Abstract
Pituitary adenomas are the most common intrasellar tumors. Patients should be identified at an early stage so that effective treatment can be implemented. The study aims at detecting the potential biomarkers with diagnostic value of pituitary adenomas. Using a total of seven gene expression profiles (GEPs) of the datasets from the Gene Expression Omnibus (GEO) database, we first screened 1980 significant differentially expressed genes (DEGs). Then, we employed the prediction analysis for microarray (PAM) algorithm to identify 340 significant DEGs able to differ pituitary tumor from normal samples, which include 208 upregulated DEGs and 132 downregulated DEGs. DAVID database was used to carry out the enrichment analysis on Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) pathways. We found that upregulated candidates were enriched in protein folding and metabolic pathways. Downregulated DEGs saw a significant enrichment in insulin receptor signaling pathway and hedgehog signaling pathway. Based on the protein-protein interaction (PPI) network as well as module analysis, we determined ten hub genes including PHLPP, ENO2, ACTR1A, EHHADH, EHMT2, FOXO1, DLD, CCT2, CSNK1D, and CETN2 that could be potential biomarkers with diagnostic value in pituitary adenomas. In conclusion, the study contributes to reliable and potential molecular biomarkers with diagnostic value. Moreover, these potential biomarkers may be used for prognosis and new therapeutic targets for the pituitary adenomas.
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Availability of Data and Materials
The datasets generated during this study are available in the online GEO database (https://www.ncbi.nlm.nih.gov/geo/).
Abbreviations
- BP:
-
Biological process
- CC:
-
Cellular constituent
- DEGs:
-
Differentially expressed genes
- EHHADH:
-
Enoyl-CoA, hydratase/3-hydroxyacyl CoA dehydrogenase
- ENO2:
-
Enolase 2
- FC:
-
Fold change
- FDR:
-
False discovery rate
- FOXO1:
-
Forkhead box O1
- GEO:
-
Gene Expression Omnibus
- GEPs:
-
Gene expression profiles
- GO:
-
Gene Ontology
- HCC:
-
Hepatocellular carcinoma cell
- KEGG:
-
Kyoto Encyclopedia of Genes and Genomes
- MF:
-
Molecular function
- PAM:
-
Prediction analysis for microarray
- PHLPP:
-
PH domain leucine-rich repeat protein phosphatase
- PPI:
-
Protein-protein interaction
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Funding
This work was supported by the National Natural Science Foundation of China (Grant No. 81702643, 81770980, 81570906), China Postdoctoral Science Foundation (Grant No. 2017M611586), Science Project of Shanghai (Grant No. 14DZ2260300), Science Project of Shanghai Municipal Commission of Health and Family Planning (Grant No. 201540173), Shanghai sailing program (Grant No.16YF1403400), and The Second Military Medical University Project (Grant No. 2017JS18).
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Peng, H., Deng, Y., Wang, L. et al. Identification of Potential Biomarkers with Diagnostic Value in Pituitary Adenomas Using Prediction Analysis for Microarrays Method. J Mol Neurosci 69, 399–410 (2019). https://doi.org/10.1007/s12031-019-01369-x
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DOI: https://doi.org/10.1007/s12031-019-01369-x