With recent advances in understanding the genomic underpinnings and oncogenic drivers of pathogenesis in different subtypes, it is increasingly clear that proper pretreatment diagnostics are essential for the choice of appropriate treatment options for
non-small cell lung cancer (NSCLC).
Tumor tissue preservation in optimal cutting temperature (OCT) compound is commonly used in the surgical suite. However,
proteins recovered from OCT-embedded specimens pose a challenge for LC-MS/MS experiments, due to the large amounts of
polymers present in OCT. Here we present a simple workflow for whole
proteome analysis of OCT-embedded NSCLC tissue samples, which involves a simple
trichloroacetic acid precipitation step. Comparisons of
protein recovery between frozen versus OCT-embedded tissue showed excellent consistency with more than 9200
proteins identified. Using an isobaric labeling strategy, we quantified more than 5400
proteins in
tumor versus normal OCT-embedded core needle biopsy samples. Gene ontology analysis indicated that a number of proliferative as well as
squamous cell carcinoma (SqCC) marker
proteins were overexpressed in the
tumor, consistent with the patient's pathology based diagnosis of "poorly differentiated SqCC". Among the most downregulated
proteins in the
tumor sample, we noted a number of
proteins with potential immunomodulatory functions. Finally, interrogation of the aberrantly expressed
proteins using a candidate approach and cross-referencing with publicly available databases led to the identification of potential druggable targets in DNA replication and DNA damage repair pathways. We conclude that our approach allows LC-MS/MS proteomic analyses on OCT-embedded
lung cancer specimens, opening the way to bring powerful proteomics into the clinic. Graphical Abstract ᅟ.