Publication highlights

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.

Immune cells such as type 1 conventional dendritic cells (cDC1) can “eat” (phagocytose) dead tumour or virally-infected cells and present associated antigens to CD8+ T cells to elicit a tumour- or virus-specific cytotoxic T cell response. How antigens from the debris get presented on MHC class I (MHC-I) molecules on cDC1 has long been puzzling as MHC-I normally presents antigens found in the cytosol. This paper shows that cDC1 use the DNGR-1 receptor to induce phagosomal rupture, releasing the debris-associated antigens into the cytosol. These findings have implications for our understanding and manipulation of immunity to infection and cancer.

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.

This manuscript was the first demonstration that irreversible commitment to cellular differentiation during early development happens unexpectedly early. The paper reflects our interdisciplinary work, combining single cell imaging, mathematical modelling and -omics approaches. We discovered a new class of genes which we termed early commitment genes (ECG) that are responsible for the pluripotency-to-differentiation transition. It was also our first manuscript in developmental biology, a new field outside of our lab’s expertise.

Research from the Scaffidi lab has developed a new strategy to identify cancer-specific vulnerabilities. They identified a group of proteins, called the male-specific lethal (MSL) acetyltransferase complex, which could be used to increase chromosomal instability in cancer cells without inducing severe adverse effects in normal tissues.

Neuroprosthetics and neuroscience research alike are limited by the bandwidth of neural recording. At the same time, ever-more powerful silicon-based technology is ubiquitous in our phones, tablets and computers. Here we showed that progress in neural recording can be coupled to this by fusing bundles of microwires to pixel array chips, lifting silicon technology to the third dimension for deep brain recording.

The first publication from our group at the Crick comprises the development of a precision tool to understand O-GalNAc glycosylation, one of the most abundant and disease-relevant types of glycans. We apply the technique to run state-of-the-art methods of biology, including chemical glycoproteomics with the Proteomics STP and a genome-wise CRISPR screen with collaborators from Stanford. We also collaborate in-house with Vivian Li to apply the probe to imaging intestinal organoids.

In this paper, led by the Sanger Institute, we characterised global human genetic diversity in whole-genomes at a greater scale and with broader diversity than before. We documented complex divergence between modern humans and archaic groups such as Neanderthals. Lead author Anders Bergström started work on the project during PhD studies at the Sanger, and continued it with my input as a Crick postdoc from April 2018 until publication in 2020.

This first research paper led by our lab presents the first large-scale study of ancient genomes from early domestic dogs. We show that dogs were domesticated prior to the agricultural transition, with a dynamic history that includes collapse of early genetic diversity of dogs in Europe, and a complex evolution of genetic adaptation to starch rich diets.

A new study from the Swanton lab identified genetic changes in tumours which could be used to predict if immunotherapy drugs would be effective in individual patients.

We demonstrate species-specific remodelling of red blood cells by the most virulent malaria-causing parasite, mediated by a species-specific expansion of an exported kinase family. Systematic deletion of all 20 members and quantitative phosphoproteomics identifies the kinase targets and supports their role in pathogenesis.

Unlike kinases, PPP-family phosphatases such as PP1 have little intrinsic specificity. PP1 acts in partnership with over 200 different PP1-interacting proteins, but it has remained unclear how they might confer sequence-specificity on PP1. We used proteomics to identify dozens of candidate Phactr1/PP1 substrates, and used structural and biochemical approaches to show that the Phactr1/PP1 holoenzyme is sequence-specific. Phactr1 binding reshapes the PP1 hydrophobic groove, thereby creating a novel composite hydrophobic surface for substrate recognition. This study explains how cofactors can enhance the reactivity of PP1 toward specific substrates, and suggests a way forward for the development of PP1 holoenzyme-specific inhibitors.