Background
The reactivation of anti-tumour responses in CD8+T-cells via PD1-targeted checkpoint inhibition is gaining widespread acceptance for treatment of lung cancer. However, patient responses are widely variable and accurate predictors of durable responses are lacking. In addition to expressing PD1 ligands, tumours deploy a host of molecular strategies to evade immune detection or to suppress immune-mediated cytotoxicy. The dynamics of these immune evasion strategies are poorly understood and model systems to enable their investigation in situ have heretofore been lacking.
The Murphy lab has recently developed a suite of genetically engineered mouse models (GEMMs) of lung cancer to begin to address this knowledge gap. The models are based on sporadic activation of conditional alleles of G12-mutant KRas along with the genome editing enzyme Apobec3b, which drives immune visibility through C->T mutagenesis of protein-coding sequences. Tumour progression is accelerated via inclusion of 1 of 3 clinically relevant co-operating oncogenic alleles: Rosa26-lsl-MYC; P53fl/fl; or Stk11fl/fl: yielding KAM; KAP; & KAS models, respectively. The 3 models show very different anti-tumour immune responses: The KAM and KAP models exhibit strongly increased survival over non-immunogenic counterparts lacking the Apobec3b allele (KM & KP) whereas the KAS model does not (compared with KS). Depletion of CD8 cells negates the survival benefit of KAM mice compared to KMs, implicating anti-tumour immunity as the source of extended survival. Notably, in lung cancer patients, p53 mutation is associated with increased sensitivity to PD1 checkpoint blockade, whereas loss of Stk11 (encoding LKB1) is linked to resistance – our GEMMs thus faithfully capture this key clinical variation.
Temporal analysis of tumour progression in the KAM mice shows a highly dynamic immune response characterized by strong tumour infiltration by T cells (both CD8 and CD4) at 8 weeks after tumour initiation but complete loss of this infiltration within an additional 4 weeks. PD1 blockade fails to restore infiltrating T cells despite widespread tumour expression of PD-L1, suggesting that additional factors are required for T cell re-engagement.
This project will use newly developed Nanostring GeoMX spatial transcriptomic analysis to investigate changes in gene expression occurring in key cell populations (tumour cells, T cell subsets, tumour-associated Macs, cancer-associated fibroblasts) over time and across the 3 model systems. Comparison with human datasets will identify cross-species conservation of immune evasion mechanisms to enable hypothesis testing and functional validation downstream within the context of an expanded research programme, supported by the MRC-funded National Mouse Genetics Network Cancer Cluster (or other means). Importantly, GeoMX technology is fully compatible with formalin fixed paraffin-embedded tissue, allowing the project to proceed with existing tissue collections already assembled by the Murphy lab. Access to the GeoMX platform will be provided through collaborations with Nigel Jamieson.
Aims
1) To determine the transcriptomic phenotypes of spatially distinct (eg. tumour-infiltrating versus tumour-excluded) T cell sub-populations across genotypes and over time.
2) To similarly investigate tumour and stromal cell transcriptional differences across genotypes and over time. This will enable spatio-temporal mapping of tumour and stroma-derived factors with cognate receptors and phenotypes of T cell sub-populations.
3) To interrogate available human lung cancer datasets (TCGA, TRACERx) for identification of conserved immune modulators that correlate with immune evasion/suppression in GEMMs.
Training outcomes
1) Direct experience with multiplex IHC required for identification of cell populations of interest and their spatial distribution in and around lung tumours
2) Up-to-the-minute training in bioinformatics, Bioconductor/R-based computational biology skillsets and Nanostring GeoMX analytical tools required for definitive assignment of transcriptomic phenotypes to specific cell subpopulations
3) Cutting-edge insight into dynamic ligand/receptor relationships and downstream signaling cascades differentially associated with active or suppressed anti-tumour immunity in lung cancer
APPLICATION INSTRUCTIONS:
This MRC programme is joint between the Universities of Edinburgh and Glasgow. You will be registered at the host institution of the primary supervisor detailed in your project selection.
All applications should be made via the University of Edinburgh, irrespective of project location. For those applying to a University of Glasgow project, your application along with any supporting documents will be shared with University of Glasgow.
http://www.ed.ac.uk/studying/postgraduate/degrees/index.php?r=site/view&id=919
Please note, you must apply to one of the projects and you must contact the primary supervisor prior to making your application. Additional information on the application process is available from the link above.
For more information about Precision Medicine visit:
http://www.ed.ac.uk/usher/precision-medicine
Application Enquiries:
Susan Mitchell/Maree Hardie
[Email Address Removed]
https://www.ed.ac.uk/usher/precision-medicine/app-process-eligibility-criteria
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