Spatial proteomics of ovarian cancer precursor lesions

High-grade serous ovarian cancer (HGSOC) is the most prevailing and lethal subtype of epithelial ovarian cancer (EOC). Despite significant research efforts, the prognosis has remained unchanged for this disease. To a significant extent, this is due to a limited understanding of the early stages of this disease. Accumulating evidence suggests that serous tubal intraepithelial carcinoma (STIC) of the fallopian tube is the main precursor lesion giving rise to HGSOC. However, not much is known about the molecular pathways that drive the transition from fallopian tube epithelium (FTE), to STIC, and then to invasive fallopian tube carcinoma (invFTC). Genomic studies have provided important knowledge on driver mutations and the genetic, clonal relationship between STIC and invFTC. However, genomics alone does not explain the functional implications of the genetic alterations. Since proteins are a closer representation of cellular state and function, proteome profiling of STICs can provide insights into how the proteome changes during the early stages of cancer. The proteomic analysis of STICs has remained challenging because they are microscopic, consisting of only a few cells, compared to established tumors. Due to a lack of workflows tailored towards proteomics of ultra-low sample input from formalin-fixed paraffin-embedded (FFPE) tissues, proteomics has not been performed yet to systematically profile STICs. To better understand the molecular processes that drive the transition from fallopian tube epithelium (FTE), to STIC, and then to HGSOC, we for the first time performed mass spectrometry-based spatial proteomics on FFPE tissue sections of a cohort of 36 patients. We characterized proteomes to a depth of 7,000 proteins from STICs as small as 50 cells. Preliminary data suggests pronounced proteome changes between FTE and STICs, but a high level of similarity between STICs and invFTC. Clustering of precursor lesions and invFTC revealed phenotypically divergent tumors with distinct enriched pathways that might contribute to the clinical outcome. Conversely, we found pronounced differences in the stroma sampled from regions directly adjacent to FTE, STICs and invFTC, suggesting a critical role of the tumor microenvironment in promoting the full transformation of pre-cancerous STICs to invasive carcinoma. Our data provides new insights into the molecular alterations that define the early stages of HGSOC development. In the future, we plan to integrate our data with genomics, and functional studies. This could ultimately help to develop strategies to intervene early and prevent HGSOC in the long term, an approach crucial in improving the disease outcome.