Proteogenomics of Colorectal Cancer Liver Metastases: Complementing Precision Oncology with Phenotypic Data

Abstract

Hotspot testing for activating KRAS mutations is used in precision oncology to select colorectal cancer (CRC) patients who are eligible for anti-EGFR treatment. However, even for KRAS wildtype tumors anti-EGFR response rates are <30%, while mutated-KRAS does not entirely rule out response, indicating the need for improved patient stratification. We performed proteogenomic phenotyping of KRAS wildtype and KRAS G12V CRC liver metastases (mCRC). Among >9000 proteins we detected considerable expression changes including numerous proteins involved in progression and resistance in CRC. We identified peptides representing a number of predicted somatic mutations, including KRAS G12V . For eight of these, we developed a multiplexed parallel reaction monitoring (PRM) mass spectrometry assay to precisely quantify the mutated and canonical protein variants. This allowed phenotyping of eight mCRC tumors and six paired healthy tissues, by determining mutation rates on the protein level. Total KRAS expression varied between tumors (0.47-1.01 fmol/µg total protein) and healthy tissues (0.13-0.64 fmol/µg). In KRAS G12V -mCRC, G12V-mutation levels were 42-100%, while one patient had only 10% KRAS G12V but 90% KRAS wildtype . This might represent a missed therapeutic opportunity: based on hotspot sequencing, the patient was excluded from anti-EGFR treatment and instead received chemotherapy, while PRM-based tumor-phenotyping indicates the patient might have benefitted from anti-EGFR therapy.

Copy number and transcriptome alterations associated with metastatic lesion response to treatment in colorectal cancer

“…While the clinical feasibility of serial biopsies is not simple, such studies are critical to guide in the identification of genomic targets that could be more easily identified in liquid biopsies. Indeed, this systematic biospecimen collection, taken in a specific clinical context, has seeded a variety of studies with both technical and clinical implications, [56][57][58][59][60] including emerging proteogenomic analyses.…”

Systematic Optimization of the iMALDI Workflow for the Robust and Straightforward Quantification of Signaling Proteins in Cancer Cells

“…This will facilitate the transfer of this technology into the clinic, where protein-based assays are becoming increasingly important for patient stratification. [10,34]…”

Proteomic Profiling and Biomarker Discovery in Colorectal Liver Metastases

“…The downstream signalling effects of genomic alterations can be characterised and evaluated by including proteomic and post-translational modification data [ 103 , 104 ]. Table 2 summarises five studies that have layered various omics in addition to proteomics to understand how cell processes in CRC are connected and communicate with each other [ 54 , 55 , 56 , 57 , 58 ]. The use of fresh frozen CRLM biospecimens and nanoscale liquid chromatography coupled to tandem mass spectrometry (nano-LC-MS/MS) characterises the few multiomic studies on CRLM to date.…”