Identification of novel gene signatures and immune cell infiltration in intervertebral disc degeneration using bioinformatics analysis

Tao Tang; Zhongyuan He; Zhengya Zhu; Fuan Wang; Hongkun Chen; Fu Zhang; Jiaxiang Zhou; Jianmin Wang; Baoliang Li; Xizhe Liu; Zhiyu Zhou; Shaoyu Liu

doi:10.3389/fmolb.2023.1169718

Identification of novel gene signatures and immune cell infiltration in intervertebral disc degeneration using bioinformatics analysis

Front Mol Biosci. 2023 Jul 14:10:1169718. doi: 10.3389/fmolb.2023.1169718. eCollection 2023.

Authors

Tao Tang^{1

2}, Zhongyuan He^{1

2}, Zhengya Zhu¹, Fuan Wang^{1

2}, Hongkun Chen¹, Fu Zhang¹, Jiaxiang Zhou³, Jianmin Wang¹, Baoliang Li^{1

2}, Xizhe Liu², Zhiyu Zhou^{1

2}, Shaoyu Liu^{1

2}

Affiliations

¹ Innovation Platform of Regeneration and Repair of Spinal Cord and Nerve Injury, Department of Orthopaedic Surgery, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China.
² Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China.
³ Department of Orthopaedic Surgery, The Affiliated Hospital of Qingdao University, Qingdao, China.

Abstract

Background: Intervertebral disc degeneration (IDD) is the leading cause of lower back pain, and an overall understanding of the molecular mechanisms related to IDD is still lacking. The purpose of this study was to explore gene signatures and immune cell infiltration related to IDD via bioinformatics analysis. Methods: A total of five expression profiles of mRNA and non-coding RNA were downloaded from the Gene Expression Omnibus (GEO) database. The potentially involved lncRNA/circRNA-miRNA-mRNA networks and protein-protein interaction networks were constructed by miRNet, circBank, STRING, and the Cytoscape database. Gene ontology, Kyoto Encyclopaedia of Genes and Genomes Analysis, Gene Set Enrichment Analysis, Gene Set Variation Analysis, Immune Infiltration Analysis, and Drug-Gene Interaction were used to analyse the top 20 hub genes. RT-qPCR was conducted to confirm the 12 differential expressions of genes both in the nucleus pulposus and annulus fibrosus tissues Results: There were 346 differentially expressed mRNAs, 12 differentially expressed miRNAs, 883 differentially expressed lncRNAs, and 916 differentially expressed circRNAs in the GEO database. Functional and enrichment analyses revealed hub genes associated with platelet activation, immune responses, focal adhesion, and PI3K-Akt signalling. The apoptotic pathway, the reactive oxygen species pathway, and oxidative phosphorylation play an essential role in IDD. Immune infiltration analysis demonstrated that the Treg cells had significant infiltration, and three levels of immune cells, including dendritic cells, Th2 cells, and tumour-infiltrating lymphocytes, were inhibited in IDD. Drug-gene interaction analysis showed that COL1A1 and COL1A2 were targeted by collagenase clostridium histolyticum, ocriplasmin, and PDGFRA was targeted by 66 drugs or molecular compounds. Finally, 24 cases of IDD tissues and 12 cases of normal disc tissues were collected, and the results of RT-qPCR were consistent with the bioinformatics results. Conclusion: Our data indicated that the 20 hub genes and immune cell infiltration were involved in the pathological process of IDD. In addition, the PDGFRA and two potential drugs were found to be significant in IDD development.

Keywords: bioinformatics analysis; druggene interaction analysis; gene signatures; immune cells infiltration; intervertebral disc degeneration.

Grants and funding

The National Natural Science Foundation of China (U22A20162,31900583, 32071351, 81772400,82102604, 81960395), foundation of Shenzhen Committee for Science and Technology Innovation (JCYJ20190809142211354), Sanming Project of Medicine in Shenzhen (SZSM201911002), the Beijing Municipal Health Commission (Grant No. BMHC-2021-6, BMHC-2019-9, BMHC-2018-4, PXM 2020_026275_000002), AO CMF CPP on Bone Regeneration (AOCMF-21-04S, supported by AO Foundation, AO CMF. AO CMF is a clinical division of the AO Foundation—an independent medically-guided not-for-profit organization), Sun Yat-sen University Clinical Research 5010 Program (2019009).