Rapid proteomic workflow for solid tumors reveals LSD1 as a drug target in an end stage cancer patient
Recent advances in mass spectrometry (MS)-based technologies are now set to transform translational cancer proteomics from an idea to a practice. Here, we present a robust proteomic workflow for the analysis of clinically relevant human cancer tissues, which allows quantitation of thousands of tumor proteins in several hours of measuring time and a total turnaround of a few days. We applied it to a chemorefractory metastatic case of the extremely rare urachal carcinoma. Quantitative comparison of lung metastases and surrounding tissue revealed several significantly upregulated proteins, among them lysine specific histone demethylase 1 (LSD1/KDM1A). LSD1 is an epigenetic regulator and is the target of active development efforts in oncology. This demonstrates that clinical cancer proteomics can rapidly and efficiently identify actionable therapeutic options. While currently described for a single case study, we envision that it can be applied broadly to other patients in a similar condition.
Sample Processing Protocol
The lung metastases were collected during surgery and were washed three times with cold PBS before flash freezing the samples in liquid nitrogen and shipping on dry ice. The samples were cut in half to enable genomic and proteomic analysis. Control and lung metastases samples were thawed on ice and prepared according to the in stage tip sample preparation method (Kulak et al. Nat Methods, 2014).
Data Processing Protocol
Samples were measured on a quadrupole Orbitrap mass spectrometer (Q Exactive HF, Thermo Fisher Scientific, Rockford, IL, USA) coupled to an EASYnLC 1200 ultra-high-pressure system (Thermo Fisher Scientific) via a nano-electrospray ion source. Data were further processed with MaxQuant with a 1% FDR at the peptide and protein level.