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

Bernhard Blank-Landeshammer,Maud Marques,Christoph H Borchers,Vincent R Richard,Alan Spatz,René P Zahedi,Ingo Feldmann,Suzan Mcnamara,Georgia Mitsa,André Leblanc,Karen Gambaro,Gerald Batist,Laxmikanth Kollipara,Albert Sickmann,Mathilde Couetoux Du Tertre

doi:10.3390/cancers11121907

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 KRASwildtype 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 KRASwildtype and KRASG12V 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 KRASG12V. 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 KRASG12V-mCRC, G12V-mutation levels were 42–100%, while one patient had only 10% KRASG12V but 90% KRASwildtype. 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.

Highlights

IntroductionIn 2018, 1.8 million people worldwide were diagnosed with colorectal cancer (CRC) [1], and
In 2018, 1.8 million people worldwide were diagnosed with colorectal cancer (CRC) [1], and860,000 people died from CRC, making it the third most common and second most deadly cancer worldwide [2]
Deep-proteomic profiling resulted in the identification of 8603 and 8330 unique proteins, at 1% protein false discovery rate, from KRASWT and KRASG12V tumors, respectively (Table S1)

Summary

Introduction

In 2018, 1.8 million people worldwide were diagnosed with colorectal cancer (CRC) [1], and. 860,000 people died from CRC, making it the third most common and second most deadly cancer worldwide [2]. 39% of CRC patients present with localized disease (5-year survival of 90%). While CRC can often be cured when diagnosed early, 50–60% of patients diagnosed with CRC will develop metastases during the course of their disease [4]. The 5-year survival rate for patients with distant metastatic disease, i.e., where the cancer has spread to the liver, lungs, or distant lymph nodes (includes Stage IV cancers), is only. Treatments for metastatic CRC (mCRC) are still largely based on toxic chemotherapy regimens, but important insights into tumor biology enabled the development of targeted cancer therapies

Methods

Results

Discussion

Conclusion