Hannon Group

Small RNAs and chromatin biology

Transposons form substantial fractions of most eukaryotic genomes. Their potentially deleterious impact on host fitness has driven the evolution of transposon control mechanisms, whose function is critical in animal germ cells. The inability to silence even a single element in Drosophila is sufficient to cause complete sterility. However, the relationship between transposons and their hosts is complex. Transposons have been co-opted to provide critical regulatory elements during development and underlie telomere maintenance in numerous species.

The piRNA pathway is a critical transposon control mechanism, vital for germ cell integrity and fertility throughout the animal kingdom. Though we have a general outline of how the pathway functions, we still have a tremendous amount to learn about many aspects of piRNA biology. We use Drosophila as a model system to deepen our mechanistic understanding of piRNA biology, drawing upon genetics, biochemistry, molecular and structural biology, high resolution and live-cell imaging, as well as computational and evolutionary biology.

As part of this research programme, we seek to understand (1) how genomic loci are defined as sources of piRNAs and how their products are fated for processing, (2) how the organization of the piRNA biogenesis machinery on the surface of mitochondria enables processing of precursor transcripts, (3) how Piwi-piRNA complexes direct co-transcriptional silencing of target loci, and (4) whether the piRNA pathway shows spatio-temporal variation in its function during different stages of development.

Early breast cancer

Ductal carcinoma in situ (DCIS) is often referred to as early-stage breast cancer. These abnormal cells are localized to the milk ducts, and as they are technically still external to the body, they are not considered an invasive cancer. However, DCIS can progress to invasive ductal carcinoma (IDC), where cells have broken out of the duct and begun to invade the breast tissue, developing into one of many subtypes of breast cancer. One of the major challenges that we are addressing is identifying what causes some women to develop IDC whereas others do not, and how best to treat women diagnosed with DCIS to avoid over treatment (Rebbeck et al., 2022). We are using a combination of laser capture microscopy, to isolate small, specific areas of breast tissue with low input RNA-seq to look for shared and distinct traits in this disease.

Aside from well-known genetic factors, what determines susceptibility to breast cancer development is still an unknown. Using a combination of approaches involving imaging, low input RNA sequencing, lineage tracing and genetic manipulation we are investigating the very early initiating events and processes that occur in response to damage and how this may differ in cells that are more, or less, vulnerable to oncogenic transformation. We are using the protective benefits of pregnancy, an evolutionary conserved phenomenon, to understand these very early initiation events with the goal to find new dependencies to target.

Tumour heterogeneity

Motivated by the importance of tumour heterogeneity to patient outcomes, but a lack of models which functionally interrogate the underlying biology, we have developed strategies to study heterogeneity in animal models of cancer.

The initial studies using DNA barcoding strategies uncovered unexpected roles for vasculogenic mimicry (VM) (Wagenblast et al., 2015) and asparagine bioavailability (Knott et al., 2018) in different stages of metastasis. These observations also inspired the development of WILD-seq to determine how tumour heterogeneity impacts therapeutic response in vivo using adaptations to our barcoding approach that facilitate simultaneous tracking of clonal lineage and gene expression using single cell RNA-sequencing (Wild et al., 2022). A major finding of this work was the identification of a metabolic vulnerability of chemotherapy resistant cells, which can be targeted therapeutically.

Ongoing work in the lab seeks to understand the role of metabolism more broadly in drug resistance and tumour progression. We are also expanding the reach of WILD-seq to diverse tumour types and model systems, including patient-derived cell and xenograft models, as well as adding new capabilities on top of lineage tracing and transcriptomics.

One functional output of tumour heterogeneity that we continue to study is vasculogenic mimicry (VM), a process by which tumours form pseudo blood vessels lined with tumour cells that have acquired endothelial-like properties. Building on our prior observations of VM driving metastasis, we recently identified FOXC2 as a master transcriptional regulator of VM (Cannell et al., 2023) that promotes ectopic endothelial gene expression in tumour cells and resistance to anti-angiogenic therapies, pointing to potential avenues to augment response to these agents. Ongoing work seeks to identify biomarkers of VM in patient-relevant models as well as understanding the complex interplay between VM, angiogenesis and hypoxia.

Technology development

The lab has always pursued technology development when existing approaches are insufficient to answer critical questions. Current technology development projects involve novel clonal tracking techniques, new and improved chromatin assays, spatial omics method development and nanobody screening platforms.

Spatial biology

Through a Cancer Grand Challenges award we have made significant investment in spatial biology developing approaches to map tumours in 3 dimensions. This laid the groundwork for a Wellcome LEAP project which seeks to understand tissue state transitions in breast cancer upon therapy.

Radiation biology

As part of the CRUK Radnet programme we are using functional genomics and clonal tracking technologies to identify ways to improve response to radiotherapy.