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Lv X, Fan Q, Li X, Li P, Wan Z, Han X, Wang H, Wang X, Wu L, Huo B, Yang L, Chen G, Zhang Y. Identification of renal ischemia reperfusion injury-characteristic genes, pathways and immunological micro-environment features through bioinformatics approaches. Aging (Albany NY) 2024; 16:2123-2140. [PMID: 38329418 PMCID: PMC10911371 DOI: 10.18632/aging.205471] [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: 09/22/2023] [Accepted: 12/15/2023] [Indexed: 02/09/2024]
Abstract
BACKGROUND Biomarkers and pathways associated with renal ischemia reperfusion injury (IRI) had not been well unveiled. This study was intended to investigate and summarize the regulatory networks for related hub genes. Besides, the immunological micro-environment features were evaluated and the correlations between immune cells and hub genes were also explored. METHODS GSE98622 containing mouse samples with multiple IRI stages and controls was collected from the GEO database. Differentially expressed genes (DEGs) were recognized by the R package limma, and the GO and KEGG analyses were conducted by DAVID. Gene set variation analysis (GSVA) and weighted gene coexpression network analysis (WGCNA) had been implemented to uncover changed pathways and gene modules related to IRI. Besides the known pathways such as apoptosis pathway, metabolic pathway, and cell cycle pathways, some novel pathways were also discovered to be critical in IRI. A series of novel genes associated with IRI was also dug out. An IRI mouse model was constructed to validate the results. RESULTS The well-known IRI marker genes (Kim1 and Lcn2) and novel hub genes (Hbegf, Serpine2, Apbb1ip, Trip13, Atf3, and Ncaph) had been proved by the quantitative real-time polymerase chain reaction (qRT-PCR). Thereafter, miRNAs targeted to the dysregulated genes were predicted and the miRNA-target network was constructed. Furthermore, the immune infiltration for these samples was predicted and the results showed that macrophages infiltrated to the injured kidney to affect the tissue repair or fibrosis. Hub genes were significantly positively or negatively correlated with the macrophage abundance indicating they played a crucial role in macrophage infiltration. CONCLUSIONS Consequently, the pathways, hub genes, miRNAs, and the immune microenvironment may explain the mechanism of IRI and might be the potential targets for IRI treatments.
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Affiliation(s)
- Xinghua Lv
- Department of Anesthesiology, First Hospital of Lanzhou University, Lanzhou, Gansu, China
| | - Qian Fan
- Tianjin Eye Hospital, Tianjin Key Lab of Ophthalmology and Visual Science, Tianjin Eye Institute, Nankai University Affiliated Eye Hospital, Nankai University Eye Institute, Nankai University, Clinical College of Ophthalmology, Tianjin Medical University, Tianjin, China
| | - Xuanjie Li
- Department of Anesthesiology, First Hospital of Lanzhou University, Lanzhou, Gansu, China
| | - Peng Li
- Department of Anesthesiology, First Hospital of Lanzhou University, Lanzhou, Gansu, China
| | - Zhanhai Wan
- Department of Anesthesiology, First Hospital of Lanzhou University, Lanzhou, Gansu, China
| | - Xuena Han
- Department of Anesthesiology, First Hospital of Lanzhou University, Lanzhou, Gansu, China
- The First Clinical Medical College of Lanzhou University, Lanzhou, Gansu Province, China
| | - Hao Wang
- Department of Anesthesiology, First Hospital of Lanzhou University, Lanzhou, Gansu, China
- The First Clinical Medical College of Lanzhou University, Lanzhou, Gansu Province, China
| | - Xiaoxia Wang
- Department of Anesthesiology, First Hospital of Lanzhou University, Lanzhou, Gansu, China
| | - Lin Wu
- Department of Anesthesiology, First Hospital of Lanzhou University, Lanzhou, Gansu, China
| | - Bin Huo
- Department of Anesthesiology, First Hospital of Lanzhou University, Lanzhou, Gansu, China
| | - Li Yang
- Lanzhou First People's Hospital, Lanzhou, Gansu, China
| | - Gen Chen
- Department of Microbiology, School of Basic Medical Sciences, Guilin Medical University, Guilin, Guangxi Zhuang Autonomous Region, China
| | - Yan Zhang
- Department of Anesthesiology, First Hospital of Lanzhou University, Lanzhou, Gansu, China
- The First Clinical Medical College of Lanzhou University, Lanzhou, Gansu Province, China
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Kimmel PL, Wendler DS. Biopsies from Healthy Volunteers to Advance Precision Medicine. N Engl J Med 2023; 389:1834-1837. [PMID: 37952126 DOI: 10.1056/nejmp2307451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2023]
Affiliation(s)
- Paul L Kimmel
- From the National Institutes of Health, Bethesda, MD
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