Deciphering ovarian cancer heterogeneity through spatial transcriptomics, single-cell profiling, and copy number variations

Abstract

High-grade serous ovarian carcinoma (HGSOC) poses a formidable clinical challenge due to multidrug resistance (MDR) caused by tumor heterogeneity. To elucidate the intricate mechanisms underlying HGSOC heterogeneity, we conducted a comprehensive analysis of five single-cell transcriptomes and eight spatial transcriptomes derived from eight HGSOC patients. This study provides a comprehensive view of tumor heterogeneity across the spectrum of gene expression, copy number variation (CNV), and single-cell profiles. Our CNV analysis revealed intratumor heterogeneity by identifying distinct tumor clones, illuminating their evolutionary trajectories and spatial relationships. We further explored the homogeneity and heterogeneity of CNV across tumors to pinpoint the origin of heterogeneity. At the cellular level, single-cell RNA sequencing (scRNA seq) analysis identified three meta-programs that delineate the functional profile of tumor cells. The communication networks between tumor cell clusters exhibited unique patterns associated with the meta-programs governing these clusters. Notably, the ligand-receptor pair MDK - NCL emerged as a highly enriched interaction in tumor cell communication. To probe the functional significance of this interaction, we induced NCL overexpression in the SOVK3 cell line and observed enhanced tumor cell proliferation. These findings indicate that the MDK - NCL interaction plays a crucial role in promoting HGSOC tumor growth and may represent a promising therapeutic target. In conclusion, this study comprehensively unravels the multifaceted nature of HGSOC heterogeneity, providing potential therapeutic strategies for this challenging malignancy.