1
|
Jia D, Wang K, Huang L, Zhou Z, Zhang Y, Chen N, Yang Q, Wen Z, Jiang H, Yao C, Wu R. Revealing PPP1R12B and COL1A1 as piRNA pathway genes contributing to abdominal aortic aneurysm through integrated analysis and experimental validation. Gene 2024; 897:148068. [PMID: 38070790 DOI: 10.1016/j.gene.2023.148068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 11/27/2023] [Accepted: 12/05/2023] [Indexed: 01/17/2024]
Abstract
BACKGROUND Abdominal aortic aneurysm (AAA) is a permanent dilation of the abdominal aorta, with a high mortality rate when rupturing. Although lots of piRNA pathway genes (piRPGs) have recently been linked to both neoplastic and non-neoplastic illnesses, their role in AAA is still unknown. Utilizing integrative bioinformatics methods, this research discovered piRPGs as biomarkers for AAA and explore possible molecular mechanisms. METHODS The datasets were obtained from the Gene Expression Omnibus and piRPGs were identified from the Genecards database. The "limma" and "clusterProfiler" R-packages were used to discover differentially expressed genes and perform enrichment analysis, respectively. Hub piRPGs were further filtered using least absolute shrinkage and selection operator regression, random forests, as well as receiver operating characteristic curve. Additionally, multi-factor logistic regression (MLR), extreme gradient boosting (XGboost), and artificial neural network (ANN) were employed to construct prediction models. The relationship between hub piRPGs and immune infiltrating cells and sgGSEA were further studied. The expression of hub piRPGs was verified by qRT-PCR, immunohistochemistry, and western blotting in AAA and normal vascular tissues and analyzed by scRNA-seq in mouse AAA model. SRAMP and cMAP database were utilized for the prediction of N6-methyladenosine (m6A) targets therapeutic drug. RESULTS 34 differentially expressed piRPGs were identified in AAA and enriched in pathways of immune regulation and gene silence. Three piRPGs (PPP1R12B, LRP10, and COL1A1) were further screened as diagnostic genes and used to construct prediction model. Compared with MLR and ANN, Xgboost showed better predictive ability, and PPP1R12B might have the ability to distinguish small and large AAA. Furthermore, the expression levels of PPP1R12B and COL1A1 were consistent with the results of bioinformatics analysis, and PPP1R12B showed a downward trend that may be related to m6A. CONCLUSION The results suggest that piRPGs might serve a significant role in AAA. PPP1R12B, COL1A1, and LRP10 had potential as diagnostic-specific biomarkers for AAA and performed better in XGboost model. The expression and localization of PPP1R12B and COL1A1 were experimentally verified. Besides, downregulation of PPP1R12B caused by m6A might contribute to the formation of AAA.
Collapse
Affiliation(s)
- Dongdong Jia
- Department of Vascular Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, PR China; National-Guangdong Joint Engineering Laboratory for Diagnosis and Treatment of Vascular Disease, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, PR China
| | - Kangjie Wang
- Department of Vascular Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, PR China; National-Guangdong Joint Engineering Laboratory for Diagnosis and Treatment of Vascular Disease, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, PR China
| | - Lin Huang
- National-Guangdong Joint Engineering Laboratory for Diagnosis and Treatment of Vascular Disease, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, PR China
| | - Zhihao Zhou
- National-Guangdong Joint Engineering Laboratory for Diagnosis and Treatment of Vascular Disease, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, PR China
| | - Yinfeng Zhang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, PR China
| | - Nuo Chen
- Department of Vascular Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, PR China
| | - Qingqi Yang
- Department of Vascular Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, PR China
| | - Zengjin Wen
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, PR China
| | - Hui Jiang
- Department of Radiation Oncology, Sun Yat-Sen University Cancer Center, Guangzhou 510060, PR China
| | - Chen Yao
- Department of Vascular Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, PR China; National-Guangdong Joint Engineering Laboratory for Diagnosis and Treatment of Vascular Disease, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, PR China
| | - Ridong Wu
- Department of Vascular Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, PR China; National-Guangdong Joint Engineering Laboratory for Diagnosis and Treatment of Vascular Disease, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, PR China.
| |
Collapse
|