J Korean Neurosurg Soc.  2022 Mar;65(2):236-244. 10.3340/jkns.2021.0169.

Bioinformatics Analysis of Autophagy and Mitophagy Markers Associated with Delayed Cerebral Ischemia Following Subarachnoid Hemorrhage

• Youn DH
• Kim BJ
• Hong EP
• Jeon JP
• on behalf of the first Korean Stroke Genetics Association Research

• KMID: 2527180
• DOI: http://doi.org/10.3340/jkns.2021.0169

Abstract

Objective
: To evaluate the interactions among differentially expressed autophagy and mitophagy markers in subarachnoid hemorrhage (SAH) patients with delayed cerebral ischemia (DCI).
Methods
: The expression data of autophagy and mitophagy-related makers in the cerebrospinal fluid (CSF) cells was analyzed by real-time reverse transcription-polymerase chain reaction and Western blotting. The markers included death-associated protein kinase (DAPK)-1, BCL2 interacting protein 3 like (BNIP3L), Bcl-1 antagonist X, phosphatase and tensin homolog-induced kinase (PINK), Unc-51 like autophagy activating kinase 1, nuclear dot protein 52, and p62. In silico functional analyses including gene ontology enrichment and the protein-protein interaction network were performed.
Results
: A total of 56 SAH patients were included and 22 (38.6%) of them experienced DCI. The DCI patients had significantly increased mRNA levels of DAPK1, BNIP3L, and PINK1, and increased expression of BECN1 compared to the non-DCI patients. The most enriched biological process was the positive regulation of autophagy, followed by the response to mitochondrial depolarization. The molecular functions ubiquitin-like protein ligase binding and ubiquitin-protein ligase binding were enriched. In the cluster of cellular components, Lewy bodies and the phagophore assembly site were enriched. BECN1 was the most connected gene among the differentially expressed markers related to autophagy and mitophagy in the development of DCI.
Conclusion
: Our study may provide novel insight into mitochondrial dysfunction in DCI pathogenesis.

Keyword

Subarachnoid hemorrhage; Autophagy; Brain ischemia; Cerebrospinal fluid; Bioinformatics

Figure

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  Fig. 1. Transmission electron microscopy showing damaged mitochondria, autophagic vacuoles, lysosomes, and peroxisomes in the cerebrospinal fluid cells of patients with subarachnoid hemorrhage. Scale bar, 2 μm.

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  Fig. 2. Gene ontology network of biological processes (A), molecular function (B), cellular components (c), and the protein-protein interaction network (d) of differentially expressed markers of autophagy and mitophagy associated with delayed cerebral ischemia following subarachnoid hemorrhage. p62 is also called SQSTM1. BNIP3L : BcL2 interacting protein 3 like, PINK1 : phosphatase and tensin homolog-induced kinase 1, SQSTM1 : sequestosome 1, dAPK : death-associated protein kinase.

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  Fig. 3. Kyoto Encyclopedia of Genes and Genomes pathway analysis of autophagy (A) and mitophagy (B). differentially expressed autophagy and mitophagy markers associated with delayed cerebral ischemia are marked in red. p62 is also designated sequestosome 1 (SQSTM1).

Reference

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