Whole transcriptome analysis identifies differentially regulated networks between osteosarcoma and normal bone samples

Abstract

We performed whole transcriptome analysis of osteosarcoma bone samples. Initially, we sequenced total RNA from 36 fresh-frozen samples (18 tumoral bone samples and 18 non-tumoral paired samples) matching in pairs for each osteosarcoma patient. We also performed independent gene expression analysis of formalin-fixed paraffin-embedded samples to verify the RNAseq results. Formalin-fixed paraffin-embedded samples allowed us to analyze the effect of chemotherapy. Data were analyzed with DESeq2, edgeR and Reactome packages of R. We found 5365 genes expressed differentially between the normal bone and osteosarcoma tissues with an FDR below 0.05, of which 3399 genes were upregulated and 1966 were downregulated. Among those genes, BTNL9, MMP14, ABCA10, ACACB, COL11A1, and PKM2 were expressed differentially with the highest significance between tumor and normal bone. Functional annotation with the reactome identified significant changes in the pathways related to the extracellular matrix degradation and collagen biosynthesis. It was suggested that chemotherapy may induce the modification of ECM with important collagen biosynthesis. Taken together, our results indicate that changes in the degradation of extracellular matrix seem to be an important mechanism of osteosarcoma and efficient chemotherapy induces the genes related to bone formation. Impact statement Osteosarcoma is a rare disease but it is of interest to many scientists all over the world because the current standard treatment still has poor results. We sequenced total RNA from 36 fresh-frozen paired samples (18 tumoral bone samples and 18 non-tumoral paired samples) from osteosarcoma patients. We found that differences in the gene expressions between the normal and affected bones reflected the changes in the regulation of the degradation of collagen and extracellular matrix. We believe that these findings contribute to the understanding of OS and suggest ideas for further studies.

Bioinformatics identification of crucial genes and pathways associated with hepatocellular carcinoma

“…For instance, Jeon et al [ 23 ] found that knockdown of ACACB could compensate for AMPK activation and facilitate anchorage-independent growth and solid tumor formation in vivo , whereas the activation of ACACB could attenuate these processes. Ho et al [ 24 ] observed that the expression level of ACACB was significantly different between osteosarcoma and normal bone samples. The above findings suggested that ACACB might be a novel gene associated with HCC.…”

Tumor cell MT1-MMP is dispensable for osteosarcoma tumor growth, bone degradation and lung metastasis

“…To our knowledge, the functional role of MT1-MMP in osteosarcoma has not been experimentally addressed, but expression studies clearly suggest an involvement in the progression of this disease. We have previously demonstrated the expression of MT1-MMP on the tumor cells in human osteosarcoma specimens using IHC 14 and in a transcriptome analysis of human osteosarcoma samples, MT1-MMP was found to be among the 10 most upregulated genes 24 . Furthermore, high MT1-MMP expression levels are correlated with poor survival in osteosarcoma patients 25,26 .…”

Analysis of Transcriptomic Similarity between Osteosarcoma Cell Lines and Primary Tumors

“…Previously published gene counts from fresh-frozen tumor were downloaded from Gene Expression Omnibus (GEO) under accession No. GSE99671 [9]. For the cell lines, raw FASTQ files were downloaded from GSE118488 [10].…”