Abstract
Protein biomarkers are widely used in cancer diagnosis, prognosis, and prediction of treatment response. Here we introduce the use of targeted multiplex proteomics (TMP) as a tool to simultaneously measure a panel of 54 proteins involved in oncogenic, tumour suppression, drug metabolism and resistance, in patients with metastatic colorectal cancer (mCRC). TMP provided valuable diagnostic information by unmasking an occult neuroendocrine differentiation and identifying a misclassified case based on abnormal proteins phenotype. No significant differences in protein levels between unpaired primary and metastatic samples were observed. Four proteins were found differentially expressed in KRAS-mutant as compared to wild-type tumours (overexpressed in mutant: KRAS, EGFR; overexpressed in wild-type: TOPO1, TOP2A). Survival analyses revealed the association between mesothelin expression and poor overall survival, whereas lack of PTEN protein expression associated with lower progression-free survival with anti-EGFR-based therapy in the first-line setting for patients with RAS wild-type tumour. Finally, outlier analysis identified putative targetable proteins in 65% of patients lacking a targetable genomic alteration. Our data show that TMP constitutes a promising, novel molecular prescreening tool in mCRC to identify protein expression alterations that may impact on patient outcomes and more precisely guide patient eligibility to clinical trials with novel targeted experimental therapies.
Highlights
Simultaneous and accurate measurement of many proteins in experimental samples is very important in descriptive and predictive biological research, including comprehensive proteomic surveys, protein network studies, validation of genomic alterations and clinical biomarker development
Our targeted panel of proteins including oncogenic, tumour suppression, drug metabolism, and drug resistance markers, among others were measured in formalin -fixed paraffin -embedded (FFPE) tissues from 50 patients with metastatic colorectal cancer (mCRC) treated at our institution and whose tumours were genomically-profiled as a prescreening strategy for clinical trial recruitment
The decision to administer standard chemotherapies in the metastatic setting (e.g. FOLFOX or FOLFIRI) remains empirical and does not rely on tumour biomarkers, which could be revealed by a novel multiplatform profiling strategy like ours
Summary
Simultaneous and accurate measurement of many proteins in experimental samples is very important in descriptive and predictive biological research, including comprehensive proteomic surveys, protein network studies, validation of genomic alterations and clinical biomarker development. Despite being a relatively easy and inexpensive approach, IHC has its limitations including reproducibility issues and very poor multiplexing capabilities It is at best a semiquantitative method and is minimally effective for comprehensive analyses. ® In the present study, we used the Liquid Tissue proteomic method to reverse formalin-induced crosslinks allowing complete solubilization of all proteins in the sample for the precise quantification[6,7]. The reliability of this approach for the analysis of proteins in patient tumour tissues has been previously demonstrated[8,9,10,11,12,13]. We performed an exploratory correlative analysis of protein levels with clinicopathological and genomic markers, investigated their association with the patient outcome – including response to standard chemotherapies and combinations with anti-EGFR agents – and assessed their potential as predictive biomarkers for novel targeted experimental therapies currently under investigation
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