News and Events
HAB Grant Project
Understanding the link between large artery mechanical properties/forces and brain volumetric changes using UK Biobank longitudinal data.
This project investigates the link between blood vessel health and brain health, focusing on how large artery stiffness (measured as aortic distensibility) may contribute to neurodegenerative changes, including dementia. Using data from the UK Biobank, the study will analyze longitudinal multi-organ imaging and genetic data to explore the causal relationship between aortic stiffness and brain atrophy. The study will also examine mechanical stress in the carotid artery as a potential mediator of these effects. Methods include MRI-based assessments of aortic distensibility and brain structure, carotid ultrasound imaging, and computational fluid dynamics modeling. Additionally, Mendelian Randomization will be used to establish causality between aortic stiffness and brain volume changes. If aortic distensibility is found to play a causal role in brain aging, this could necessitate new therapeutic strategies, as traditional cardiovascular risk reduction methods may not effectively address arterial stiffness and its impact on cognitive decline.
Gonadal sex reversal at single-cell resolution in Znrf3-deficient mice
The role of anti-WNT ZNRF3 is central to determining gonadal fate: XY mice lacking functional ZNRF3 exhibit a highly variable gonadal sex reversal phenotype in the fetal period, characterised by appearance of ovarian tissue. To investigate this sex reversal further, we used single-cell RNA-seq to examine the transcriptomes of XY Znrf3-deficient gonads during the mouse sex-determining period. Analyses of cell trajectories in mutant gonads reveal the failure of pre-supporting cells to commit to the Sertoli cell fate, XY granulosa cell development, unstable commitment in those cells that reach the Sertoli path and enhanced contribution to a supporting-like cell fate. By developing a machine learning-based score for transcriptomic similarity to Sertoli and granulosa, we show pervasive disruption to acquisition of testicular cell fate in the mutant supporting cell lineage, with large numbers of cells co-expressing pro-Sertoli and pro-granulosa markers. These data reveal that loss of Znrf3 results in transcriptomic and cellular heterogeneity, with shifts in cellular sex identity that undermine a simple binary model in which mutant supporting cell precursors achieve either Sertoli or granulosa cell differentiation.
Read the full paper here!
Making sense of the linear genome, gene function and TADs
HAB Grant Project
The role of SETD1B in somatic hypermutation and germinal center physiology
The genome contains an organism’s complete genetic information, and while mutations can disrupt normal function, they are essential in one biological process—adaptive immunity. When the immune system encounters foreign elements like viruses or vaccines, B cells undergo somatic hypermutation in germinal centers (found in lymphoid tissues such as the spleen, tonsils, and lymph nodes). This process introduces mutations in antibody genes, altering their shape and binding strength (affinity) to antigens. Affinity selection ensures that B cells with higher-affinity antibodies are preserved, driving an accelerated evolutionary process that enhances immunity. However, key questions remain about how somatic hypermutation and germinal centers function. This proposal aims to investigate a newly identified gene critical to both processes.
HAB Grant Project
Investigating immune cell interactions in early fibrotic lung disease using spatial transcriptomics
This study aims to understand the role of immune cells in the early stages of pulmonary fibrosis to develop new therapeutic strategies. Interstitial lung abnormalities (ILA), detected incidentally on CT scans, offer a unique opportunity to study the disease’s origins, as 25% of patients with ILA develop pulmonary fibrosis within four years. Using well-characterized FFPE lung tissue sections from lung cancer resections, the study will apply single-cell spatial transcriptomics via the NanoString CosMX SMI platform to create an ILA cell atlas, identify functional cell states, and examine cell-cell interactions driving fibrosis. Additionally, AI-powered CT scan analysis (‘e-Lung’ by Brainomix) will help identify imaging biomarkers, integrating radiomics with spatial transcriptomics to develop the first multi-omic predictive model of ILA progression. The pilot study will guide a prospective study using bronchoscopy samples. The patient cohort, sourced from a London-based tertiary referral center, consists of an equal number of male and female participants with a mean age of 74, reflecting at-risk demographics, with additional demographic data to be collected in the first phase.
HAB LAUNCH EVENT
The HAB Launch Event was a resounding success! Held on December 4th, the event brought together members of the bioinformatics community to celebrate the official opening of the Hub for Applied Bioinformatics.
The afternoon featured insightful presentations from HAB leadership, including an overview of HAB activities, highlights from the training program, and discussions on community engagement. Attendees also heard inspiring success stories from researchers who have benefited from HAB’s support. The event concluded with networking over refreshments, fostering new connections and future collaborations.
A huge thank you to everyone who joined us—we look forward to growing this community together!
Python for Biologists Workshop
First in-person training at the HAB
PhD students from several research groups attended the first training session at the HAB after completing the online “Basic R” course. During this immersive 5-hour workshop, Dr. Vigilante took students through a hands-on tutorial on data manipulation and visualization, using a range of example datasets. Building on the foundational skills they gained online, students had the chance to dive into more advanced analyses, including correlation studies and Principal Component Analysis (PCA). This session was an incredible opportunity for students to solidify their R programming skills, ask questions and network.