Abstract A15: Generation of clonal replica tumors to interrogate complexity of human cancer in vivo
Authors: Seth Sahil , Li Chieh-Yuan , Corti Denise , Loponte Sara , Ho I-Lin , Poggetto Edoardo Del , Peoples Michael , Bristow Christopher , Marszalek Joseph , Heffernan Timothy , Genovese Giannicola , Draetta Giulio , Carugo Alessandro , Viale Andrea 
Published: May 2018

Tumor evolution and adaptation, especially in response to therapy, are well-established concepts in clinical oncology and a major causes of treatment failure. The inability of current experimental models, including genetically engineered mouse models, to inform on the breadth of functional heterogeneity within human tumors has substantially limited our understanding of the evolution of tumor architecture under perturbations such as pharmacologic treatments with a profound negative impact on cancer drug discovery research, where drug efficacy continues to be measured in terms of tumor volume.

To address this technologic gap, we developed a new approach based on clonal tracking to model human tumors in vivo supporting the dissection of functional heterogeneity at the clonal level as well as the study of tumor evolution and clonal dynamics in response to external perturbations in real time. Lentivirus-based systems have been extensively used as a tool to investigate the clonal dynamics and tumor cell heterogeneities of solid tumors, but they have been limited by a lack of sensitivity and the impossibility of tracking identical clones in different animals. Using a revised strategy to barcode patient-derived pancreatic cancer cells coupled with deep-sequencing analysis, we created PDX cohorts harboring Clonal Replica Tumors (hereafter CRTs), in which all mice bear human tumors maintained by the same clones. Because they are maintained by thousands of common clones and are virtually identical, CRTs enable the evaluation of single- and combined-therapy approaches as well as mechanistic studies where the evolution and dynamics of single clones can be tracked with extremely high precision to monitor the contribution of even low-represented clones to tumor growth and relapse. Since functional heterogeneity in tumors can only be fully appreciated upon different perturbations, the availability of large cohorts of animals bearing clonally identical tumors makes CRTs a critical instrument to investigate tumor complexity in vivo. Further, another advancement supported by the CRT platform is the isolation and expansion of any clone of interest identified in vivo through bioinformatics analysis. High-throughput isolation and functional characterization of virtually every clonal population of cells within a CRT provides an invaluable tool to identify exploitable vulnerabilities of resistant clones.

In conclusion, CRTs represent an innovative approach to dissect the complexity of human tumors at an unprecedented level of resolution, enabling the investigation of mechanisms of tumor evolution and drug resistance. Understanding clonal dynamics, tumor composition, and adaptive mechanisms, and how these factors may influence treatment response, is essential to reach new horizons in cancer care.

Citation Format: Sahil Seth, Chieh-Yuan Li, Denise Corti, Sara Loponte, I-Lin Ho, Edoardo Del Poggetto, Michael Peoples, Christopher Bristow, Joseph Marszalek, Timothy Heffernan, Giannicola Genovese, Giulio Draetta, Alessandro Carugo, Andrea Viale. Generation of clonal replica tumors to interrogate complexity of human cancer in vivo [abstract]. In: Proceedings of the AACR Special Conference: Advances in Modeling Cancer in Mice: Technology, Biology, and Beyond; 2017 Sep 24-27; Orlando, Florida. Philadelphia (PA): AACR; Cancer Res 2018;78(10 Suppl):Abstract nr A15.