Abstract
BackgroundRhabdomyosarcoma (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.MethodsThe 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).ResultsA 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.ConclusionsThese 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.
Highlights
Rhabdomyosarcoma (RMS), a common soft-tissue malignancy in pediatrics, presents high invasiveness and mortality
Functional enrichment of differentially expressed genes (DEGs) To understand the changes in DEGs function, we mapped all of the genes to the DAVID database
Gene ontology (GO) functional analysis of RMS and normal striated muscle DEGs revealed that up-regulated genes in biological processes (BP) are largely enriched in cell or nuclear division, G2/M transition in cell cycle and transcription
Summary
Rhabdomyosarcoma (RMS), a common soft-tissue malignancy in pediatrics, presents high invasiveness and mortality. Other prognostic (e.g. MYOD1 mutation, RAS pathway mutation, NCOA2 or VGLL2 gene fusion) and diagnostic (e.g. intermediate silk proteins [desmin, vimentin and nestin], muscle proteins [myoglobin and actin] and myocyte determinant-coding genes [MYOD1 and myogenin]) markers have been found in RMS [3, 7]. These biomarkers play a considerable role in RMS, the 5-year survival rate of RMS sufferer is still lower than 20% [4,5,6]. The study used immunohistochemistry (IHC) to further verify that more than 80% of RMS clinical samples showed increased expression of CDK1 and CCNB1 protein levels, and the CCNB1 gene was associated with the age and location of RMS patients
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