Abstract A087: Empowering precision medicine in metastatic colorectal cancer: preliminary results from the FUNNEL platform
Authors: Martino Cosimo , Berrino Enrico , Dell'Aglio Carmine , Casorzo Laura , Panero Mara , Siena Salvatore , Sartore-Bianchi Andrea , Cassingena Andrea , Zagonel Vittorina , Lonardi Sara , Loupakis Fotios , Tonini Giuseppe , Racca Patrizia , Trusolino Livio , Bertotti Andrea , Depetris Ilaria , Balsamo Antonella , Sapino Anna , Marsoni Silvia 
Published: August 2018

Abstract
Background: Metastatic colorectal cancer still has a dismal 5-yr survival of less than 10%. Chemotherapy, targeted therapies, and immune-checkpoint inhibitors are effective in only a fraction of patients, and even in responders, long-term remission are rare. To harness insight into the evolving heterogeneity of mCRC, and to combat it therapeutically, we have established the logistic research matrix FUNNEL that integrates the topographic acquisition of patient samples with the clinical validation of hypothesis-driven trials in primary or secondary resistance disease. Methods: FUNNEL will follow 1000 sequential cases from diagnosis to death, acquiring biologic specimens, imaging, and clinical data at critical steps along the disease continuum. At diagnosis of metastatic disease, patients are genotyped with a CRC-specific panel designed to map the landscape of primary resistance to anti-EGFR therapies (Bertotti A. et al,, Nature 2015). Paraffin samples are centrally processed and tested using Sequenom® (with a 5% detection sensitivity for 168 mutations in KRAS, BRAF, NRAS, PIK3CA, EGFR, HER2, IDH1, MEK1) and NanoString® technologies [measuring gene copy number variation (CNV) for RAF1, EGFR, FGRF1/2/3, HER2, IGF1/2, IGF1R, KRAS, MET, and NF1]. Genes are considered amplified with a CNV ≥ 10 cut-off validated by FISH. Dynamic data of centralized disease assessments imaging coupled with longitudinal liquid biopsies are also collected at significant clinical events (baseline, response to therapy, and progression of sequential treatment’s lines). Proteomics and neoantigenic profile of cancer cells in parallel with function and tumor specificity of infiltrating T cells will also be determined in retrospectively selected patients. Results: From 7/2015 to 6/2017, 428 patients have been successfully genotyped. Overall we found 52% mutated and 6% amplified tumors (2% both amplified and mutated). Of these, 81% (N 180) had a single gene mutation in KRAS (67%), BRAF (13%), PIK3CA (11%), or NRAS (9%). Remaining cases had a double gene alteration in PIK3CA (N 38) and KRAS (81%) or BRAF (7%) or NRAS (5%), or BRAF (N3: KRAS, NRAS, IDH1 ). 29% of the 24 amplified tumors showed concomitant mutations, while 16% had multiple amplifications. Interestingly, 2 out of 13 HER2-amplified tumors also harbored KRAS (G12D) and PIK3CA mutations (E542K and E545A). Conclusion: Upfront genotyping detected 44% multiple wild type and 9% patients with potentially actionable drivers including HER2, FGFR1 and 3, EGFR, MET, IGF1 and 2, and IGF1R. Two embedded trials for HER2-amplified (HERACLES - EudraCT 2012-002128-33, NCT03225937) and multiple wild type patients (CHRONOS EudraCT 2016-002597-12, NCT03227926) are ongoing. Beyond "molecular triage" purposes, FUNNEL is also building an integrated repository of lifetime clinical and molecular information, that all together will allow a comprehensive insight of mCRC clonal evolution, laying the groundwork to design further innovative trials, and, eventually, inform patient care. Funded by AIRC Grant 9970; Italian Ministry of Health grant NET-2011-02352137.
Citation Format: Cosimo Martino, Enrico Berrino, Carmine Dell'Aglio, Laura Casorzo, Mara Panero, Salvatore Siena, Andrea Sartore-Bianchi, Andrea Cassingena, Vittorina Zagonel, Sara Lonardi, Fotios Loupakis, Giuseppe Tonini, Patrizia Racca, Livio Trusolino, Andrea Bertotti, Ilaria Depetris, Antonella Balsamo, Anna Sapino, Silvia Marsoni. Empowering precision medicine in metastatic colorectal cancer: preliminary results from the FUNNEL platform [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2017 Oct 26-30; Philadelphia, PA. Philadelphia (PA): AACR; Mol Cancer Ther 2018;17(1 Suppl):Abstract nr A087.