Characterizations of DNA copy number variations and spatio-temporal intra tumor heterogeneity in liver metastasis from colorectal cancer patients
Authors: M. Marques, K. Gambaro, M. Couetoux du Tertre, M. Witcher, B. Samson, B. Lesperance, Y. Ko, R. Dalfen, E. St-Hilaire, L. Sideris, F. Couture, S. Tejpar, R. Burkes, M. Harb, T. Alcindor, E. Camlioglu, A. Gologan, V. Pelsser, S. McNamara, P. Kavan, C. Kleinman, G. Batist
Journal: Annals of Oncology (2018)

Introduction: Metastatic colorectal cancers (mCRC) are highly heterogeneous, representing a challenge in treatment management. Studies have largely investigated the genomic landscape of primary tumors at diagnosis. As metastasis is responsible for 90% of cancer patient deaths, this highlights the need to characterize the genomic landscape of metastasis over time of treatment to decipher their evolution and role in therapeutic resistance. Methods: Metastatic liver tissue samples were collected at baseline (pre-biopsies) and at relapse (post-biopsies) in responder and non-responder mCRC patients undergoing the same treatment. Paired pre/post biopsies were collected from 14 patients (4 of them had multiple post-biopsies) to assess intra-patient, inter-tumour and intra-tumour heterogeneity following treatment exposure. Biopsies were profiled using RNA and whole exome sequencing (WES) as well as high-density Single-Nucleotide Polymorphism (SNP) array. Results: Profiling of 45 samples with both high-density SNP array and WES revealed 97.4% similarity between both technologies in the identification of genes targeted by copy number (CN) changes. The metastatic and primary tumor had similar somatic copy number aberration (SCNA) profiles. Using chemo-naïve biopsies, we identified 120 CN gains and 47 CN losses that were significantly associated with patient progression free survival. Integrative analysis with transcriptomic data from the same samples revealed that only 10% of the CN gains and 17% of the CN loss regions showed concordance between SCNA and expression levels. Similarly, at the gene level, higher concordance between SCNAs and expression change was observed in CN deletions compared to CN amplifications (11% vs 4.2%), suggesting other regulatory mechanisms involved. Interestingly, some of the genes showing high correlation between SCNA and gene expression were previously known for their involvement in cancer such as MYC and CD44. For each paired sample pre/post or post/post from the same patient, we computed a heterogeneity score (HS) based on SCNA calling using as two parameters, identical type of event called and 70% reciprocal overlap. We found high temporal intra-tumor heterogeneity in our cohort with a mean value of HS = 0.84 (range: 0.47-0.98). As expected, we observed more heterogeneity when comparing intra-patient inter-tumors heterogeneity (mean = 0.89, range: 0.77-0.95). Interestingly, the intrinsically resistant lesion had a lower score, and pre/post samples from the same or different lesion having the same response to treatment were less heterogeneous. This implies that acquisition of resistance correlates with an increase in genomic changes. Conclusion: Overall, we showed that liver metastasis and primary tumors from mCRC patients have similar SCNA profiles. From a technical perspective, we concluded that the use of WES data to identify genes located in SCNAs (gain and loss) is comparable to high-density SNP array. From a clinical point of view, we showed that approximately 10% of the genes affected by SCNA showed concordant changes in expression and therefore the use of CN results may not be suitable for making therapeutic decision. Furthermore, the high intra-tumor heterogeneity observed following treatment exposure highlights the importance of post-treatment biopsies to identify and understand mechanisms of mCRC resistance.