The final, formatted version of the article will be published soon.
ORIGINAL RESEARCH article
Front. Immunol.
Sec. Systems Immunology
Volume 15 - 2024 |
doi: 10.3389/fimmu.2024.1441028
Machine learning-based diagnostic model of lymphatics-associated genes for new therapeutic target analysis in intervertebral disc degeneration
Provisionally accepted- 1 Lanzhou University Second Hospital, Lanzhou, China
- 2 Department of Orthopaedics, Lanzhou University Second Hospital, Lanzhou, Gansu Province, China
Background: Low back pain resulting from intervertebral disc degeneration (IVDD) represents a significant global social problem. There are notable differences in the distribution of lymphatic vessels (LV) in normal and pathological intervertebral discs. Nevertheless, the molecular mechanisms of lymphatics-associated genes (LAGs) in the development of IVDD remain unclear. An in-depth exploration of this area will help to reveal the biological and clinical significance of LAGs in IVDD and may lead to the search for new therapeutic targets for IVDD. Methods: Data sets were obtained from the Gene Expression Omnibus (GEO) database. Following quality control and normalization, the datasets (GSE153761, GSE147383, and GSE124272) were merged to form the training set, with GSE150408 serving as the validation set. LAGs from GeneCards, MSigDB, Gene Ontology, and KEGG database. The Venn diagram was employed to identify differentially expressed lymphatic-associated genes (DELAGs) that were differentially expressed in the normal and IVDD groups. Subsequently, four machine learning algorithms (SVM-RFE, Random Forest, XGB, and GLM) were used to select the method to construct the diagnostic model. The receiver operating characteristic (ROC) curve, nomogram, and Decision Curve Analysis (DCA) were used to evaluate the model effect. In addition, we constructed a potential drug regulatory network and competitive endogenous RNA (ceRNA) network for key LAGs. Results: A total of 15 differentially expressed LAGs were identified. By comparing four machine learning methods, the top five genes of importance in the XGB model (MET, HHIP, SPRY1, CSF1, TOX) were identified as lymphatics-associated gene diagnostic signatures. This signature was used to predict the diagnosis of IVDD with strong accuracy and an area under curve (AUC) value of 0.938. Furthermore, the diagnostic model was validated in an external dataset (GSE150408), with an AUC value of 0.772. The nomogram and DCA further prove that the diagnosis model has good performance and predictive value. Additionally, drug regulatory networks and ceRNA networks were constructed, revealing potential therapeutic drugs and post-transcriptional regulatory mechanisms. Conclusion: We developed and validated a lymphatics-associated genes diagnostic model by machine learning algorithms that effectively identify IVDD patients. These five key LAGs may be potential therapeutic targets for IVDD patients.
Keywords: Intervertebral Disc Degeneration, machine learning, Diagnostic model, lymphatic-associated gene, Therapeutic target
Received: 31 May 2024; Accepted: 11 Nov 2024.
Copyright: © 2024 Lin, Li, Wang, Zheng, Hu, Zhang, Song and Zhou. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence:
Shaolong Li, Department of Orthopaedics, Lanzhou University Second Hospital, Lanzhou, 730030, Gansu Province, China
Yabin Wang, Lanzhou University Second Hospital, Lanzhou, China
Guan Zheng, Lanzhou University Second Hospital, Lanzhou, China
Fukang Hu, Lanzhou University Second Hospital, Lanzhou, China
Qiang Zhang, Lanzhou University Second Hospital, Lanzhou, China
Pengjie Song, Department of Orthopaedics, Lanzhou University Second Hospital, Lanzhou, 730030, Gansu Province, China
Haiyu Zhou, Department of Orthopaedics, Lanzhou University Second Hospital, Lanzhou, 730030, Gansu Province, China
Disclaimer: All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article or claim that may be made by its manufacturer is not guaranteed or endorsed by the publisher.