Decoding neuronal genes in stroke-induced pain: insights from single-nucleus sequencing in mice

Abstract

Background The role of neurons in central post-stroke pain (CPSP) following thalamic hemorrhage remains unclear. This study aimed to identify key genes associated with post-thalamic hemorrhage pain and to explore their functions in neurons. Single-nucleus RNA sequencing (snRNA-seq) data from a mouse model was used for this analysis. Methods First, snRNA-seq data were analyzed to identify cell types associated with CPSP induced by thalamic hemorrhage. Differentially expressed genes (DEGs) in neurons were then screened between control and model groups, followed by the construction of a protein-protein interaction (PPI) network for the DEGs. CytoNCA was used to assess node connectivity in the PPI network, and the top 5 key genes were identified. Subsequently, transcription factor (TF)-mRNA and miRNA-mRNA networks were constructed, and small-molecule drugs potentially targeting these key genes were predicted. Finally, the expression differences of key genes in neurons were compared between the model and control groups. Results A total of 13 cell clusters were identified, categorized into 8 cell types: T cells, endothelial cells, monocytes, neural progenitor cells (NPCs), microglia, astrocytes, neurons, and oligodendrocytes. A total of 228 DEGs were detected in neurons when comparing the model group with the control group. The PPI network of the DEGs consisted of 126 nodes and 209 edges, identifying the top 5 key genes: Dlgap1, Cacna1c, Gria2, Hsp90ab1, and Gapdh. The miRNA-mRNA network included 68 miRNA-mRNA pairs, 62 miRNAs, and 5 mRNAs, while the TF-mRNA network consisted of 66 TF-mRNA pairs, 56 TFs, and 5 mRNAs. Drug prediction identified 110 small-molecule drugs (e.g., purpurogallin, nifedipine, and novobiocin) potentially targeting these key genes. Additionally, Cacna1c were significantly upregulated in model mice. Conclusion This study identified the role of key genes in thalamic hemorrhage-induced CPSP through snRNA-seq, providing a scientific basis for further exploration of the molecular mechanisms underlying CPSP. Supplementary Information The online version contains supplementary material available at 10.1186/s12883-024-03965-w.