Abstract 4380: Integrative genomics analysis of metastatic colorectal cancer
Authors: Marla Lipsyc, Walid Chatila, Jaclyn F. Hechtman, Francisco Sanchez-Vega, Sumit Middha, Andrea Cercek, Zsofia Stadler, Ritika Kundra, Aijazuddin Syed, David M. Hyman, Ahmet Zehir, Armin Shahrokni, Anna Varghese, Diane Reidy, Neil H. Segal, Efsevia Vakiani, David B. Solit, Marc Ladanyi, Michael F. Berger, Nancy Kemeny, Leonard Saltz, Nikolaus Schultz, Rona Yaeger
Journal: Cancer Research (2017)

Abstract We performed an integrated clinical and bioinformatic analysis of colorectal cancers (CRCs) genotyped at our institution from 4/2014-7/2016 to comprehensively characterize genomic alterations in metastatic CRC (mCRC). We analyzed 1008 samples (474 primaries, 534 metastases) from 985 mCRC patients and 128 early stage CRCs sequenced with MSK-IMPACT, a hybridization capture next generation sequencing assay. Metastatic CRCs were divided into 3 groups by mutation burden and MSIsensor algorithm score: microsatellite stable (MSS) (n=939; 95%), microsatellite-high (MSI-H) (n=41; 4%), and ultra-mutated (n=5; 1%). Early stage CRC were enriched for MSI-H due to clinical selection and were 53% MSS, 44% MSI-H, and 4% ultra-mutated. Ultra-mutated tumors exhibited &amp;gt;100 mutations and harbored hotspot mutations in POLE in 8 cases and a potential novel POLE alteration in 1 case. We evaluated the frequency of oncogenic alterations in MSI-H and MSS mCRCs. The frequency of the resistance biomarkers KRAS and NRAS did not vary between MSI-H and MSS mCRCs (46% v 41%, p=0.6). Potentially actionable alterations were enriched in MSI-H tumors (78% v 33%, p&amp;lt;0.001). Metastases did not have more actionable alterations than primary tumors. We classified clinically relevant targets using the OncoKB classification as level 2B (FDA-approved target in another disease type), 3A (target with compelling early clinical evidence in CRC), and 3B (target with compelling early clinical evidence in another disease type). Twelve percent (109/939) of MSS mCRCs had a level 2B target: BRAF V600E (5%), ERBB2 amplification (AMP) (4%), MET AMP (1%), BRCA1/BRCA2 alteration (1%), TSC1/TSC2 mutation (1%), EGFR mutation (&amp;lt;1%), RET fusion (&amp;lt;1%); there was significant enrichment of BRAF V600E (24%) and BRCA1/BRCA2 alterations (29%) in MSI-H versus MSS mCRC (p&amp;lt;0.001). NTRK fusions, the main 3A alteration identified, occurred in 7% of MSI-H and &amp;lt;1% MSS CRC (p&amp;lt;0.01). Level 3B alterations at ≥ 1% in MSS CRC included PIK3CA (15%), NRAS (3%), AKT1 (1%), MAP2K1 (1%), and ERBB2 (1%) mutations and FGFR1 AMP (2%). PIK3CA and PTCH1 mutations were both enriched in MSI-H versus MSS mCRC (32% v 15%, p&amp;lt;0.01; 27%,v &amp;lt;1%, p&amp;lt;0.001, respectively). Analysis of mutation frequencies in 3 MSS CRC disease states - early stage resected primary (The Cancer Genome Atlas, TCGA), primary site of mCRC, and metastatic site - found significant depletion of FBXW7 mutations in metastases. We also found significant and progressive enrichment of TP53 alterations (58% TCGA, 73% primaries of mCRC, 79% metastases) and BRAF mutations (4% TCGA, 9% primaries of mCRC, 10% metastases) in advanced disease, suggesting a role of these genes in aggressive disease. One third of the BRAF mutations in our cohorts were not V600 but known to be oncogenic. In this large dataset, we identified markers of advanced CRC and found that while MSI-H and MSS CRC have a similar frequency of resistance biomarkers, MSI-H CRC more commonly harbor actionable alterations. Citation Format: Marla Lipsyc, Walid Chatila, Jaclyn F. Hechtman, Francisco Sanchez-Vega, Sumit Middha, Andrea Cercek, Zsofia Stadler, Ritika Kundra, Aijazuddin Syed, David M. Hyman, Ahmet Zehir, Armin Shahrokni, Anna Varghese, Diane Reidy, Neil H. Segal, Efsevia Vakiani, David B. Solit, Marc Ladanyi, Michael F. Berger, Nancy Kemeny, Leonard Saltz, Nikolaus Schultz, Rona Yaeger. Integrative genomics analysis of metastatic colorectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4380. doi:10.1158/1538-7445.AM2017-4380