Bioinformatic analysis and clinical verification of related genes and signaling pathways in primary myelofibrosis
10.3760/cma.j.cn115356-20231211-00097
- VernacularTitle:原发性骨髓纤维化相关基因和信号通路的生物信息学分析及临床验证
- Author:
Jing XU
1
;
Xueying WAN
;
Fanggang REN
;
Jinyi FENG
;
Hongwei WANG
Author Information
1. 山西医科大学医学细胞生物与遗传学教研室，太原 030001
- Keywords:
Primary myelofibrosis;
Molecular biology;
Computational biology
- From:
Journal of Leukemia & Lymphoma
2024;33(10):610-616
- CountryChina
- Language:Chinese
-
Abstract:
Objective:To explore the genes related to primary myelofibrosis (PMF) and signaling pathways as well as the possible clinical significance.Methods:A total of 3 mRNA expression datasets of PMF (GSE26049, GSE61629 and GSE53482) were downloaded from Gene Expression Omnibus (GEO) database, including the data of peripheral blood samples from 55 PMF patients and 58 controls. The differentially expressed genes (DEG) between PMF patients and the controls were identified by using online tool GEO2R. Gene ontology (GO) annotation, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were performed on the common DEG of the 3 datasets, and then protein interaction (PPI) network was constructed. The key nodes of the common DEG in PPI network were calculated by using MCC method and Degree method in cytoHubba program; finally the top 10 hub genes were selected and the hub genes shared by the 2 methods were obtained. Peripheral blood samples of 25 PMF patients and 10 controls (normal hematopoietic stem cell transplant donors or iron deficiency anemia patients) admitted to the Second Hospital of Shanxi Medical University from September 2017 to June 2021 were retrospectively collected. Reverse transcription-fluorescence quantitative polymerase chain reaction (RT-qPCR) was used to detect the expression levels of 10 screened common hub genes in each sample, and the expressions of all genes at transcriptional level of the two groups were compared.Results:A total of 239 common DEG between PMF patients and the controls were screened out in the 3 datasets, including 153 downregulated DEG and 86 upregulated DEG. The GO enrichment analysis showed that the common downregulated DEG were significantly enriched in negative regulation of transcription, translation and fibroblast proliferation, while the upregulated DEG were mainly enriched in protein ubiquitination and ubiquitin-dependent protein catabolic process. The KEGG pathway analysis indicated that the upregulated common DEG and downregulated common DEG were both enriched in PI3K/Akt signaling pathway, cancer pathways and transcriptional misregulation in cancer. There were 8 common hub genes shared by the 2 methods among the top 10 genes ranked by MCC and Degree methods, including 6 downregulated common DEG (TP53, MYC, ATM, FYN, PTPRC and ATRX) and 2 upregulated common DEG (VEGFA and FOXO3). These above 8 common hub genes were mainly involved in PI3K/Akt signaling pathway, cell cycle and cancer transcriptional regulation signaling pathways. RT-qPCR detection of clinical peripheral blood samples showed that the relative expression levels of mRNA in 6 downregulated common DEG of PMF patients were lower compared with those in controls, while the differences were not statistically significant (all P > 0.05); the relative expression levels of mRNA in 2 upregulated common DEG of PMF patients were higher compared with those in controls, and the differences were statistically significant ( U value was 33.00, 36.00, respectively; P value was 0.021, 0.033, respectively). Conclusions:Bioinformatics and clinical sample verification show that VEGFA and FOXO3 are up-regulated in PMF patients, which are mainly involved in the PI3K/Akt signaling pathway, cell cycle and cancer transcriptional regulation signaling pathway. Both genes may be related to the development of PMF and may become potential therapeutic targets.
