Ablation of Death-Associated Protein Kinase 1 Changes the Transcriptomic Profile and Alters Neural-Related Pathways in the Brain

Abstract

Death-associated protein kinase 1 (DAPK1), a Ca²⁺/calmodulin-dependent serine/threonine kinase, mediates various neuronal functions, including cell death. Abnormal upregulation of DAPK1 is observed in human patients with neurological diseases, such as Alzheimer's disease (AD) and epilepsy. Ablation of DAPK1 expression and suppression of DAPK1 activity attenuates neuropathology and behavior impairments. However, whether DAPK1 regulates gene expression in the brain, and whether its gene profile is implicated in neuronal disorders, remains elusive. To reveal the function and pathogenic role of DAPK1 in neurological diseases in the brain, differential transcriptional profiling was performed in the brains of DAPK1 knockout (DAPK1-KO) mice compared with those of wild-type (WT) mice by RNA sequencing. We showed significantly altered genes in the cerebral cortex, hippocampus, brain stem, and cerebellum of both male and female DAPK1-KO mice compared to those in WT mice, respectively. The genes are implicated in multiple neural-related pathways, including: AD, Parkinson's disease (PD), Huntington's disease (HD), neurodegeneration, glutamatergic synapse, and GABAergic synapse pathways. Moreover, our findings imply that the potassium voltage-gated channel subfamily A member 1 (Kcna1) may be involved in the modulation of DAPK1 in epilepsy. Our study provides insight into the pathological role of DAPK1 in the regulatory networks in the brain and new therapeutic strategies for the treatment of neurological diseases.

Keywords: brain; death-associated protein kinase 1 (DAPK1); differential transcriptional profiling; neurodegeneration; neuronal functions.

Figure 1

Transcriptional profiling of tissues from different brain regions in DAPK1-KO mice. (A) DAPK1 protein levels in tissues from four different brain regions of WT and DAPK1-KO male and female mice by immunoblotting analysis. (B) Differential gene expression volcano plots of tissues from each brain region of male mice by the edgeR method. The horizontal dotted line refers to the threshold of statistical significance with log, while the vertical dotted line refers to the threshold of the differential expressed ratio. (C) Number of DEGs in tissues of four brain regions for male mice.

Figure 2

Chromosome distribution of significantly regulated genes in different regions of male DAPK1-KO mouse brain tissues. Chromosome distribution of DEGs in the cerebral cortex (A), hippocampus (B), brain stem (C) and cerebellum (D).

Figure 3

Venn analysis of the differentially expressed genes in different brain region tissues of male (A) and female (B) DAPK1-KO mice.

Figure 4

Gene ontology enrichment analysis of the DEGs in the cerebral cortex (A) and hippocampus (B) of male DAPK1-KO mice. The GO categories were biological process (BP), cellular component (CC), and molecular function (MF).

Figure 5

Gene ontology enrichment analysis of the DEGs in the brain stem (A) and cerebellum (B) of male DAPK1-KO mice. The GO categories were biological process (BP), cellular component (CC), and molecular function (MF).

Figure 6

KEGG pathway analysis of the DEGs in the cerebral cortex (A) and hippocampus (B) of male DAPK1-KO mice.

Figure 7

KEGG pathway analysis of the DEGs in the brain stem (A) and cerebellum (B) of male DAPK1-KO mice.

Figure 8

Validation of gene expression by qRT-PCR in DAPK1-KO mice. qRT-PCR analysis of Aff2, Zkscan16, Kcna1, Pcdhac2, and Pcdhga8 in the cerebral cortex, hippocampus, brain stem, and cerebellum for males (A) and females (B). Each data point represents the mean ± standard deviation (SD) of three mice.