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Identification of renal ischemia reperfusion injury-characteristic genes, pathways and immunological micro-environment features through bioinformatics approaches.
Lv, Xinghua; Fan, Qian; Li, Xuanjie; Li, Peng; Wan, Zhanhai; Han, Xuena; Wang, Hao; Wang, Xiaoxia; Wu, Lin; Huo, Bin; Yang, Li; Chen, Gen; Zhang, Yan.
Afiliación
  • Lv X; Department of Anesthesiology, First Hospital of Lanzhou University, Lanzhou, Gansu, China.
  • Fan Q; 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.
  • Li X; Department of Anesthesiology, First Hospital of Lanzhou University, Lanzhou, Gansu, China.
  • Li P; Department of Anesthesiology, First Hospital of Lanzhou University, Lanzhou, Gansu, China.
  • Wan Z; Department of Anesthesiology, First Hospital of Lanzhou University, Lanzhou, Gansu, China.
  • Han X; Department of Anesthesiology, First Hospital of Lanzhou University, Lanzhou, Gansu, China.
  • Wang H; The First Clinical Medical College of Lanzhou University, Lanzhou, Gansu Province, China.
  • Wang X; Department of Anesthesiology, First Hospital of Lanzhou University, Lanzhou, Gansu, China.
  • Wu L; The First Clinical Medical College of Lanzhou University, Lanzhou, Gansu Province, China.
  • Huo B; Department of Anesthesiology, First Hospital of Lanzhou University, Lanzhou, Gansu, China.
  • Yang L; Department of Anesthesiology, First Hospital of Lanzhou University, Lanzhou, Gansu, China.
  • Chen G; Department of Anesthesiology, First Hospital of Lanzhou University, Lanzhou, Gansu, China.
  • Zhang Y; Lanzhou First People's Hospital, Lanzhou, Gansu, China.
Aging (Albany NY) ; 16(3): 2123-2140, 2024 02 06.
Article en En | MEDLINE | ID: mdl-38329418
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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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: MicroARNs / Serpina E2 Tipo de estudio: Diagnostic_studies / Prognostic_studies Límite: Animals Idioma: En Revista: Aging (Albany NY) Asunto de la revista: GERIATRIA Año: 2024 Tipo del documento: Article País de afiliación: China Pais de publicación: Estados Unidos
Texto completo
Añadir a Mi BVS
Imprimir
XML
PubMed Links
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: MicroARNs / Serpina E2 Tipo de estudio: Diagnostic_studies / Prognostic_studies Límite: Animals Idioma: En Revista: Aging (Albany NY) Asunto de la revista: GERIATRIA Año: 2024 Tipo del documento: Article País de afiliación: China Pais de publicación: Estados Unidos