WP2. Allan Balmain, UCSF, USA.

Mouse models of tumour initiation and promotion.

The Balmain lab has accumulated a tissue bank of >4000 samples representing all stages of carcinogenesis from a genetically heterogeneous mouse population that mimics human diversity. They will work with WP6, WP7 and WP8 to investigate the mechanisms by which known or suspected environmental promoting factors function at the single cell level to activate cells with pre-existing critical driver mutations.

WP3. Marc Gunter, ICL, United Kingdom Impact of changes in cancer risk factors on the molecular architecture of normal tissues.

The Gunter lab will conduct human intervention studies to investigate the impact of changes in two important cancer risk factors (obesity and smoking) on normal tissue biology. This will involve collection of serial biopsies from volunteers undergoing lifestyle modifications related to weight loss and smoking cessation. His group will provide fresh tissue samples for organoid culture (WP8), and for analysis of genetic, transcriptomic and proteomic changes with WP4 and WP5.

WP4. Emma Lundberg, KTH, Sweden. Multi-omics imaging of human tissue samples.

Dr Lundberg is co-Director of the Human Protein Atlas Program, and will use their proteome-wide collection of antibodies and multiplexed imaging to study proteome differences of normal and tumour tissue samples from WP1, WP2 and WP3, with a focus on cell cycle, inflammatory and stem cell markers. She will develop new assays to test hypotheses emerging from the functional screens from mouse or organoid models of tumour promotion. She will also perform in situ sequencing to detect mutations in single cells. This work will be performed in the new Spatial Omics facility at SciLifeLab that she is co-leading with Prof. Mats Nilsson.

WP5. Nuria Lopez-Bigas, IRB, Barcelona, Spain. Deriving molecular signatures of cancer promotion.

The Lopez-Bigas lab has developed computational methods to identify cancer genes, driver mutations and mutational signatures of cancer treatments. She will investigate the effects of cancer therapeutics on clonal selection of cells in normal hematopoietic tissue that carry pre-existing cancer driver mutations (with WP1, WP2, WP3 and WP4). Her lab will lead the bulk total RNA, duplex and single cell sequencing of human samples, and will manage the joint data repository from all work packages. This work package will deliver innovative computational technologies for the joint analysis of mutations, RNA and protein expression, using molecular evolution and machine learning models.

WP6. Chris Counter, Duke University, USA. Exploiting genetically engineered mouse models to identify promoting events and Promolytics targets.

The Counter laboratory employs genetically engineered mouse models to study how oncogenic mutations arise and initiate tumorigenesis. He will exploit novel oncogenic murine alleles that promote proliferation of normal cells in vivo. This will be achieved by determining the effects of environmental, metabolic, inflammatory, and genetic stresses, by ultra-sensitive sequencing of driver mutations, single-cell transcriptomics and proximity labelling, on in vivo promotion from the dormant to tumorigenic state (with WP2, WP4, and WP7). This work will identify mechanisms of promoter action, potential biomarkers, and Promolytic targets.

WP7. Luke Gilbert, UCSF, USA. CRISPR functional genomics screens for analysis of gene targets that promote or restrain the activity of environmental tumour promoters.

The Gilbert lab has developed genome-wide CRISPR/Cas functional genomics screens for identification of the direct targets and pathways activated by cancer drugs or metabolic intermediates. He will develop genome-scale CRISPRi/a, CRISPRon/off and Perturb-seq screening tools for genetic interaction mapping and identification of the exact molecular targets of agents known to act as promoters or anti-promoting factors. He will work extensively with WP2 and WP8.

WP8. Calvin Kuo, Stanford, USA. Human organoids for analysis of mutation selection in human cancers.

The Kuo lab at Stanford has generated novel organoid systems that allow en bloc culture of human epithelial cells together with immune cells and other stromal constituents. This holistic culture method has been used to transform normal tissue to cancer by introduction of mutations in oncogenes and tumour suppressors, as well as to model immune checkpoint inhibition. He will collaborate with WP4 on spatial imaging, with WP3 on organoid generation from human interventions, and with WP2, WP6 and WP7 on carcinogen and tumour promoter exposure and high throughput functional genomics CRISPR screens.