Background Osteosarcoma has been a common bone malignancy
occurring in
children and adolescents. Attributing to high tumor heterogeneity, none specific breakthrough has been received in targeted gene therapy for osteosarcoma, although it’s still of great potential for immunotherapy in clinical application. In the study, 5 GEO profiles containing transcriptome information of 109 osteosarcoma samples, single cell sequencing data composed of 6 cases of samples, as well as 43 cases of local hospital tissue samples were combine used to identify the promising immune related candidate genes in osteosarcoma.
Methods Based on
osteosarcoma transcriptome microarrays from GEO database as well as immune related gene profile from IMMPORT database, differently expressed meanwhile immune related gene candidates in osteosarcoma comparing to normal control samples were identified. Then, protein-protein interaction network (PPI), survival analysis followed by LASSO analysis were in succession applied to construct a gene signature based on the selected candidate genes. After understanding the basic genetic physicochemical properties and evaluating the prognosis risk association of the gene signature using local hospital cancer samples, its association with immune microenvironment features including macrophages included various immune cells infiltration, different immune checkpoints expression, immune related signaling pathways involvement were next step assessed.
Results
From GEO transcriptome datasets which contains a total of 109 osteosarcoma samples, a total of 108 high level differently expressed meanwhile immune related gene candidates were identified. Then, PPI network and LASSO analysis highlighted a 6 genes containing cluster from the 108 candidate genes. Further, ROC curve as well as Cox regression analysis assisted scaled the 6 hub genes down to 2 key genes, namely STC2 and FPR1, and a gene signature was constructed based on them. After understanding the basic genetic physicochemical properties of STC2 and FPR1, double staining immunochemistry (IHC) experiment based on 43 cases of local hospital samples and single cell sequencing date of 6 tissue samples revealed that STC2 was mainly expressed in osteosarcoma cancer cells, meanwhile, FPR1 was mostly enriched in macrophages focused immune cells which has also been the main immune cell type in osteosarcoma microenvironment. Moreover, the combining STC2/FPR1 dual genes signature was also associated with distribution of multiple immune checkpoints, especially TIM-3. Further, the correlation between the signature and other immune features including immune related cell death (ICD) and ESTIMATE immune score were additionally evaluated.
Conclusions
Based on osteosarcoma transcriptome genes analysis, a dual genes containing signature composed of STC2 and FPR1 genes was constructed. Immune correlation analysis indicated the signature was associated with the macrophages infiltration which has been a main immune cell type in osteosarcoma, ans it was also related with TIM-3 included multiple immune checkpoints expression. The results shall benefit further osteosarcoma immune researches and assist revealing promising prediction markers for clinical immunotherapy.
