| Literature DB >> 31058188 |
Wenlei Ye1, Wei Shen1, Wei Yan1, Su Zhou1, Jing Cheng1,2, Guangxin Pan1,3, Meng Wu1, Lingwei Ma1, Aiyue Luo1, Shixuan Wang1.
Abstract
There are about 1-2 million follicles presented in the ovary at birth, while only around 1000 primordial follicles are left at menopause. The ovarian function also decreases in parallel with aging. Folliculogenesis is vital for ovarian function, no matter the synthesis of female hormones or ovulation, yet the mechanisms for its changing with increasing age are not fully understood. Early follicle growth up to the large preantral stage is independent of gonadotropins in rodents and relies on intraovarian factors. To further understand the age-related molecular changes in the process of folliculogenesis, we performed microarray gene expression profile analysis using total RNA extracted from young (9 weeks old) and old (32 weeks old) mouse ovarian secondary follicles. The results of our current microarray study revealed that there were 371 (≥2-fold, q-value ≤0.05) genes differentially expressed in which 174 genes were upregulated and 197 genes were downregulated in old mouse ovarian secondary follicles compared to young mouse ovarian secondary follicles. The gene ontology and KEGG pathway analysis of differentially expressed genes uncovered critical biological functions such as immune system process, aging, transcription, DNA replication, DNA repair, protein stabilization, and apoptotic process were affected in the process of aging. The considerable changes in gene expression profile may have an adverse influence on follicle quality and folliculogenesis. Our study provided information on the processes that may contribute to age-related decline in ovarian function.Entities:
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Year: 2019 PMID: 31058188 PMCID: PMC6463680 DOI: 10.1155/2019/3842312
Source DB: PubMed Journal: Biomed Res Int Impact factor: 3.411
Figure 1Box and whisker plot (Box plot). We performed the comparison of gene expression with a total of six samples from young (n=3) and old (n=3) mouse ovarian secondary follicles by using Affymetrix 3' IVT Expression Arrays (Mouse Genome 430 2.0 array) at Bioassay Laboratory of CapitalBio Corporation. Robust multiarray average (RMA) algorithm was used to eliminate the variation in the arrays from noisy data. Box plot was constructed to illustrate the distribution of normalized probe hybridization signal intensities (log ratios) for all six arrays (young and old mouse ovarian secondary follicles). The probe distribution by 0-100% quantiles as whiskers, the 25-75% quantiles as different color boxes, and the 50% quantile as horizontal line within the box indicated a similar range of signal intensities and confirmed perfect hybridization.
Figure 2Heat map visualization for selected differentially expressed genes. Heat map was produced by unsupervised hierarchical-clustering analysis from microarray data for top 50 upregulated genes and top 50 downregulated genes in old mouse ovarian secondary follicles compared to young. The relative expression levels of each gene are mentioned in different colors. The red lines represent high expression, while blue lines represent low expression. The numbers in the right side, corresponding to the different colors, represent the relative expression levels of each gene.
Functional enrichment analysis of upregulated genes in the old mouse ovarian secondary follicles compared to young mouse.
| Category | Term | Count | % | P Value |
|---|---|---|---|---|
| GOTERM_BP_DIRECT | GO:0035458~cellular response to interferon-beta | 15 | 8.6 | 5.62E-21 |
| GOTERM_BP_DIRECT | GO:0009615~response to virus | 18 | 10.3 | 6.73E-21 |
| GOTERM_BP_DIRECT | GO:0051607~defense response to virus | 21 | 12.1 | 1.15E-19 |
| GOTERM_BP_DIRECT | GO:0002376~immune system process | 24 | 13.8 | 1.01E-15 |
| GOTERM_BP_DIRECT | GO:0045087~innate immune response | 23 | 13.2 | 2.70E-14 |
| GOTERM_BP_DIRECT | GO:0071346~cellular response to interferon-gamma | 9 | 5.2 | 1.80E-08 |
| GOTERM_BP_DIRECT | GO:0042832~defense response to protozoan | 6 | 3.4 | 1.60E-06 |
| GOTERM_BP_DIRECT | GO:0006952~defense response | 8 | 4.6 | 1.36E-05 |
| GOTERM_BP_DIRECT | GO:0032870~cellular response to hormone stimulus | 6 | 3.4 | 1.57E-05 |
| GOTERM_BP_DIRECT | GO:0034097~response to cytokine | 7 | 4.0 | 1.79E-05 |
| GOTERM_CC_DIRECT | GO:0020005~symbiont-containing vacuole membrane | 5 | 2.9 | 1.46E-07 |
| GOTERM_CC_DIRECT | GO:0005829~cytosol | 28 | 16.1 | 7.00E-05 |
| GOTERM_CC_DIRECT | GO:0005737~cytoplasm | 65 | 37.4 | 6.61E-04 |
| GOTERM_CC_DIRECT | GO:0005634~nucleus | 58 | 33.3 | 2.75E-03 |
| GOTERM_CC_DIRECT | GO:0048471~perinuclear region of cytoplasm | 12 | 6.9 | 8.23E-03 |
| GOTERM_CC_DIRECT | GO:0072562~blood microparticle | 5 | 2.9 | 1.34E-02 |
| GOTERM_CC_DIRECT | GO:0031225~anchored component of membrane | 5 | 2.9 | 1.63E-02 |
| GOTERM_CC_DIRECT | GO:0009897~external side of plasma membrane | 7 | 4.0 | 2.23E-02 |
| GOTERM_MF_DIRECT | GO:0003725~double-stranded RNA binding | 9 | 5.2 | 2.62E-08 |
| GOTERM_MF_DIRECT | GO:0003690~double-stranded DNA binding | 11 | 6.3 | 3.33E-08 |
| GOTERM_MF_DIRECT | GO:0003924~GTPase activity | 11 | 6.3 | 1.81E-06 |
| GOTERM_MF_DIRECT | GO:0005525~GTP binding | 12 | 6.9 | 6.76E-05 |
| GOTERM_MF_DIRECT | GO:0008134~transcription factor binding | 10 | 5.7 | 5.97E-04 |
| GOTERM_MF_DIRECT | GO:0003723~RNA binding | 15 | 8.6 | 9.40E-04 |
| GOTERM_MF_DIRECT | GO:0003677~DNA binding | 25 | 14.4 | 1.58E-03 |
| GOTERM_MF_DIRECT | GO:0001730~2′-5′-oligoadenylate synthetase activity | 3 | 1.7 | 2.48E-03 |
| GOTERM_MF_DIRECT | GO:0016817~hydrolase activity, acting on acid anhydrides | 3 | 1.7 | 2.48E-03 |
| GOTERM_MF_DIRECT | GO:0001077~transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding | 8 | 4.6 | 2.65E-03 |
Number of enriched genes in each term. The top ten terms based on P value were chosen in each category.
Functional enrichment analysis of downregulated genes in the old mouse ovarian secondary follicles compared to young mouse.
| Category | Term | Count | % | P value |
|---|---|---|---|---|
| GOTERM_BP_DIRECT | GO:0006355~regulation of transcription, DNA-templated | 42 | 21.3 | 7.02E-05 |
| GOTERM_BP_DIRECT | GO:0016311~dephosphorylation | 8 | 4.1 | 9.84E-05 |
| GOTERM_BP_DIRECT | GO:0006351~transcription, DNA-templated | 35 | 17.8 | 3.19E-04 |
| GOTERM_BP_DIRECT | GO:0045893~positive regulation of transcription, DNA-templated | 16 | 8.1 | 5.56E-04 |
| GOTERM_BP_DIRECT | GO:0030335~positive regulation of cell migration | 9 | 4.6 | 8.87E-04 |
| GOTERM_BP_DIRECT | GO:0006470~protein dephosphorylation | 7 | 3.6 | 2.39E-03 |
| GOTERM_BP_DIRECT | GO:0043154~negative regulation of cysteine-type endopeptidase activity involved in apoptotic process | 5 | 2.5 | 4.21E-03 |
| GOTERM_BP_DIRECT | GO:0030177~positive regulation of Wnt signaling pathway | 4 | 2.0 | 5.61E-03 |
| GOTERM_BP_DIRECT | GO:0043065~positive regulation of apoptotic process | 10 | 5.1 | 5.85E-03 |
| GOTERM_BP_DIRECT | GO:0097194~execution phase of apoptosis | 3 | 1.5 | 6.92E-03 |
| GOTERM_CC_DIRECT | GO:0005634~nucleus | 106 | 53.8 | 3.23E-13 |
| GOTERM_CC_DIRECT | GO:0005737~cytoplasm | 100 | 50.8 | 4.49E-08 |
| GOTERM_CC_DIRECT | GO:0005654~nucleoplasm | 44 | 22.3 | 9.26E-08 |
| GOTERM_CC_DIRECT | GO:0070062~extracellular exosome | 50 | 25.4 | 3.19E-06 |
| GOTERM_CC_DIRECT | GO:0043234~protein complex | 19 | 9.6 | 3.26E-05 |
| GOTERM_CC_DIRECT | GO:0071013~catalytic step 2 spliceosome | 6 | 3.0 | 2.24E-03 |
| GOTERM_CC_DIRECT | GO:0005925~focal adhesion | 11 | 5.6 | 4.30E-03 |
| GOTERM_CC_DIRECT | GO:0005829~cytosol | 29 | 14.7 | 5.76E-03 |
| GOTERM_CC_DIRECT | GO:0030529~intracellular ribonucleoprotein complex | 9 | 4.6 | 1.17E-02 |
| GOTERM_CC_DIRECT | GO:0005911~cell-cell junction | 7 | 3.6 | 1.26E-02 |
| GOTERM_MF_DIRECT | GO:0005515~protein binding | 77 | 39.1 | 6.99E-09 |
| GOTERM_MF_DIRECT | GO:0044822~poly(A) RNA binding | 30 | 15.2 | 2.52E-06 |
| GOTERM_MF_DIRECT | GO:0003723~RNA binding | 20 | 10.2 | 3.71E-04 |
| GOTERM_MF_DIRECT | GO:0003677~DNA binding | 35 | 17.8 | 4.23E-04 |
| GOTERM_MF_DIRECT | GO:0004725~protein tyrosine phosphatase activity | 7 | 3.6 | 4.62E-04 |
| GOTERM_MF_DIRECT | GO:0046982~protein heterodimerization activity | 15 | 7.6 | 7.77E-04 |
| GOTERM_MF_DIRECT | GO:0000166~nucleotide binding | 35 | 17.8 | 9.78E-04 |
| GOTERM_MF_DIRECT | GO:0016791~phosphatase activity | 7 | 3.6 | 1.29E-03 |
| GOTERM_MF_DIRECT | GO:0019903~protein phosphatase binding | 6 | 3.0 | 2.02E-03 |
| GOTERM_MF_DIRECT | GO:0005524~ATP binding | 28 | 14.2 | 2.62E-03 |
Number of enriched genes in each term. The top ten terms based on P value were chosen in each category.
Pathway enrichment analysis of differentially expressed genes in old mouse ovarian secondary follicles compared to young mouse.
| Category | Term | Count | % | P value |
|---|---|---|---|---|
| Up-regulated | ||||
| KEGG_PATHWAY | mmu05164:Influenza A | 15 | 8.6 | 2.25E-11 |
| KEGG_PATHWAY | mmu05168:Herpes simplex infection | 15 | 8.6 | 3.13E-10 |
| KEGG_PATHWAY | mmu05162:Measles | 11 | 6.3 | 6.23E-08 |
| KEGG_PATHWAY | mmu05160:Hepatitis C | 11 | 6.3 | 6.23E-08 |
| KEGG_PATHWAY | mmu04380:Osteoclast differentiation | 8 | 4.6 | 4.40E-05 |
| KEGG_PATHWAY | mmu05161:Hepatitis B | 8 | 4.6 | 1.12E-04 |
| KEGG_PATHWAY | mmu04622:RIG-I-like receptor signaling pathway | 6 | 3.4 | 1.58E-04 |
| KEGG_PATHWAY | mmu04668:TNF signaling pathway | 7 | 4.0 | 1.69E-04 |
| KEGG_PATHWAY | mmu04620:Toll-like receptor signaling pathway | 6 | 3.4 | 9.93E-04 |
| KEGG_PATHWAY | mmu05133:Pertussis | 5 | 2.9 | 2.38E-03 |
| Down-regulated | ||||
| KEGG_PATHWAY | mmu04151:PI3K-Akt signaling pathway | 14 | 7.1 | 4.14E-04 |
| KEGG_PATHWAY | mmu05200:Pathways in cancer | 14 | 7.1 | 1.31E-03 |
| KEGG_PATHWAY | mmu04550:Signaling pathways regulating pluripotency of stem cells | 8 | 4.1 | 1.69E-03 |
| KEGG_PATHWAY | mmu04520:Adherens junction | 6 | 3.0 | 2.03E-03 |
| KEGG_PATHWAY | mmu04015:Rap1 signaling pathway | 9 | 4.6 | 5.33E-03 |
| KEGG_PATHWAY | mmu04390:Hippo signaling pathway | 7 | 3.6 | 1.16E-02 |
| KEGG_PATHWAY | mmu05145:Toxoplasmosis | 6 | 3.0 | 1.36E-02 |
| KEGG_PATHWAY | mmu04510:Focal adhesion | 8 | 4.1 | 1.51E-02 |
| KEGG_PATHWAY | mmu04022:cGMP-PKG signaling pathway | 7 | 3.6 | 2.04E-02 |
| KEGG_PATHWAY | mmu03040:Spliceosome | 6 | 3.0 | 2.57E-02 |
Number of enriched genes in each term. The top ten terms based on P value were chosen in each category.
Figure 3Protein-protein interaction (PPI) network complex. Using the Search Tool for the retrieval of Interacting Genes (STRING) database online database, 187 out of 371 differentially expressed genes (DEGs) (upregulated genes are displayed in red and downregulated genes in green) were filtered into the DEGs protein-protein interaction (PPI) network complex.
Figure 4Overlapping protein complexes in the protein interaction. The most significant module consisted of 35 nodes and 286 edges, and all genes in this module were upregulated (in red).
Figure 5Gene regulatory network modeling for selected differentially expressed genes by using Cytoscape software (version 3.6.1). Gene regulatory network modeling of selected genes such as BRCA1, RPA2, STAT3, JUN, AKT1, STK3, SOX4, TCF3, S100A8, and IFIT2 showed their genetic interactions by various pathways. Circles indicate genes, red color indicates upregulation, and green color indicates downregulation.