Cortex-specific transcriptome profiling reveals upregulation of interferon-regulated genes after deeper cerebral hypoperfusion in mice

Zengyu Zhang; Zimin Guo; Zhilan Tu; Hualan Yang; Chao Li; Mengting Hu; Yuan Zhang; Pengpeng Jin; Shuangxing Hou

doi:10.3389/fphys.2023.1056354

Cortex-specific transcriptome profiling reveals upregulation of interferon-regulated genes after deeper cerebral hypoperfusion in mice

Front Physiol. 2023 Mar 13:14:1056354. doi: 10.3389/fphys.2023.1056354. eCollection 2023.

Authors

Zengyu Zhang¹, Zimin Guo¹, Zhilan Tu¹, Hualan Yang¹, Chao Li², Mengting Hu¹, Yuan Zhang³, Pengpeng Jin⁴, Shuangxing Hou¹

Affiliations

¹ Department of Neurology, Shanghai Pudong Hospital, Fudan University, Shanghai, China.
² School of Pharmacy, Hubei University of Science and Technology, Hubei, China.
³ Department of Vascular Surgery, Shanghai Pudong Hospital, Fudan University, Shanghai, China.
⁴ Department of Chronic Disease Management, Shanghai Pudong Hospital, Fudan University, Shanghai, China.

Abstract

Background: Chronic cerebral hypoperfusion (CCH) is commonly accompanied by brain injury and glial activation. In addition to white matter lesions, the intensity of CCH greatly affects the degree of gray matter damage. However, little is understood about the underlying molecular mechanisms related to cortical lesions and glial activation following hypoperfusion. Efforts to investigate the relationship between neuropathological alternations and gene expression changes support a role for identifying novel molecular pathways by transcriptomic mechanisms. Methods: Chronic cerebral ischemic injury model was induced by the bilateral carotid artery stenosis (BCAS) using 0.16/0.18 mm microcoils. Cerebral blood flow (CBF) was evaluated using laser speckle contrast imaging (LSCI) system. Spatial learning and memory were assessed by Morris water maze test. Histological changes were evaluated by Hematoxylin staining. Microglial activation and neuronal loss were further examined by immunofluorescence staining. Cortex-specific gene expression profiling analysis was performed in sham and BCAS mice, and then validated by quantitative RT-PCR and immunohistochemistry (IHC). Results: In our study, compared with the sham group, the right hemisphere CBF of BCAS mice decreased to 69% and the cognitive function became impaired at 4 weeks postoperation. Besides, the BCAS mice displayed profound gray matter damage, including atrophy and thinning of the cortex, accompanied by neuronal loss and increased activated microglia. Gene set enrichment analysis (GSEA) revealed that hypoperfusion-induced upregulated genes were significantly enriched in the pathways of interferon (IFN)-regulated signaling along with neuroinflammation signaling. Ingenuity pathway analysis (IPA) predicted the importance of type I IFN signaling in regulating the CCH gene network. The obtained RNA-seq data were validated by qRT-PCR in cerebral cortex, showing consistency with the RNA-seq results. Also, IHC staining revealed elevated expression of IFN-inducible protein in cerebral cortex following BCAS-hypoperfusion. Conclusion: Overall, the activation of IFN-mediated signaling enhanced our understanding of the neuroimmune responses induced by CCH. The upregulation of IFN-regulated genes (IRGs) might exert a critical impact on the progression of cerebral hypoperfusion. Our improved understanding of cortex-specific transcriptional profiles will be helpful to explore potential targets for CCH.

Keywords: RNA-seq; bilateral carotid artery stenosis; cerebral cortex; chronic cerebral hypoperfusion (CCH); type I interferon.

Grants and funding

This work was supported by grants from the Key Discipline Project of Shanghai Pudong Hospital (zdxk2020-09), the Science and Technology Development Fund of Shanghai Pudong New Area (Grant No. PKJ2020-Y51), the Shanghai Sailing Program (Grant No. 20YF1443100), the Research and Popularization of Appropriate Intervention Techniques for Stroke High-risk Groups in China by the Stroke Prevention and Treatment Engineering Committee of the National Health Commission (GN-2018R0008), and Beijing Emerging Health Industry Development Foundation Project (XXCY2018-011).