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Published on: February 6, 2018
Identification and immuno-infiltration analysis of cuproptosis regulators in human spermatogenic dysfunction
Ming Zhao1,2, Wen-Xiao Yu2, Sheng-Jing Liu2
1Graduate School, Beijing University of Chinese Medicine, Beijing, China.
Insights
Cuproptosis, a cell death process, is linked to human spermatogenic dysfunction (SD). Researchers identified key cuproptosis-related genes and developed a 5-gene predictive model for SD, showing promising accuracy in validation.
Area of Science:
- Biochemistry and Molecular Biology
- Reproductive Medicine
- Immunology
Background:
- Cuproptosis (copper-induced cell death) is implicated in various disease pathologies.
- Spermatogenic dysfunction (SD) significantly impacts male fertility.
- Understanding the molecular mechanisms linking cuproptosis and SD is crucial for potential therapeutic targets.
Purpose of the Study:
- To investigate the role of cuproptosis-related genes in human spermatogenic dysfunction.
- To analyze immune cell infiltration patterns in SD.
- To construct and validate a predictive model for SD based on cuproptosis regulators.
Main Methods:
- Utilized Gene Expression Omnibus (GEO) datasets (GSE4797, GSE45885) for male infertility patients.
- Identified differentially expressed cuproptosis-related genes (deCRGs) and analyzed immune cell infiltration.
- Employed Weighted Gene Co-expression Network Analysis (WGCNA) and Gene Set Variation Analysis (GSVA).
- Developed and validated a machine learning model (eXtreme Gradient Boosting - XGB) using nomograms, calibration curves, and decision curve analysis (DCA).
Main Results:
- Identified 11 deCRGs in SD, with specific genes like ATP7A and PDHA1 upregulated.
- Discovered two distinct molecular clusters in SD exhibiting immune infiltration heterogeneity.
- Cluster 2 showed elevated expression of certain cuproptosis genes and increased resting memory CD4+ T cells.
- A 5-gene XGB model achieved an AUC of 0.812 on an external validation dataset, demonstrating high predictive accuracy for SD.
Conclusions:
- Cuproptosis plays a preliminary role in the pathogenesis of spermatogenic dysfunction.
- A novel, accurate predictive model for SD has been developed using cuproptosis-related genes.
- This research provides insights into the molecular mechanisms of SD and potential diagnostic tools.
Abstract:
Introduction: Cuproptosis seems to promote the progression of diverse diseases. Hence, we explored the cuproptosis regulators in human spermatogenic dysfunction (SD), analyzed the condition of immune cell infiltration, and constructed a predictive model. Methods: Two microarray datasets (GSE4797 and GSE45885) related to male infertility (MI) patients with SD were downloaded from the Gene Expression Omnibus (GEO) database. We utilized the GSE4797 dataset to obtain differentially expressed cuproptosis-related genes (deCRGs) between SD and normal controls. The correlation between deCRGs and immune cell infiltration status was analyzed. We also explored the molecular clusters of CRGs and the status of immune cell infiltration. Notably, weighted gene co-expression network analysis (WGCNA) was used to identify the cluster-specific differentially expressed genes (DEGs). Moreso, gene set variation analysis (GSVA) was performed to annotate the enriched genes. Subsequently, we selected an optimal machine-learning model from four models. Finally, nomograms, calibration curves, decision curve analysis (DCA), and the GSE45885 dataset were utilized to verify the predictions' accuracy. Results: Among SD and normal controls, we confirmed that there are deCRGs and activated immune responses. Through the GSE4797 dataset, we obtained 11 deCRGs. ATP7A, ATP7B, SLC31A1, FDX1, PDHA1, PDHB, GLS, CDKN2A, DBT, and GCSH were highly expressed in testicular tissues with SD, whereas LIAS was lowly expressed. Additionally, two clusters were identified in SD. Immune-infiltration analysis showed the existing heterogeneity of immunity at these two clusters. Cuproptosis-related molecular Cluster2 was marked by enhanced expressions of ATP7A, SLC31A1, PDHA1, PDHB, CDKN2A, DBT, and higher proportions of resting memory CD4+ T cells. Furthermore, an eXtreme Gradient Boosting (XGB) model based on 5-gene was built, which showed superior performance on the external validation dataset GSE45885 (AUC = 0.812). Therefore, the combined nomogram, calibration curve, and DCA results demonstrated the accuracy of predicting SD. Conclusion: Our study preliminarily illustrates the relationship between SD and cuproptosis. Moreover, a bright predictive model was developed.
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