Background

The genomics revolution has offered unprecedented insight in to the pathways that are dysregulated in cancer. A recurrent observation from these studies is that certain mutations are frequently associated with malignancies in specific tissues but are virtually absent from others.

Put another way, tissues show strong preference for different palettes of driver mutations.

How and why this tropism exists remains largely unknown, but it strongly suggests that bottlenecks to tumorigenesis are tissue specific and that the processing of information conferred by driver mutations is dependent on the molecular milieu.

Understanding the mechanisms that underpin the way different tissues respond to mutations is an issue which – if tackled – could transform the way cancers are managed, from prevention through to treatment.

At the heart of the issue lies a fundamental question; what gives a tissue its identity?

Tissue-specific epigenetic landscapes

Stephen Elledge and his team believe that epigenetic architecture assembled during development creates a tissue-specific molecular circuitry which dictates how the information from oncogenic drivers is processed and responded to. As such, they posit that the epigenetic landscape of the cell will confer targetable tissue-specific vulnerabilities.

Cancer Grand Challenges has enabled him to assemble an international constellation of world-leading tumour biologists, geneticists, computational biologists and more to test this hypothesis.

The scale of funding afforded by Cancer Grand Challenges has allowed him to devise an ambitious plan – called SPECIFICANCER – to breach the boundaries of traditional, single investigator-led approaches, and create synergy on an unparalleled scale.

Their overall approach is to integrate data from functional genomic screens, in vivo models and cancer genomics studies to build rich tissue-specific datasets to interrogate why specific responses are evoked following oncogenic mutation.

Permissive versus non-permissive tissues

To flush out genes involved in establishing the cancer phenotype across cell types, the team will embark on a suite of unbiased screens – the largest ever performed in healthy tissue. Oncogenic driver libraries, together with ORF and CRISPR libraries will be used to identify genes driving proliferation and survival in eight different cell types taken from seven (brain, breast, colon, kidney, lung, pancreas and skin) organs.

Promising hits will be further scrutinised with organoid panels – which are amenable to high-throughput oncogenic library screens – allowing the team to validate their results in models which more closely mimic the tumour environment.

To unveil the specific molecular constituents of permissive and non-permissive states, the group will next introduce individual oncogenic mutants (KRAS, HRAS, BRAF, EZH2), or knock-out tumour suppressor genes (APC, SETD2 and PRC2) into an array of different tissue types using an inducible CRISPR system.

These isogenic lines will be subjected to exhaustive transcriptomic (RNAseq), proteomic (whole and phospho-proteome) and epigenetic (ChIP seq and ATAC seq) analyses of cell in the presence or absence of each oncogenic insult.

Next, these genetically engineered cells will be used as the basis for the first ever systematic review of synthetic lethality across human tissues – using both ORF and CRISPR libraries – to identify driver-specific lethals that are tissue-selective or promiscuous across different tissue types.

Finally, commonly observed combinations of driver mutations will be introduced into permissive and non-permissive tissues, which will then be subjected to large-scale compound screens to further delineate targetable tissue-specific vulnerabilities.

Together, these experiments will allow the group to discern the ‘ground-state’ for each different cell type and elucidate how this molecular circuitry is perturbed by driver events.

They’ll also allow the team to see whether re-creating this circuitry in non-permissive tissues could drive transformation and importantly, whether short-circuiting these networks might abort or reverse tumorigenesis.

In vivo veritas

The team will next focus efforts on three pathways which display exquisite tissue-specific mutational profiles in cancer: KRAS/MAPK, WNT/β-Catenin and EZH2/PRC2, the latter of which is itself an epigenetic modifier that is frequently mutated in many tumour types.

Using genetically-engineered mouse models, the aim will be to discern the biological consequences of driver mutations in permissive and non-permissive tissues in well-defined, genetically tractable in vivo settings.

Talk to the tissue

Not only will this project reveal novel tissue-specific targets, its findings might also help explain why certain treatments have therapeutic benefit in some tumor types but fail to do so in others.

In recent years, the idea of treating tumours according to their genetic profile rather than their anatomical site has gained significant traction. But while the hypothesis is solid in principle, it has not yet lived up to its promise in the clinic; targeted treatments have shown wildly different effects in different tissue types, even those with identical driver mutations.

Elledge asserts that these disparities are down to the tissue-specific epigenetic ‘ground-state’ and that the project will provide the rationale for a new era of ‘tropo-genetic’ medicine which considers oncogenic mutations, and crucially, the tissue context in which they exist.

When cartography and biology collide

The vast amounts of data generated will integrated to produce functional maps, which will provide – for the first time – a comprehensive and robust way to compare and interrogate tissue-specific networks.

The team hope that the community will be able to use these maps to provide genomics data into deeper biological context and unveil novel therapeutic strategies that are rooted in the biology of tissues.

Wider impact

The team will generate a number of resources – including cells, organoids, genomic libraries and datasets – all which will be made freely available to the wider community.

Elledge’s team is hopeful that the project will establish a new doctrine for the way tumours are approached both in the lab and in the clinic. Although the project focuses on a subset of cancers, it’s easy to see how lessons learned could percolate across disease types, revealing insights into how cancer develops and might be targeted.

But it’s not only cancer research that is likely to be enriched by this work. By offering a tissue-specific lens through which to view cell behaviour, this project has the potential to drive innovation and discovery across the field of metazoan biology. As Elledge himself predicts: “It’s going to make a lot of things possible that weren’t before.”