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The whole transcriptome analysis using FFPE and fresh tissue samples identifies the molecular fingerprint of osteosarcoma

ABSTRACT: 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.

ORGANISM(S): Homo sapiens

PROVIDER: GSE253548 | GEO | 2024/07/10

REPOSITORIES: GEO

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Project description:For the effectiveness of targeted immunotherapy, which is currently one of the most promising treatments for brain tumors, it is necessary to know specific tumor-associated antigens (TAA). This project aimed to validate the suitability of formalin-fixed and paraffin-embedded (FFPE) material instead of fresh-frozen material for RNA sequencing and downstream TAA identification. Purpose: Detect potential oligodendroglioma-associated antigens using both fresh-frozen and FFPE brain tissues; assess the suitability of the FFPE material for TAA identification. Results: A comparative analysis based on the RNA-seq of canine oligodendroglioma showed that formalin fixation of the samples had a significant effect on the RNA-seq library in terms of quality. Read distribution analysis showed that the FFPE samples contained fewer reads mapping to exonic regions and were enriched with reads mapped to introns and intergenic regions, while the fresh-frozen samples were mostly enriched in reads mapping to exons. Mismatch profile and SNVs calling analyses revealed some substitution artefacts present in the FFPE samples and absent in the corresponding fresh-frozen samples. However, according to the Principal Component Analysis, 36% of the variance between the samples could be explained by the types of conservation, while 43% of the variance could still be attributed to different expression profiles between oligodendroglioma and control conditions. A differential expression analysis of fresh-frozen oligodendroglioma versus fresh-frozen control samples identified 62 potential TAA strongly up-regulated in tumor tissue. The same analysis using the FFPE samples showed 80% of these genes (49/62) also to be differentially expressed. Comparative analysis showed good agreement between FFPE and fresh-frozen RNA-seq libraries in terms of the accuracy of gene expression measurements indicating that archived FFPE tissue can be used for identification of TAA candidates by RNA-seq providing a wealthy source of clinical samples for research. The following 10 genes encoding cell surface proteins have been identified by both approaches as potential TAA candidates based on their strong overexpression in oligodendrogliomas: PDGFRA, NOTCH1, DLL1, GPER1, TNR, IQGAP3, CD44, ERBB3, BCAS1 and ROR2. Future projects still need to investigate their suitability as TAA for targeted immunotherapy. Conclusion: Formalin fixation of the samples had a significant impact on the RNA-seq quality in terms of the accuracy of gene expression measurements, as well as the quality of the nucleotide sequences. Nevertheless, the comparative analysis showed good agreement between FFPE and fresh-frozen RNA-seq libraries.

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The whole transcriptome analysis using FFPE and fresh tissue samples identifies the molecular fingerprint of osteosarcoma

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