Publication highlights

The priming signals in sterile chronic inflammatory diseases remained elusive. Moreover, NETs were mostly thought to serve as an antimicrobial defence mechanism. This work showed that NETs are proinflammatory and provide the priming signals for inflammation in atherosclerosis. It has important implications for our understanding of the mechanisms driving many inflammatory conditions and the important amplification mechanisms involving neutrophil-macrophage crosstalk.

The paper was a broad collaboration with a team from one of our Partner Institutions and others, and illustrates how our learning from insights in the PKC field, here concerning kinase nucleotide pocket occupation, can impact our understanding of the broader kinome. Specifically the work demonstrates that the pseudokinase HER3 which is upregulated in cancer and drug resistance settings, undergoes essential nucleotide pocket occupation dependent changes in conformation to drive HER2 partner dependent signalling. Of importance clinically, the paper offers a route to small molecule-based intervention and also raises questions of inhibitor liability associated with HER3.

The paper unravels the cell cycle dependent input to PKCe engagement and its proximal action through AuroraB. The non-apoptotic M-Phase role of caspase7 in cleaving a chromatin-associated pool of PKCe, alongside the site switching mechanism that plays out in the control of Topo2A by AuroraB are unusual and distinctive features of this cell cycle programme. The mechanistic insights into this transformation-associated pathway provide a specific steer to intervention oppportunities in cancer.

We demonstrated aberrant intron retention in ALS-causing mutations. This is the first description of abnormal intron retention in ALS. The most significantly retained intron in is the SFPQ transcript, which 'drags' SFPQ protein out of the nucleus. SFPQ nuclear loss is a new universal molecular hallmark of ALS across iPSC, mouse models and in sporadic ALS post-mortem tissue.

This paper demonstrates the power of neural networks in deconvoluting complex biological data. We developed an easy-to-use integrated software suite, DIA-NN, that exploits deep neural networks and new quantification and signal correction strategies for the processing of data-independent acquisition (DIA) proteomics experiments. DIA-NN improves the identification and quantification performance in conventional DIA proteomic applications, and is particularly beneficial for high-throughput applications, as it is fast and enables deep and confident proteome coverage when used in combination with fast chromatographic methods.

Point-of-care diagnostic classifiers for COVID-19 are urgently required. Here, we present a platform for ultra-high-throughput serum and plasma proteomics that can be implemented in regulated clinical laboratories. We use our platform to identify 27 potential biomarkers that are differentially expressed depending on the WHO severity grade of COVID-19. They include complement factors, the coagulation system, inflammation modulators, and pro-inflammatory factors upstream and downstream of interleukin 6. All protocols and software for implementing our approach are freely available. This work supports the development of routine proteomic assays to aid clinical decision making and generate hypotheses about potential COVID-19 therapeutic targets.

This is the first paper from my lab. We showed that layer 5 pyramidal neurons, the main cell type in the cortex, are functionally more diverse than previously thought. This has wide-ranging implications for the modular organisation and cortex and for computational capabilities. Furthermore, using numerical modelling, we discovered how the shape of neurons governs their computational ability, a simple, yet very powerful finding.

The paper establishes isoform specificity of the action of Hypoxia Inducible Factors in specific physiological control mechanisms; specifically the non-redundant role of HIF2 in ventilatory acclimatisation to sustained hypoxia. It also establishes that pharmaceutical antagonism of HIF2 using agents which are undergoing trials in clinical renal cancer have the ability to disrupt normal human ventilatory control.

In this paper we showed that cDC1 recruitment and infiltration in several mouse tumour models depends on the chemokines CCL5 and XCL1 produced by NK cells. In human cancers, CCL5/XCL chemokine transcripts correlate with gene signatures for NK cells and cDC1 and predict overall survival in melanoma, head and neck cancer, breast cancer and lung adenocarcinoma. Therefore, our data uncovered a mechanism for cDC1 recruitment into tumours that is translatable to humans and cancer patient survival.

In this paper, we uncovered a potent mechanism of cancer immune evasion, namely cyclooxygenase (COX)-dependent secretion of prostaglandin E2 (PGE2) by tumour cells. We further showed that the growth of PGE2-secreting tumours in mice can be reversed by a combination of checkpoint blockade immunotherapy and COX inhibitors, suggesting that COX inhibition might be a useful addition to both conventional and immune-based therapy of cancer. This paper led to seven clinical trials worldwide to test combinations of prostaglandin E2 inhibition with checkpoint blockade cancer therapies.

In collaboration with GSK and the Crick-GSK LInkLabs we selected single-domain antibodies (dAbs) based on a human scaffold that recognise the catalytic domain of HOIP, a subunit of the multi-component E3 ligase LUBAC. We used these dAbs to interrogate the ubiquitin transfer mechanism of HOIP, and as crystallisation chaperones to crystallise a HOIP RBR/dAb complex. This complex now serves as a robust platform for soaking of ligands that target the active site cysteine of HOIP, thereby providing easy access to structure-based ligand design for this important class of E3 ligases.

The influenza HA is one of two glycoproteins on the surface of influenza virus and mediates receptor binding and membrane fusion during viral entry.In order to understand the function of HA in influenza infectivity it is necessary to understand the mechanism of endocytosis. It has previously been established that endocytosis involves a large conformational rearrangement of the HA protein that can be triggered by a change in pH, revealed by structures of initial and final states. Here, we directly image structural transformations in the HA at the pH of membrane fusion and solve the structure of three structural intermediates including a 150 Å-long triple-helical coiled coil of the HA2 transmembrane subunit. This was a long sought-after result and showed new, surprising concerted conformational rearrangements important to the membrane fusion mechanism.

In this study, we used our bank of patient-dervied stromal fibroblasts to ask why some fibroblasts generate highly aligned extra-cellular matrices and other do not. We were able to show how cell migration and cell-cell collisions can dictate the patterns formed by fibroblasts, and that furthermore, the higher order organisation of fibroblasts and matrix is associated with millimetre scale contraction of reconstituted tissues and cancer invasion. The quantitative tool developed during the course of this work and a related study is now being tested for its prognostic value in simple histological stains of breast and prostate cancers.

We set up a complex model for lung alveoli by co-culturing lung fibroblasts and alveolar epithelial type I and type II cells on a gas permeable support, with the expectation that the fibroblasts would strongly influence the behaviour of cancer cells introduced into the system. However, we discovered that the largest effect came from the alveolar epithelial cells, and we then used a range of approaches to delineate the signalling mechanisms involved. This work, together with a concomitant study from the Malanchi group, established the role of epithelial cells in the tumour microenvironment of indolent and micro-metastases.

This work shows why stromal fibroblasts are an important source of inflammatory modulators in tumours. We show fibroblasts can respond to cGAMP produced by cancer cells, but only when the two cell types are in direct contact. This in turn promotes the STING and IRF3 dependent expression of interferon beta and various chemokines. The subsequent up-regulation of interferon-stimulated gene expression undermines the efficacy of oncolytic viruses. We propose the requirement for direct contact represents a ‘tissue level’ mechanism for triggering this response specifically in the context of tissue damage, as in healthy tissue, the basement membrane precludes such interactions.