Publication highlights

Through an analysis of TRACERx, extended from our haplotyping analysis, we developed an algorithm called LOHHLA which infers allele specific copy number aberrations in HLA. We find HLA loss occurs in 40% of early stage lung cancers, usually as a subclonal event, and is permissive for branched evolution associated with expansion of mutations predicted to bind the lost HLA allele.

We demonstrated that mechanical forces and not enzymatic liberation are the physiological mechanism for acquisition of antigens by B cells from live presenting cells. Using DNA-based nanosensors we showed that B cell affinity discrimination is regulated by physical properties of the antigen-presenting cells and identified follicular dendritic cells as a stiff antigen presenting subset that promotes B cell affinity discrimination in germinal centres.

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.

The first pan-tumour study to evaluate the contribution of fremashift mutations to generation of immunogenic peptides and anti-tumour immunity. Patent arising.

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.

Here, we described a technique for reversing infertility in XXY (Klinefelter) and XYY (Jacob) syndrome mice. We showed that reprogramming of fibroblasts from these mice resulted in elimination of the extra sex chromosome, and that resulting XY cells could be converted by in vitro gametogenesis into functional sperm. Reprogramming could also chromosomally correct cells from Down syndrome mice and patients. The work revealed an unexpected role for reprogramming as a form of chromosome therapy.

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.

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.

Transcription factors typically activate transcription by recruiting cofactors, but our data in this paper illustrate a new function. We show that the sequence-specific transcription factor Rap1 prevents regulatory elements from initiating transcription in the divergent direction. We define a novel mechanism for providing directionality towards productive transcription, as Rap1 promotes directionality, at least in part, by directly interfering with transcription initiation in the divergent direction. Our study reveals a new important layer of regulation, describing how genomes restrict the accumulation of aberrant transcripts and ensure productive coding gene expression.

In this paper we show that the ability of cells to survive glutamine depletion depends on aspartate metabolism, which is supported by the aspartate/glutamate transporter SLC1A3. The tumor suppressor p53 is shown to induce the expression of SLC1A3, explaining in part how p53 can help cancer cells survive under glutamine starvation.

The generation of CRISPR-Cas9 GEN1 k/o cell lines (supplemented with MUS81 siRNA) allowed us to develop the first model system to analyse the phenotypes of ‘resolvase-deficient’ human cells. We discovered that recombination intermediates persist until anaphase (despite the presence of the BLM-TopoIII-RMI1-RMI2 dissolvasome) where they form ultra-fine bridges (UFBs). These UFBs represent a new class of ultrafine bridges (we termed them HR-UFBs) distinct from replication stress induced UFBs or centromeric UFBs. HR-UFBs were targeted and processed by PICH/BLM, leading to the formation of ssDNA bridges that were broken at cytokinesis. Loss of GEN1 and MUS81 activity led to synthetic lethality.

First description of the SMX tri-nuclease that resolves recombination intermediates. Composed of SLX1-SLX4, MUS81-EME1 and XPF-ERCC1, the six-subunit complex was purified following baculovirus expression in insect cells. Characterization of the Holliday junction cleavage reaction revealed that the first incision was introduced by SLX1-SLX4, while the second was mediated by MUS81-EME1. We also found that MUS81-EME1 was activated by interaction with the SLX4 scaffold, ensuring that the second cut occurs in concert with SLX1-SLX4’s initial incision. The formation of SMX and activation of MUS81-EME1 provides a mechanistic basis for restriction of SMX activity to the later stages of the cell cycle.