Machine learning-based characterization of cuprotosis-related biomarkers and immune infiltration in Parkinson's disease

Songyun Zhao; Li Zhang; Wei Ji; Yachen Shi; Guichuan Lai; Hao Chi; Weiyi Huang; Chao Cheng

doi:10.3389/fgene.2022.1010361

Machine learning-based characterization of cuprotosis-related biomarkers and immune infiltration in Parkinson's disease

Front Genet. 2022 Oct 17:13:1010361. doi: 10.3389/fgene.2022.1010361. eCollection 2022.

Authors

Songyun Zhao¹, Li Zhang², Wei Ji¹, Yachen Shi², Guichuan Lai³, Hao Chi⁴, Weiyi Huang¹, Chao Cheng¹

Affiliations

¹ Department of Neurosurgery, Wuxi People's Hospital Affiliated to Nanjing Medical University, Wuxi, Jiangsu, China.
² Department of Neurology, Wuxi People's Hospital Affiliated to Nanjing Medical University, Wuxi, Jiangsu, China.
³ Department of Epidemiology and Health Statistics, School of Public Health, Chongqing Medical University, Chongqing, China.
⁴ Clinical Medicine College, Southwest Medical University, Luzhou, China.

Abstract

Background: Parkinson's disease (PD) is a neurodegenerative disease commonly seen in the elderly. On the other hand, cuprotosis is a new copper-dependent type of cell death that can be observed in various diseases. Methods: This study aimed to identify potential novel biomarkers of Parkinson's disease by biomarker analysis and to explore immune cell infiltration during the onset of cuprotosis. Gene expression profiles were retrieved from the GEO database for the GSE8397, GSE7621, GSE20163, and GSE20186 datasets. Three machine learning algorithms: the least absolute shrinkage and selection operator (LASSO), random forest, and support vector machine-recursive feature elimination (SVM-RFE) were used to screen for signature genes for Parkinson's disease onset and cuprotosis-related genes (CRG). Immune cell infiltration was estimated by ssGSEA, and cuprotosis-related genes associated with immune cells and immune function were examined using spearman correlation analysis. Nomogram was created to validate the accuracy of these cuprotosis-related genes in predicting PD disease progression. Classification of Parkinson's specimens using consensus clustering methods. Result: Three PD datasets from the Gene Expression Omnibus (GEO) database were combined after eliminating batch effects. By ssGSEA, we identified three cuprotosis-related genes ATP7A, SLC31A1, and DBT associated with immune cells or immune function in PD and more accurate for the diagnosis of Parkinson's disease course. Patients could benefit clinically from a characteristic line graph based on these genes. Consistent clustering analysis identified two subtypes, with the C2 subtype exhibiting higher immune cell infiltration and immune function. Conclusion: In conclusion, our study reveals that several newly identified cuprotosis-related genes intervene in the progression of Parkinson's disease through immune cell infiltration.

Keywords: PD; bioinformatics analysis; consensus clustering; cuprotosis; immune cell infiltration.