Results of text mining, biological process and pathway analysis.
In exploring potential drugs for EMT-induced infertility, 550 genes were found to be related to EMT-induced infertility from the text mining searches.
We uploaded DEGs to the online website GeneCodis to identify GO Terms and KEGG pathways and classified them into three functional categories: biological process (BP), cellular component (CC), and molecular function (MF; Fig. 1). During this process, to ensure that only the most enriched annotations were chosen, a P‑value cutoff (P = 1.00E‑06) was set. As shown in Fig. 1A and Table 1, GO analysis showed that the DEGs were most significantly enriched in response to the organic substance. Moreover, the upregulated DEGs were significantly enriched in biological process, including muscle system process, muscle contraction, and regulation of muscle contraction (Fig. 1A and Table 2); Among the most significantly enriched GO Terms above the cutoff, those most relevant to EMT-induced infertility based on the available literature and research were selected. Therefore, the six most enriched biological process annotations were: i) ‘response to organic substance’ (P = 3.90E-127);ii) ‘cellular response to chemical stimulus’ (P = 1.29E-112); iii) ‘regulation of cell proliferation’ (P = 1.43E-98); iv) ‘cellular response to organic substance’ (P = 1.01E-95); v) ‘cell proliferation’ (P = 3.58E-94); and vi) ‘response to oxygen-containing compound’ (P = 1.48E-92), containing 328, 304, 227, 261, 241 and 215 genes from the query set, respectively. And the six most enriched cellular component annotations were: i) ‘extracellular space’ (P = 1.87E-63);ii) ‘extracellular region’ (P = 2.15E-39); iii) ‘cell surface’ (P = 5.22E-38); iv) ‘extracellular region part’ (P = 1.70E-34); v) ‘external side of plasma membrane’ (P = 6.97E-22); and vi) ‘side of membrane’ (P = 2.16E-20), containing190, 305, 110, 265, 48 and 62 genes from the query set, respectively. What is more, the six most enriched molecular function annotations were: i) ‘receptor binding’ (P = 8.64E-75); ii) ‘cytokine receptor binding’ (P = 3.76E-48); iii) ‘cytokine activity’ (P = 5.29E-37); iv) ‘growth factor activity’ (P = 4.88E-24); v) ‘identical protein binding’ (P = 2.24E-19); and vi) ‘enzyme binding’ (P = 1.57E-18), containing200, 76, 60, 41, 111 and 130 genes from the query set, respectively.
Table 1
The Gene Ontology of the genes involved in EM-induced infertility.
Category | Term | Count | PValue |
GOTERM_BP_FAT | GO:0010033 ~ response to organic substance | 328 | 3.90E-127 |
GOTERM_BP_FAT | GO:0070887 ~ cellular response to chemical stimulus | 304 | 1.29E-112 |
GOTERM_BP_FAT | GO:0042127 ~ regulation of cell proliferation | 227 | 1.43E-98 |
GOTERM_BP_FAT | GO:0071310 ~ cellular response to organic substance | 261 | 1.01E-95 |
GOTERM_BP_FAT | GO:0008283 ~ cell proliferation | 241 | 3.58E-94 |
GOTERM_BP_FAT | GO:1901700 ~ response to oxygen-containing compound | 215 | 1.48E-92 |
GOTERM_CC_FAT | GO:0005615 ~ extracellular space | 190 | 1.87E-63 |
GOTERM_CC_FAT | GO:0005576 ~ extracellular region | 305 | 2.15E-39 |
GOTERM_CC_FAT | GO:0009986 ~ cell surface | 110 | 5.22E-38 |
GOTERM_CC_FAT | GO:0044421 ~ extracellular region part | 265 | 1.70E-34 |
GOTERM_CC_FAT | GO:0009897 ~ external side of plasma membrane | 48 | 6.97E-22 |
GOTERM_CC_FAT | GO:0098552 ~ side of membrane | 62 | 2.16E-20 |
GOTERM_MF_FAT | GO:0005102 ~ receptor binding | 200 | 8.64E-75 |
GOTERM_MF_FAT | GO:0005126 ~ cytokine receptor binding | 76 | 3.76E-48 |
GOTERM_MF_FAT | GO:0005125 ~ cytokine activity | 60 | 5.29E-37 |
GOTERM_MF_FAT | GO:0008083 ~ growth factor activity | 41 | 4.88E-24 |
GOTERM_MF_FAT | GO:0042802 ~ identical protein binding | 111 | 2.24E-19 |
GOTERM_MF_FAT | GO:0019899 ~ enzyme binding | 130 | 1.57E-18 |
Abbreviation: EM,endometriosis. |
Table 2
Signaling Pathway Enrichment Analysis of involved in EM-induced infertility.
Category | Term | Count | PValue |
KEGG_PATHWAY | bta04060:Cytokine-cytokine receptor interaction | 65 | 2.41E-32 |
bta05200:Pathways in cancer | 74 | 6.92E-23 |
bta05205:Proteoglycans in cancer | 51 | 1.45E-21 |
bta05323:Rheumatoid arthritis | 33 | 1.60E-18 |
bta05161:Hepatitis B | 39 | 2.95E-17 |
bta04151:PI3K-Akt signaling pathway | 60 | 6.44E-17 |
bta04668:TNF signaling pathway | 33 | 1.14E-16 |
bta05142:Chagas disease (American trypanosomiasis) | 33 | 7.56E-16 |
bta04066:HIF-1 signaling pathway | 29 | 1.74E-14 |
bta05321:Inflammatory bowel disease (IBD) | 24 | 2.40E-13 |
bta04068:FoxO signaling pathway | 32 | 4.42E-13 |
bta05144:Malaria | 21 | 4.53E-13 |
bta05133:Pertussis | 24 | 2.34E-12 |
bta05140:Leishmaniasis | 23 | 3.11E-12 |
bta04630:Jak-STAT signaling pathway | 33 | 3.67E-12 |
bta05212:Pancreatic cancer | 22 | 3.94E-12 |
bta05206:MicroRNAs in cancer | 42 | 1.63E-11 |
bta05152:Tuberculosis | 34 | 1.23E-10 |
In the process of KEGG pathway enrichment analysis, those most relevant to EMT-induced infertility based on the available literature and research were selected. The analysis of enriched pathway annotations resulted in 18 pathways containing a total of 74 unique genes (Table 2). The six most significantly enriched pathways were: i) ‘cytokine-cytokine receptor interaction’ (P = 2.41E-32); ii) ‘pathways in cancer’ (P = 6.92E-23); and iii) ‘proteoglycans in cancer’ (P = 1.45E-21), iv) ‘rheumatoid arthritis’ (P = 1.60E-18); v) ‘hepatitis B’ (P = 2.95E-17); and vi) ‘PI3K-Akt signaling pathway’ (P = 6.44E-17), containing 65, 74, 51, 33 ,39 and 60 genes from the query set, respectively.
Results of protein-protein interaction.
The protein-protein interaction network of the 452 target genes was illustrated based on the STRING online database (http://string-db.org) and Cytoscape software (Fig. 2). PPI network complexly contained 452 nodes and 2758 edges (Fig. 2A). Finally, 39 genes were selected to form a strong interaction network based on the MCODE. The significant module (39 nodes 384 edges, Fig. 2B) from the PPI network was selected, as determined by Cytoscape. The 39 genes included CXCR3, NPY, BMP4, IGFBP1, APOA1, IL6, PROC, APOE, POMC, TIMP1, AHSG, CXCL8, CX3CR1, TF, CXCL1, F5, DRD2, CCL5, GPER1, AFP, AGTR2, CXCL10, CXCL11, CXCL12, CCR5, CASR, SPP1, ALB, CCL19, CCL25, CCL21, C3, CCL20, AGT, LGALS1, MSLN, CSF1, BMP15 and MFGE8.
Results of drug-gene interactions.
They used the final list of 39 genes as the potential targets in the drug-gene interaction analysis, a list of 49 drugs meeting the standard requirements for drug treatments for EMT-induced infertility (Table 3). They included: Acepromazine, Acetophenazine, Alizapride, Amantadine hydrochloride, Amisulpride, Apomorphine, Aripiprazole, Bifeprunox, Brexpiprazole, Cabergoline, Cinacalcet, Clozapine, Haloperidol, Iloperidone, Levodopa, Levomepromazine, Lisuride, Loxapine, Maraviroc, Menadione, Mesoridazine, Minaprine, Olanzapine, Paliperidone, Perphenazine, Pimozide, Pipotiazine, Promazine, Propiomazine, Remoxipride, Risperidone, Rivanicline, Ropinirole, Rotigotine, Siltuximab, Sodium tetradecyl sulfate, Tasosartan, Thioproperazine, Thiothixene, Tinzaparin sodium, Triflupromazine, Velcalcetide and Zuclopenthixol.
Table 3
Candidate drugs targeting genes with EM-induced infertility.
Number | Drug | Gene | Drug-gene interaction | Score* | Approved? | Approved FDA | Reference (PubMed ID) |
1 | Acepromazine | DRD2 | antagonist | 7 | Yes | Yes | 15694263 |
2 | Acetophenazine | DRD2 | antagonist | 9 | Yes | Yes | 6147851 |
3 | Alizapride | DRD2 | antagonist | 5 | Yes | No | 7865862 |
4 | Amantadine hydrochloride | DRD2 | agonist | 5 | Yes | No | 10443547 |
5 | Amisulpride | DRD2 | antagonist | 8 | Yes | No | 12404702 |
6 | Apomorphine | DRD2 | agonist | 12 | Investigational | Yes | 11343576 |
7 | Aripiprazole | DRD2 | antagonist | 12 | Yes | Yes | 9083792 |
8 | Bifeprunox | DRD2 | agonist | 6 | Investigational | No | 17393144 |
9 | Brexpiprazole | DRD2 | agonist | 5 | Yes | No | 24947465 |
10 | Cabergoline | DRD2 | agonist | 14 | Yes | Yes | 12721865 |
11 | Cinacalcet | CASR | agonist | 15 | Yes | Yes | 19261825 |
12 | Clozapine | DRD2 | antagonist | 14 | Yes | Yes | 15781964 |
13 | Dihydromorphine | POMC | agonist | 3 | Experimental | No | 6292632 |
14 | Domperidone | DRD2 | antagonist | 10 | Investigational | No | 15894081 |
15 | Droperidol | DRD2 | antagonist | 8 | Yes | Yes | 2527092 |
16 | Drotrecogin alfa | F5 | inhibitor | 13 | Investigational | Yes | 11893230 |
17 | Fluspirilene | DRD2 | antagonist | 9 | Yes | Yes | 8935801 |
18 | Ginseng | IL6 | antagonist | 3 | Yes | / | 17436372 |
19 | Haloperidol | DRD2 | antagonist | 7 | Yes | Yes | 12887421 |
20 | Iloperidone | DRD2 | antagonist | 7 | Yes | Yes | 12861482 |
21 | Levodopa | DRD2 | agonist | 10 | Yes | Yes | 11978145 |
22 | Levomepromazine | DRD2 | antagonist | 5 | Yes | No | 2870716 |
23 | Lisuride | DRD2 | agonist | 6 | Yes | No | 18691132 |
24 | Loxapine | DRD2 | antagonist | 13 | Yes | Yes | 9570468 |
25 | Maraviroc | CCR5 | antagonist | 13 | Yes | Yes | 16298345 |
26 | Menadione | PROC | activator | 8 | Yes | Yes | 17215245 |
27 | Mesoridazine | DRD2 | antagonist | 8 | Yes | Yes | 15357957 |
28 | Minaprine | DRD2 | agonist | 5 | Yes | No | 17139284 |
29 | Olanzapine | DRD2 | antagonist | 15 | Yes | Yes | 14575800 |
30 | Paliperidone | DRD2 | antagonist | 12 | Yes | Yes | 11132243 |
31 | Perphenazine | DRD2 | antagonist | 12 | Yes | Yes | 2573104 |
32 | Pimozide | DRD2 | antagonist | 14 | Yes | Yes | 8301582 |
33 | Pipotiazine | DRD2 | antagonist | 9 | Yes | / | 15694263 |
34 | Promazine | DRD2 | antagonist | 6 | Yes | Yes | 17139284 |
35 | Propiomazine | DRD2 | antagonist | 5 | Yes | Yes | 17139284 |
36 | Remoxipride | DRD2 | antagonist | 7 | Yes | No | 8665533 |
37 | Risperidone | DRD2 | antagonist | 13 | Investigational | Yes | 17059881 |
38 | Rivanicline | CXCL8 | antagonist | 2 | Investigational | No | 16715250 |
39 | Ropinirole | DRD2 | agonist | 11 | Investigational | Yes | 10446316 |
40 | Rotigotine | DRD2 | agonist | 7 | Yes | Yes | 18691132 |
41 | Siltuximab | IL6 | inhibitor | 4 | Yes | Yes | 8823310 |
42 | Sodium tetradecyl sulfate | PROC | inhibitor | 5 | Yes | Yes | 11752352 |
43 | Tasosartan | AGTR2 | antagonist | 2 | Yes | No | 11683476 |
44 | Thioproperazine | DRD2 | antagonist | 7 | Yes | No | 15694263 |
45 | Thiothixene | DRD2 | antagonist | 9 | Yes | Yes | 15694263 |
46 | Tinzaparin sodium | CXCL12 | binder | 2 | Yes | Yes | 18991783 |
47 | Triflupromazine | DRD2 | antagonist | 6 | Yes | Yes | 17139284 |
48 | Velcalcetide | CASR | agonist | 4 | Investigational | No | 24235081 |
49 | Zuclopenthixol | DRD2 | antagonist | 8 | Yes | Yes | 17535043 |
Each individual instance of a drug-gene interaction was evaluated in the context of the gene’s relationship to EMT-induced infertility and the drug’s relationship to the gene, thus ensuring any putative drug would be expected to have the desired directional effect on the condition. Drugs and compounds which met the criteria of targeting one of the candidate genes by an appropriate interaction were collected in a final list |
*The score is the combined number of database sources and PubMed references supporting a given interaction |
Potential gene targets of the drugs in this list are DRD2 (37 drugs), PROC, IL6 and CASR (2 drugs each), POMC, F5, CXCL8, CXCL12, CCR5and AGTR2 (1 drug each). Common previously approved uses for these drugs include the treatment of hemostasis, nausea, vomit, mental disease, chronic kidney disease, Parkinson's disease, and Alzheimer's disease. A total of 25 drugs on the list are used for anti-mental disease therapy. Next, we verified whether the drugs identified by our analysis could target pathways associated with EMT-induced infertility.