| Literature DB >> 31281445 |
Jun Qiao1, Yuan Sun2, Jinfang Wu3, Li Wang2.
Abstract
Ketamine elicits a rapid antidepressant effect in treatment-refractory affective disorders. The aim of the present study was to elucidate the underlying mechanism of this effect and to identify potential targets of ketamine for antidepressant effects. GSE73798 and GSE73799 datasets were downloaded from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) were identified in hippocampus or striatum samples treated with ketamine, phencyclidyne or memantine compared with a saline or normal group at 1, 2, 4 and 8 h. The overlapping DEGs were the DEGs in both hippocampus and striatum samples. Kyoto Encyclopedia of Genes and Genomes and BioCyc databases were used to perform functional annotation and pathway analyses. Protein-protein interactions (PPIs) were predicted using Search Tool for the Retrieval of Interacting Genes/Proteins version 9.1 for the DEGs in the striatum samples treated with ketamine, phencyclidine or memantine compared with normal samples. Reverse transcription-quantitative polymerase chain reaction was performed to determine mRNA levels. Perilipin 4 (Plin4), serum/glucocorticoid regulated kinase 1 (Sgk1), kruppel like factor 2 (Klf2) and DDB1 and CUL4 associated factor 12 like 1 (Dcaf12l1) were the overlapping DEGs in the striatum samples treated with the three drugs at different time points. The mRNA expression levels of Plin4, Sgk1 and Klf2 were significantly higher (P<0.05), and the mRNA expression level of Dcaf12l1 was significantly lower in the striatum samples of the ketamine-treated group compared with the control group in an in vivo experiment. Both Sgk1 and Klf2 were enriched in the 'forkhead box O (FoxO) signaling pathway', and Sgk1 was additionally enriched in the 'mechanistic target of rapamycin kinase (mTOR) signaling pathway'. PPI networks of DEGs in the striatum samples treated with ketamine, phencyclidine and memantine compared with normal samples were constructed, and Klf2 was involved in more pairs and was therefore a gene hub in the three networks. The four genes, Plin4, Sgk1, Klf2 and Dcaf12l1, were differentially expressed in all of the groups that treated with the three drugs and their expression levels were verified in in vivo experiments. The FoxO and mTOR signaling pathways may be involved in the underlying mechanism of the antidepressant effects of ketamine, and Plin4, Sgk1, Klf2 and Dcaf12l1 may be potential biomarkers for depression in N-methyl-D-aspartic acid receptor antagonist treatment.Entities:
Keywords: antidepressant effect; ketamine; molecular profile
Year: 2019 PMID: 31281445 PMCID: PMC6580107 DOI: 10.3892/etm.2019.7633
Source DB: PubMed Journal: Exp Ther Med ISSN: 1792-0981 Impact factor: 2.447
Gene numbers of the 48 sets of DEGs in hippocampus or striatum samples individually treated with ketamine, phencyclidine or memantine compared with the saline or normal group at 1, 2, 4 and 8 h, respectively.
| Hippocampus | Striatum | ||||||||
|---|---|---|---|---|---|---|---|---|---|
| Drug | Control | 1 h | 2 h | 4 h | 8 h | 1 h | 2 h | 4 h | 8 h |
| Ketamine | Saline | 13 (2,11) | 7 (6,1) | 2 (2,0) | 0 (0,0) | 113 (23,90) | 122 (30,92) | 235 (121,114) | 103 (41,62) |
| Normal | 7 (6,1) | 12 (5,7) | 8 (8,0) | 2 (1,1) | 50 (36,14) | 91 (47,44) | 64 (47,17) | 26 (23,3) | |
| Phencyclidine | Saline | 10 (3,7) | 4 (4,0) | 4 (1,3) | 0 (0,0) | 87 (46,41) | 106 (18,88) | 243 (119,124) | 98 (44,53) |
| Normal | 8 (4,4) | 14 (3,11) | 15 (10,5) | 5 (2,3) | 50 (41,9) | 43 (9,34) | 38 (21,17) | 31 (27,4) | |
| Memantine | Saline | 4 (4,0) | 18 (16,2) | 11 (6,5) | 1 (0,1) | 104 (13,91) | 99 (31,68) | 520 (241,279) | 89 (44,45) |
| Normal | 7 (7,0) | 16 (16,0) | 7 (7,0) | 1 (1,0) | 19 (14,5) | 43 (30,13) | 134 (60,74) | 13 (11,2) | |
Data are presented as the total number of DEGs (upregulated DEGs, downregulated DEGs). DEGs, differentially expressed genes.
Gene numbers of the overlapping genes in three drug groups compared with both the saline and normal groups.
| Hippocampus | Striatum | |||||||
|---|---|---|---|---|---|---|---|---|
| Drug | 1 h | 2 h | 4 h | 8 h | 1 h | 2 h | 4 h | 8 h |
| Ketamine | 3 (2,1) | 1 (0,1) | 2 (2,0) | 0 (0,0) | 10 (7,3) | 26 (19,7) | 7 (5,2) | 6 (6,0) |
| Phencyclidine | 4 (2,2) | 0 (0,0) | 4 (1,3) | 0 (0,0) | 20 (18,2) | 11 (3,8) | 2 (1,1) | 9 (7,2) |
| Memantine | 4 (4,0) | 9 (9,0) | 5 (5,0) | 0 (0,0) | 5 (4,1) | 14 (10,4) | 40 (18,22) | 2 (1,1) |
Overlapping genes at the four time points.
| Tissue | Drug | Upregulated | Downregulated |
|---|---|---|---|
| Hippocampus | Ketamine Phencyclidine | ||
| Memantine | |||
| Striatum | Ketamine | ||
| Phencyclidine | |||
| Memantine | |||
| Megf9, Cdkn1a, Nostrin, BAI3, Ism1, Cfp, Ramp2, Txnip, Bcl6, Sult1a1, Tsc22d3, LOC100044968, 9930108O06Rik, Adipor2, Thbd, Ddit4 |
Figure 1.Relative expression levels of Plin4, Skg1, Klf2 and Dcaf12l1 in the striatum samples. ***P<0.001, **P<0.01 and *P<0.05 as indicated. -ketamine, ketamine-treated striatum samples; -control, saline-treated striatum samples; SGK1, serum/glucocorticoid regulated kinase 1; Plin4, perilipin 4; Klf2, Kruppel like factor 2; Dcaf12l1, DDB1 and CUL4 associated factor 12 like 1.
Figure 2.Expression of Plin4 in the hippocampus samples treated with KET, PHE and MEM. KET, ketamine; PHE, phencyclidine; MEM, memantine; Plin4, perilipin 4.
Figure 3.Expression of Plin4 in the striatum samples treated with KET, PHE and MEM. KET, ketamine; PHE, phencyclidine; MEM, memantine; Plin4, perilipin 4.
mRNA levels of Plin4, Sgk1, Klf2 and Dcaf12l1 in the striatum samples.
| Relative expression value | ||||
|---|---|---|---|---|
| Group | Sgk1 | Klf2 | ||
| Ketamine group | 3.77±0.38 | 4.87±0.19 | 3.27±0.36 | 1.23±0.21 |
| Control group | 2.28±0.25 | 3.46±0.27 | 2.53±0.23 | 2.31±0.34 |
| P-value | <0.0001 | <0.0001 | 0.0402 | 0.0018 |
| T-value | 8.76 | 12.81 | −3.68 | 7.87 |
The enriched GO terms of Sgk1 and Klf2.
| Gene | GO term | Function |
|---|---|---|
| GO:0004672 | ‘Protein kinase activity’ | |
| GO:0004674 | ‘Protein serine/threonine kinase activity’ | |
| GO:0005524 | ‘ATP binding’ | |
| GO:0016301 | ‘Kinase activity′’ | |
| GO:0016740 | ‘Transferase activity’ | |
| GO:0003677 | ‘DNA binding’ | |
| GO:0003700 | ‘Transcription factor activity, sequence-specific DNA binding’ | |
| GO:0008270 | ‘Zinc ion binding’ | |
| GO:0046872 | ‘Metal ion binding’ |
GO, gene ontology; SGK1, serum/glucocorticoid regulated kinase 1; Klf2, Kruppel like factor 2.
Figure 4.Protein-protein interaction network of differentially expressed genes in the striatum samples treated with ketamine. Small nodes represent proteins of unknown 3D structure, large nodes represent proteins with known or predicted 3D structure. Colored nodes represent query proteins and the first shell of interactors. Interactors with purple edges represent known experimentally determined interactions, brilliant green edges represent textmining interactions and dark edges represent co-expression interactions. STRING, search tool for the retrieval of interacting genes/proteins.
Figure 6.Protein-protein interaction network of differentially expressed genes in the striatum samples treated with memantine. Small nodes represent proteins of unknown 3D structure, large nodes represent proteins with known or predicted 3D structure; colored nodes represent query proteins and first shell of interactors; interactors with light blue lines represent known interactions from STRING databases, purple edges represent known experimentally determined interactions, brilliant green edges represent textmining interactions, dark edges represent co-expression interactions. STRING, search tool for the retrieval of interacting genes/proteins.
Enriched KEGG pathways of Plin4, Sgk1 and Klf2.
| Gene | KEGG pathway | Name |
|---|---|---|
| mmu04068 | ‘FoxO signaling pathway’ | |
| mmu04150 | ‘mTOR signaling pathway’ | |
| mmu04151 | ‘PI3K-Akt signaling pathway’ | |
| mmu04960 | ‘Aldosterone-regulated sodium reabsorption’ | |
| mmu03320 | ‘PPAR signaling pathway’ | |
| mmu04068 | ‘FoxO signaling pathway’ | |
| mmu04371 | ‘Apelin signaling pathway’ | |
| mmu05418 | ‘Fluid shear stress and atherosclerosis’ |
KEGG, Kyoto Encyclopedia of Genes and Genomes; SGK1, serum/glucocorticoid regulated kinase 1; Plin4, perilipin 4; Klf2, Kruppel like factor 2.