The whole transcriptome analysis using FFPE and fresh tissue samples identifies the molecular fingerprint of osteosarcoma
Osteosarcoma is a form of bone cancer that predominantly impacts osteoblasts, the cells responsible for creating fresh bone tissue. Typical indications include bone pain, inflammation, sensitivity, mobility constraints, and fractures. Utilizing imaging techniques such as X-rays, MRI scans, and CT scans can provide insights into the size and location of the tumor. Additionally, a biopsy is employed to confirm the diagnosis. Analyzing genes with distinct expression patterns unique to osteosarcoma can be valuable for early detection and the development of effective treatment approaches. In this research, we conducted a comprehensive examination of the entire transcriptome and pinpointed genes with altered expression profiles specific to osteosarcoma.The study mainly aimed to identify the molecular fingerprint of osteosarcoma. In this study, we processed a total of 90 FFPE samples from PathWest of which 45 were OS and equal number of healthy tissues. RNA was extracted from Paraffin-embedded tissue; RNA was sequenced, the sequencing data was analysed and gene expression was compared to healthy of the same patients. Differentially expressed genes in osteosarcoma derived samples were identified and the functions of those genes were explored. This result was combined to perform meta-analysis with our previous studies based on FFPE and fresh samples. We identified 1,500 identical differentially expressed genes in PathWest osteosarcoma samples when compared with normal tissue sample of the same patients. Meta-analysis with combined fresh issue samples identified 504 differentially expressed genes. IFITM5, MMP13, PANX3, MAGEA6 were some of the most overexpressed genes in osteosarcoma samples while SLC4A1, HBA1, HBB, AQP7 genes were some of the top downregulated genes. Through the metanalysis, 504 differentially expressed genes were identified to be identical among FFPE (105 FFPE samples) and 36 fresh bone samples. These 504 differentially expressed genes can be taken as a molecular fingerprint of osteosarcoma. Overall design: We performed whole transcriptome analysis on 90 FFPE osteosarcoma samples, 50 tumours and 40 controls.