Utilizing bulk and single-cell RNA sequencing to identify potential biomarkers linked to angiogenesis and integrated stress response in chondrosarcoma

Chondrosarcoma (CS) is the second most common bone sarcoma with a cartilage matrix. Angiogenesis and integrated stress response (ISR) exert a vital influence on the development of CS. This research aimed to conduct a comprehensive analysis to pinpoint angiogenesis and ISR-related potential biomarkers in CS and to elucidate their potential molecular mechanisms. CS data were from GEO. Potential biomarkers were identified and confirmed using differential expression analysis, WGCNA, and expression assessment. Moreover, enrichment analysis was employed to examine relevant pathways. Molecular regulatory network, compound prediction, and molecular docking analyses further explored the key regulatory roles of potential biomarkers in CS. GSE184118 was used to determine key cells and perform pseudo-time and cell communication analyses. Finally, RT-qPCR was used to confirm potential biomarker expression levels. Overall, three potential biomarkers (HSPA8, LMNA and SERPINH1) were determined, and their expression trends were consistent across the GSE30835 and GSE22855 datasets. Potential biomarkers were significantly enriched in the pathways like "medicus variant mutation caused aberrant HTT to 26S proteasome mediated protein degradation" in CS. Moreover, 9 transcription factors (TFs) (like STAT1), 69 key microRNAs (miRNAs) (like hsa-miR-361-3p), and 78 long non-coding RNAs (lncRNAs) (like NEAT1) were found to have relationships with potential biomarkers, and potential biomarkers had stable binding affinity with adenosine diphosphate (ADP) and lonafarnib. Moreover, pseudo-time analysis demonstrated a notable correlation between potential biomarkers' expression and differentiation status of key cells (stromal cells (excluding leucocytes)), and cell communication revealed the strong interactions between stromal cells and chondroid clusters 1. Importantly, RT-qPCR confirmed higher expression of HSPA8, LMNA and SERPINH1 in CS patients. The findings suggested that HSPA8, LMNA and SERPINH1 might offer novel insights for the development of targeted therapies for CS associated with angiogenesis and ISR.