骨肉瘤是一种骨癌，主要影响成骨细胞，即负责产生新鲜骨组织的细胞。典型的适应症包括骨痛、炎症、敏感、活动受限和骨折。利用 X 射线、MRI 扫描和 CT 扫描等成像技术可以深入了解肿瘤的大小和位置。此外，还采用活检来确认诊断。分析具有骨肉瘤特有的独特表达模式的基因对于早期检测和开发有效的治疗方法具有重要意义。在这项研究中，我们全面检查了整个转录组，并查明了骨肉瘤特有的表达谱发生改变的基因。该研究主要旨在鉴定骨肉瘤的分子指纹。在这项研究中，我们处理了来自 PathWest 的 90 个 FFPE 样本，其中骨肉瘤和健康组织的数量几乎相等。从石蜡包埋的组织中提取RNA；对RNA进行测序，分析测序数据，并将基因表达与同一患者的健康样本进行比较。鉴定了骨肉瘤来源的样本中的差异表达基因，并探索了这些基因的功能。该结果与我们之前基于 FFPE 和新鲜样本的研究相结合，进行了荟萃分析。与同一患者的正常组织样本相比，我们在 PathWest 骨肉瘤样本中鉴定出了 1,500 个相同的差异表达基因。结合新鲜组织样本的荟萃分析鉴定出 530 个差异表达基因。 IFITM5、MMP13、PANX3 和 MAGEA6 是骨肉瘤样本中过度表达最多的基因，而 SLC4A1、HBA1、HBB、AQP7 基因是下调最多的基因。通过荟萃分析，鉴定出 FFPE（105 个 FFPE 样本）和 36 个新鲜骨样本中的 530 个差异表达基因相同。使用单细胞 RNAseq 数据进行反卷积分析证实了 FFPE 样品中特定细胞簇的存在。我们建议将这 530 个 DEG 作为骨肉瘤的分子指纹。版权所有 © 2024 Poudel 和 Koks。

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. Utilising imaging techniques such as X-rays, MRI scans, and CT scans can provide insights into the size and location of the tumour. Additionally, a biopsy is employed to confirm the diagnosis. Analysing 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 comprehensively examined 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 90 FFPE samples from PathWest with an almost equal number of osteosarcoma and healthy tissues. RNA was extracted from Paraffin-embedded tissue; RNA was sequenced, the sequencing data was analysed, and gene expression was compared to the healthy samples 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 with our previous studies based on FFPE and fresh samples to perform a meta-analysis. We identified 1,500 identical differentially expressed genes in PathWest osteosarcoma samples compared to normal tissue samples of the same patients. Meta-analysis with combined fresh tissue samples identified 530 differentially expressed genes. IFITM5, MMP13, PANX3, and 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 meta-analysis, 530 differentially expressed genes were identified to be identical among FFPE (105 FFPE samples) and 36 fresh bone samples. Deconvolution analysis with single-cell RNAseq data confirmed the presence of specific cell clusters in FFPE samples. We propose these 530 DEGs as a molecular fingerprint of osteosarcoma.Copyright © 2024 Poudel and Koks.