Classification of Molecular Subtypes of High-Grade Serous Ovarian Cancer by MALDI-Imaging

SIMPLE SUMMARY: High-grade serous ovarian cancer (HGSOC) accounts for 70% of ovarian carcinomas with sobering survival rates. The mechanisms mediating treatment efficacy are still poorly understood with no adequate biomarkers of response to treatment and risk assessment. This variability of treatment response might be due to its molecular heterogeneity. Therefore, identification of biomarkers or molecular signatures to stratify patients and offer personalized treatment is of utmost priority. Currently, comprehensive gene expression profiling is time- and cost-extensive and limited by tissue heterogeneity. Thus, it has not been implemented into clinical practice. This study demonstrates for the first time a spatially resolved, time- and cost-effective approach to stratifying HGSOC patients by combining novel matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI-IMS) technology with machine-learning algorithms. Eventually, MALDI-derived predictive signatures for treatment efficacy, recurrent risk, or, as demonstrated here, molecular subtypes might be utilized for emerging clinical challenges to ultimately improve patient outcomes. ABSTRACT: Despite the correlation of clinical outcome and molecular subtypes of high-grade serous ovarian cancer (HGSOC), contemporary gene expression signatures have not been implemented in clinical practice to stratify patients for targeted therapy. Hence, we aimed to examine the potential of unsupervised matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI-IMS) to stratify patients who might benefit from targeted therapeutic strategies. Molecular subtyping of paraffin-embedded tissue samples from 279 HGSOC patients was performed by NanoString analysis (ground truth labeling). Next, we applied MALDI-IMS paired with machine-learning algorithms to identify distinct mass profiles on the same paraffin-embedded tissue sections and distinguish HGSOC subtypes by proteomic signature. Finally, we devised a novel approach to annotate spectra of stromal origin. We elucidated a MALDI-derived proteomic signature (135 peptides) able to classify HGSOC subtypes. Random forest classifiers achieved an area under the curve (AUC) of 0.983. Furthermore, we demonstrated that the exclusion of stroma-associated spectra provides tangible improvements to classification quality (AUC = 0.988). Moreover, novel MALDI-based stroma annotation achieved near-perfect classifications (AUC = 0.999). Here, we present a concept integrating MALDI-IMS with machine-learning algorithms to classify patients according to distinct molecular subtypes of HGSOC. This has great potential to assign patients for personalized treatment.