Intratumor heterogeneity causes spatial proteome variation in NSCLC patients

Non-small cell lung cancer (NSCLC) accounts for around 85% of all lung cancer instances, with patients encountering poor prognoses. It is subclassified as squamous (SQ) and non-SQ cell carcinoma, the latter of which splits again into the subtypes of large cell carcinoma and adenocarcinoma. NSCLC subtypes do not show particularly distinct genetic profiles and have mostly been identified by their morphological properties. NSCLC evolves in an environment with low selection pressure which maximizes the existence of more diverse cell clones, eventually leading to intratumor heterogeneity (ITH). ITH causes therapeutic resistance and unfavorable treatment outcomes in patients. Mass spectrometry (MS)-based proteomic analysis has become a key technology in systems biology and thus in cancer research. MS-based proteomics focussed, for many years, on analyzing "bulk" material, e.g. patient tumor samples or whole tissue sections. This also applies to clinical tumor samples, which usually contain a mixture of tumor and tumor-associated cells, resulting in an average proteome representation of the tumor. Hence, ITH blurs the picture of tumor cell diversity, which can only be addressed by low-input/single-cell approaches. The recently developed Deep Visual Proteomics (DVP) approach (Mund and Coscia et al. 2022) is an innovative technology that combines high-end microscopy with state-of-the-art high-sensitivity MS-based proteomics. It allows precise isolation of small areas /single cells from formalin-fixed and paraffin-embedded (FFPE) tissue samples via laser microdissection (LMD), based on their phenotypic appearance while maintaining spatial information. Subsequent liquid-chromatography (LC)-MS analysis will provide a clearer picture of the underlying proteome of phenotypically different tumor regions. This study serves as proof of relevance for the utilization of the DVP method in lung cancer studies. We compare the proteome of phenotypically different tumor and stroma regions to identify proteomic variances and uncover key aspects of spatial cellular regulation within the diverse tumor landscape of NSCLC subtypes.