CDK1 and CCNB1 as potential diagnostic markers of rhabdomyosarcoma: validation following bioinformatics analysis

• Published in: BMC medical genomics Vol. 12; no. 1; p. 198
• Main Authors: Li, Qianru, Zhang, Liang, Jiang, Jinfang, Zhang, Yangyang, Wang, Xiaomeng, Zhang, Qiaochu, Wang, Yang, Liu, Chunxia, Li, Feng
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 23-12-2019; BioMed Central; BMC
• Subjects: 1-Phosphatidylinositol 3-kinase; AKT protein; Alveoli; Analysis; Biochemistry; Bioinformatics; Bioinformatics analysis; Biological markers; Biomarkers; Biomarkers, Tumor - genetics; CCNB1; CDC2 Protein Kinase - genetics; CDK1; Cell cycle; Child; Child, Preschool; Computational Biology; Computer programs; Cyclin B1 - genetics; Diagnosis; Extracellular matrix; Female; FOXO1 protein; Fusion protein; Gene expression; Gene Expression Regulation, Neoplastic; Genes; Health aspects; Hub genes; Humans; Immunohistochemistry; Invasiveness; Male; Malignancy; Molecular modelling; Mortality; Muscle contraction; Mutation; Ontology; p53 Protein; Patients; Pax3 protein; Pediatrics; Polymerase chain reaction; Proliferating cell nuclear antigen; Protein Interaction Mapping; Proteins; Rhabdomyosarcoma; Rhabdomyosarcoma - diagnosis; Rhabdomyosarcoma - genetics; Rhabdomyosarcoma - metabolism; Sarcoma; Skeletal muscle; Software; Survival Analysis; Tumor proteins; Tumors; China; Bioinformatics analysis; CDK1; CCNB1; Hub genes; Diagnosis; Rhabdomyosarcoma
• ISSN: 1755-8794; 1755-8794
• DOI: 10.1186/s12920-019-0645-x

Rhabdomyosarcoma (RMS), a common soft-tissue malignancy in pediatrics, presents high invasiveness and mortality. However, besides known changes in the PAX3/7-FOXO1 fusion gene in alveolar RMS, the molecular mechanisms of the disease remain incompletely understood. The purpose of the study is to recognize potential biomarkers related with RMS and analyse their molecular mechanism, diagnosis and prognostic significance.
The Gene Expression Omnibus was used to search the RMS and normal striated muscle data sets. Differentially expressed genes (DEGs) were filtered using R software. The DAVID has become accustomed to performing functional annotations and pathway analysis on DEGs. The protein interaction was constructed and further processed by the STRING tool and Cytoscape software. Kaplan-Meier was used to estimate the effect of hub genes on the ending of sarcoma sufferers, and the expression of these genes in RMS was proved by real-time polymerase chain reaction (RT-PCR). Finally, the expression of CDK1 and CCNB1 in RMS was validated by immunohistochemistry (IHC).
A total of 1932 DEGs were obtained, amongst which 1505 were up-regulated and 427were down-regulated. Up-regulated genes were largely enriched in the cell cycle, ECM-receptor interaction, PI3K/Akt and p53 pathways, whilst down-regulated genes were primarily enriched in the muscle contraction process. CDK1, CCNB1, CDC20, CCNB2, AURKB, MAD2L1, HIST2H2BE, CENPE, KIF2C and PCNA were identified as hub genes by Cytoscape analyses. Survival analysis showed that, except for HIST2H2BE, the other hub genes were highly expressed and related to poor prognosis in sarcoma. RT-PCR validation showed that CDK1, CCNB1, CDC20, CENPE and HIST2H2BE were significantly differential expression in RMS compared to the normal control. IHC revealed that the expression of CDK1 (28/32, 87.5%) and CCNB1 (26/32, 81.25%) were notably higher in RMS than normal controls (1/9, 11.1%; 0/9, 0%). Moreover, the CCNB1 was associated with the age and location of the patient's onset.
These results show that these hub genes, especially CDK1 and CCNB1, may be potential diagnostic biomarkers for RMS and provide a new perspective for the pathogenesis of RMS.