Publication highlights

This paper, and another published the same year (Gentsch GE et al. (2019) iScience, 16, 485-498), analysed gene activation in the early Xenopus embryo and asked what causes cells to become competent to respond to Wnt, Nodal and BMP signalling. We identified regulatory DNA sequences associated with early-expressed genes, and deduced from them that the maternal pluripotency factors Pou5f3 and Sox3 remodel compacted chromatin before the onset of inductive signalling. This remodelling includes the opening and marking of thousands of regulatory elements, extensive chromatin looping, and the co-recruitment of signal-mediating transcription factors. Our work informs our understanding of how pluripotent stem cells interpret inductive signals.

This paper demonstrates a cell intrinsic role for AHR in intestinal stem cells. AHR deficiency in intestinal epithelium causes dysregulation of the Wnt pathway, overproliferation of crypt stem cells and impaired epithelial differentiation following injury, culminating in tumorigenesis.

SCAF4 and SCAF8 were isolated in the mid-90s as proteins that bind the RNAPII C-terminal repeat domain (CTD) but little or nothing was known about their cellular function. This paper describes their function as the first eukaryotic mRNA anti-terminator proteins. Together, SCAF4 and SCAF8 coordinate the transition between elongation and termination, ensuring correct polyA site selection and RNAPII transcriptional termination in human cells.

We analysed the first 100 TRACERx patients to unravel how escape from adaptive immunity occurs in non-small cell lung cancer. Immune ‘hot’ tumours, characterised by a brisk lymphoid infiltrate, had been selected for HLA LOH or deleterious mutations in the antigen presentation machinery. In contrast immune ‘cold’ tumours with an absent lymphoid infiltrate had lost clonal neoantigens through DNA copy number loss events. We found evidence for negative selection of subclones early in tumour evolution harbouring neoantigens in genes essential for non-small cell lung cancer viability. Patient outcome was worse for tumours with evidence of an immune evasion event.

This paper represents an important step forward in our understanding of ATG9, the only multi-spanning autophagy protein and a major focus of my lab’s current work. Here we discovered the composition of the ATG9 vesicle and uncovered an important role for a protein which can induce membrane curvature and a lipid kinase. I chose this work as it has provided us with important insights into the function of ATG9A.

This paper follows on from our work on WAC and the role of centrosomes in autophagy. We discovered an important centriolar protein has a specific motif (LIR motif) enabling its binding to a key autophagy protein. In collaborative work, we determined the structure and the important features of the LIR motif, and extended the findings to a group of autophagy proteins to provide an important advance on our understanding of selective autophagy. I chose this work because it is a tour de force of structure and biochemistry and a very substantial collaboration between Structural Biology and Peptide Chemistry STPs

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.

The MRTF-SRF and the YAP-TEAD transcriptional regulatory networks both respond to extracellular signals and mechanical stimuli: the MRTFs are controlled directly by G-actin, while YAP activity is somehow potentiated by F-actin. Cancer-associated fibroblasts play an important pro-invasive role in stimulating cancer progression, and previous studies have shown that this involves YAP-TEAD signalling. This paper shows that CAFs also exhibit mechanically-dependent MRTF activation, which is also required for their contractile and pro-invasive activity. The two pathways are mutually dependent, requiring recruitment of MRTF and YAP to DNA via their respective DNA-binding partners, and reflecting their ability to control cytoskeletal gene expression.

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.

This paper shows that the ArhGAP9/12/15/27 and ArhGAP32/33 families of rhoGAPs are RPEL proteins whose activity is coupled to G-actin concentration. G-actin forms a 1:1 complex with these ArhGAPs, interacting with an RPEL motif located between the PH and GAP domains, thereby inhibiting their GAP activity. Mutations that block G-actin binding exhibit elevated GAP activity towards their substrate GTPases Rac and Cdc42. Strikingly, treatment of cells with drugs enhancing or inhibiting G-actin/ArhGAP interaction has corresponding effects on Rac GTP loading. These results establish a novel homeostatic feedback loop, in which ArhGAP12-family (and presumably ArhGAP32-family) GAP activity increases when G-actin levels become limiting.

Fs-indels that escape the nonsense-mediated decay (NMD) pathway, can elicit anti-tumor immune responses, especially those the highly elongated neo open reading frames. NMD-escape fs-indels represent an attractive target for biomarker optimisation and immunotherapy design.

This is the first prospective study in any cancer type that resolved the origin of the metastasising clone in the primary tumour characterising its genetic features and uncovering high risk events that confer risk of death.

This is the largest genomic study ever to be conducted in renal cell cancer and the first to show how evolutionary features of the tumour impact the clinical phenotype. Patent arising.

Aneuploidy is remarkably common in human embryos, and most often results from defective recombination in the maternal germ line. There is therefore great interest in determining mechanisms that eliminate recombination-defective oocytes, and how defects in these mechanisms cause chromosome abnormalities in offspring. In this study, we showed that recombination-defective oocytes are eliminated via the BCL-2 pathway components Puma, Noxa and Bax. Our findings raised the possibility that allelic variants of the BCL-2 pathway could influence the risk of embryonic aneuploidy.

Single-cell RNA sequencing of embryos can resolve the transcriptional landscape of development at unprecedented resolution, but such studies of mammalian embryos had focused exclusively on placental species. Analysis of mammalian outgroups might identify deeply-conserved lineage specification and pluripotency factors. In this study, we performed the first single-cell RNA-sequencing in a marsupial, which diverged from eutherians 160 million years ago. We identified many critical developmental regulators pre-dating the placental-marsupial separation which are thus likely to be especially important for embryogenesis. Our study has important implications for understanding the high rates of miscarriage in humans and for developing improved conditions for assisted reproduction.

In this study we showed that the Dp1Tyb mouse model of DS has locomotor defects, mapped the causative genes to a 25-gene region and identified that Dyrk1a is one of these. Furthermore, we found an unexpected progressive loss of motor neurons in these mice and showed that a similar loss is seen in humans with DS.

Building on our successful biochemical reconstitution of topological cohesin loading onto DNA, we completed the reconstitution of both dynamic loading as well as unloading. We realised that both loading and unloading follow a very similar trajectory through sequential ATPase and kleisin gates, only one of which can be open at any one time. This formed the basis for our unified DNA passage proposal both into and out of the ring.

Cohesin is a ring-shaped protein complex that topologically entraps DNA to fulfil key functions in chromosome architecture. In a collaborative and multidisciplinary approach, we used cryo-EM, biochemical and biophysical techniques to describe how ATP-fuelled structural changes of the cohesin complex drive the DNA entry reaction into the cohesin ring. This solves one of the outstanding riddles in molecular biology.

One of the major surprises of our iCLIP studies was the major role that transposable elements play as hubs for RNP assembly. Here, we uncover multiple roles of LINEs in RNP assembly, and show how this helps to create repressive environment in introns, while also driving the evolution of new tissue-specific exons.

We showed that active YAP1 in radial glia derived neural precursor cells induces ependymoma-like tumours in mice. We demonstrated that YAP1 is necessary and sufficient using mouse models. We found that transcription coactivator HOPX, a factor consistently suppressed in malignancies, is highly expressed in our mouse models and in YAP1-fusion human ependymoma. HOPX differentiates YAP1-fusion subtype from the highly malignant RELA-fusion human ependymomas. This supports the notion for subtype-specific care for ependymoma.