Towards a holistic and mechanistic understanding of tumourigenesis via genetically engineered mouse models Ashna Alladin and Martin Jechlinger Abstract Mouse models have been an invaluable tool to systematically study tumour progression upon expression of an oncogene or knockdown of tumour suppressors in an immune-proficient microenvironment. Today, tractable genetically engineered mouse models (GEMMs) of human disease permit the regu- lation of cancer inducing genes at a given time-point in a tissue specific manner and can be combined with cell type specific marking approaches to follow, isolate and study cells during disease. Organoid cultures of primary cells taken directly from these mice are capable of preserving the original architecture and signalling events within the tumour, allowing in-depth mechanistic analysis. Here we present an overview of com- bined approaches, involving GEMMs that expand on our knowledge obtained from patient material and contribute to our in-depth understanding of human cancer. Addresses EMBL, Cell Biology and Biophysics Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany Corresponding author: Jechlinger, Martin (martin.jechlinger@embl.de) Current Opinion in Systems Biology 2017, 6:74 – 79 This review comes from a themed issue on Systems Biology of Model Organisms (2017) Edited by Jens Nielsen and Kiran Raosaheb Patil For a complete overview see the Issue and the Editorial Available online 7 November 2017 https://doi.org/10.1016/j.coisb.2017.10.004 2452-3100/© 2017 Published by Elsevier Ltd. Keywords Genetically engineered mouse models (GEMMs), Organoid technology, Multi-omic analysis, Intra-vital microscopy, Minimal residual disease. Introduction Despite major advances in diagnostics and treatment options, cancer remains one of the leading causes of morbidity and mortality worldwide. Moreover, the number of new cases is expected to rise by 70% in the next 2 decades [1], emphasizing the need to intensify research efforts on the causes and mechanisms of carcinogenesis. Recent advances in the genomic analysis of human cancers, including single cell sequencing approaches, has led to a much better understanding of tumour evolution and heterogeneity, has aided better classification of cancer subtypes [2] and-in conjunction with sophisticated histological analysis [3]- also helped to shed light on the role of the tumour microenviron- ment. However, large sample numbers have to be ob- tained to analyse vaguely defined human tumour subtypes, confounding lifestyle factors have to be considered and ethical hurdles to be overcome. Further, a mechanistic analysis of tumour progression and ther- apy response is hard to achieve with independent pa- tient samples, since they reflect only a snap shot of these dynamic processes. To this end, mouse models have proved to be an invaluable resource to systematically and reproducibly analyse mechanisms in tumourigenesis [4,5]. Specifically genet- ically engineered mouse models permit us to delineate the cell of origin in lineage tracing approaches and to study as well as visualize the outcome of drug treatment. They also serve as a tool to understand late tumour stages by giving access to minimal residual disease following therapy and homing metastatic cells, both cellular substrates that largely remain elusive in patient samples (see Table 1). Tumour initiation Despite our increased understanding of tumour pro- gression, the initiating and driving cancer cells remain largely uncharacterized, as does their evolution via accumulation of mutations. It is imperative to under- stand contextual evolution of tumours to develop effi- cient therapeutics for the different tumour subpopulations, including tumour re-initiating cells (so called cancer stem cells). Lineage tracing approaches in mouse models are used to elucidate the mechanisms of tumour initiation and pro- gression into pre-neoplastic disease and involve marking a single cell with a label that is transferred to all its progeny and retained stably over time [6,7]. For this, the Cre-loxP system adapted from bacteriophage P1 is widely used. In short, Cre recombinase is expressed under the control of a tissue/cell type-specific promoter and will excise a loxP-STOP-loxP (“floxed” STOP) sequence to activate expression of a reporter gene. Temporal control of Cre activity can be achieved by inducible recombina- tion systems like Cre-ER and Cre-PR fusion proteins. These systems have been carefully developed over the years, both in terms of preventing “leakiness” of Cre- induction [8] and development of robust reporter genes as well as multi-label approaches [9]. Available online at www.sciencedirect.com ScienceDirect Current Opinion in Systems Biology Current Opinion in Systems Biology 2017, 6:74 – 79 www.sciencedirect.com