Harnessing single-cell transcriptomics analysis to determine cellular heterogeneity, progression, and early markers of conventional chondrosarcoma

Abstract

Chondrosarcoma is a cancer of cartilage producing cells and is relatively rare. Conventional chondrosarcomas including central (75%), peripheral (10%), periosteal (1%) variants are the most common form of chondrosarcoma that can arise from a benign tumour. However, there is currently no clear diagnostic marker for malignant transformation and clinical decision making. We used single-cell RNA sequencing (scRNA-seq) to characterize primary tumour tissues from five patients with central chondrosarcoma, one patient with a benign tumour, as well as a chondroblastic osteosarcoma and a fetal femur as controls. This atlas of 25,739 single cells was analysed to identify tumour heterogeneity, malignant transformation, and early markers of central chondrosarcoma. Based on inter-tumoral heterogeneity at single-cell resolution, we found that differentiated tumours were enriched for two distinct neoplastic cell clusters. One cluster resembled normal resting chondrocytes from the foetal femur while the other, which was subjected to cellular reprograming and endoplasmic reticulum stress (ER), indicated malignant transformation. Further single-cell analysis on additional central, peripheral, and dedifferentiated chondrosarcomas revalidated ER stress as a specific early marker for central chondrosarcoma. In addition, we revalidated the cancer development trajectory that the NF-B pathway regulated the survival of chondrosarcoma cells by alleviating ER stress-induced apoptosis. Importantly, coupled with a large cohort of bulk expression profiles, we proposed a prognostic model and identified DNA Damage Inducible Transcript 3 (DDIT3), commonly known as CHOP which mediates ER stress-induced apoptosis, as an early marker for chondrosarcoma. Overall, these findings help decipher tumour heterogeneity and malignant transformation and provide molecular signatures for the diagnosis and grading of chondrosarcoma.