q, Tan X, Tang J. Sorafenib inhibits LPS-induced inflammation by regulating Lyn-MAPK-NF-kB/AP-1 pathway and TLR4 expression. Cell Death Discovery. 2022;8(1):281.
Gomes SA, Lowrie M, Targett M. Single dose epidural methylprednisolone as a treatment and predictor of outcome following subsequent decompressive surgery in degenerative lumbosacral stenosis with foraminal stenosis. Veterinary journal (London, England: 1997) 2020, 257:105451.
Harmon MD, Ramos DM, Nithyadevi D, Bordett R, Rudraiah S, Nukavarapu SP, Moss IL, Kumbar SG. Growing a backbone - functional biomaterials and structures for intervertebral disc (IVD) repair and regeneration: challenges, innovations, and future directions. Biomaterials Sci. 2020;8(5):1216–39.
Teixeira GQ, Yong Z, Kuhn A, Riegger J, Goncalves RM, Ruf M, Mauer UM, Huber-Lang M, Ignatius A, Brenner RE, et al. Interleukin-1β and cathepsin D modulate formation of the terminal complement complex in cultured human disc tissue. Eur Spine Journal: Official Publication Eur Spine Soc Eur Spinal Deformity Soc Eur Sect Cerv Spine Res Soc. 2021;30(8):2247–56.
Feng SH, Xie F, Yao HY, Wu GB, Sun XY, Yang J. The mechanism of Bushen Huoxue decoction in treating intervertebral disc degeneration based on network pharmacology. Annals of Palliative Medicine. 2021;10(4):3783–92.
Feng Y, Wang H, Chen Z, Chen B. High glucose mediates the ChREBP/p300 transcriptional complex to activate proapoptotic genes Puma and BAX and contributes to intervertebral disc degeneration. Bone. 2021;153:116164.
Hwang HS, Kim HA. Chondrocyte apoptosis in the pathogenesis of Osteoarthritis. Int J Mol Sci. 2015;16(11):26035–54.
Chen S, Lei L, Li Z, Chen F, Huang Y, Jiang G, Guo X, Zhao Z, Liu H, Wang H, et al. Grem1 accelerates nucleus pulposus cell apoptosis and intervertebral disc degeneration by inhibiting TGF-β-mediated Smad2/3 phosphorylation. Exp Mol Med. 2022;54(4):518–30.
Mohassel P, Donkervoort S, Lone MA, Nalls M, Gable K, Gupta SD, Foley AR, Hu Y, Saute JAM, Moreira AL, et al. Childhood amyotrophic lateral sclerosis caused by excess sphingolipid synthesis. Nat Med. 2021;27(7):1197–204.
Xia B, Xing J, Ai Q, Li H, Xu M, Hou T. [Expression profile of intervertebral disc degeneration-specific genes: a transcriptome sequencing-based analysis]. Nan fang yi ke da xue xue bao = Journal of Southern Medical University. 2021;41(6):883–90.
Acknowledgements
Thanks to the GEO database for sharing data and code.
Funding
This study was supported by the National Nature Science Foundation of China (grant no. 82172472).
Author information
Authors and Affiliations
Contributions
Yifeng Wang designed the study, analyzed the data and wrote the manuscript. Xiongsheng Chen was responsible for proofreading the manuscript. Zhiwei Wang, Yifan Tang, Yong Chen, Chuanyuan Fang and Zhihui Li analyzed the data and participated in the writing of this manuscript. Genlong Jiao participated in the writing and proofreading the manuscript. All authors reviewed the manuscript.
Corresponding authors
Ethics declarations
Ethics approval and consent to participate
All methods were carried out in accordance with relevant guidelines and regulations. No human subject was directly involved in this study.
Consent for publication
All participants gave written informed consent for their details to be published in this study.
Competing interests
The authors declare that they have no competing interests.
Additional information
Publisher’s Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Rights and permissions
Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
About this article
Cite this article
Wang, Y., Wang, Z., Tang, Y. et al. Diagnostic model based on key autophagy-related genes in intervertebral disc degeneration. BMC Musculoskelet Disord 24, 927 (2023). https://doi.org/10.1186/s12891-023-06886-w
Received:
Accepted:
Published:
DOI: https://doi.org/10.1186/s12891-023-06886-w