Achievements

ISMB Commentary: Using deep learning and single cell tracking to understand competitive interactions in cell populations

Cell competition is a quality-control mechanism through which tissues eliminate unfit cells. Cell competition can result from short-range biochemical inductions or long-range mechanical cues. However, little is known about how cell-scale interactions give rise to population shifts in tissues, due to the lack of experimental and computational tools to efficiently characterize interactions at the single-cell level. Here, we address these challenges by combining long-term automated microscopy with deep-learning image analysis to decipher how single-cell behavior determines tissue makeup during competition. Using our high-throughput analysis pipeline, we show that competitive interactions between MDCK wild-type cells and cells depleted of the polarity protein scribble are governed by differential sensitivity to local density and the cell type of each cell’s neighbors. We find that local density has a dramatic effect on the rate of division and apoptosis under competitive conditions. Strikingly, our analysis reveals that proliferation of the winner cells is up-regulated in neighborhoods mostly populated by loser cells. These data suggest that tissue-scale population shifts are strongly affected by cellular-scale tissue organization. We present a quantitative mathematical model that demonstrates the effect of neighbor cell–type dependence of apoptosis and division in determining the fitness of competing cell lines.

Dr Alan Lowe

Ref: Local cellular neighbourhood controls proliferation in cell competition
Bove, A., Gradeci, D., Fujita, Y., Banerjee, S., Charras, G., Lowe, A.R.
Mol. Biol. Cell (2017) 28: 3215-3228

This video by the Alan Lowe lab demonstrates the data acquired and software developed as part of the work.

 

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ISMB Research could spell new approach to preventing progression of Huntington’s disease

June 2018

New research from scientists at Birkbeck and UCL points the way to a new approach in preventing progression of Huntington’s disease (HD), by manipulating the mutated protein associated with the disease.

HD is an inherited neurodegenerative disease, thought to affect about 7000 people in the UK. There is currently no treatment or cure for the disease, which causes progressive movement disorders and early death.

The disease is caused by a single mutation, which occurs in a gene that encodes the information to make a protein called huntingtin. The mutation causes this protein to form clumps and this process is associated with the damage to brain cells seen in HD. These clumps – or ‘aggregates’ – have been found in the brains of individuals with HD, but it is not clear how they form.

Using a fluorescent tag to track the mutated protein, the researchers found that it can first form a liquid-like cluster that subsequently converts into the harmful aggregates, which are solid and fibrous. Crucially, the researchers showed, both in isolation and in cells, that the aggregates can be easily dissolved when exposed to a chemical called hexanediol when it is in its early liquid-like form – but the chemical does not have any effect once the clusters have ‘solidified’ into aggregates.

Professor Helen Saibil, who led the study, said: “Our findings suggest that the harmful aggregates associated with Huntington’s disease emerge from a form which could be reversible. If the protein behaves similarly in brain cells, it might be possible to target the liquid clusters and prevent the protein from forming the aggregates which are associated with developing Huntington’s. This could have major implications for slowing or preventing disease progression in the future.”

The research formed the PhD project of Dr Tom Peskett (who was a student on the ISMB’s Wellcome Trust PhD programme) and is published in Molecular Cell. It was also the subject of an article in the Evening Standard on 29 June 2018.

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Promotion of ISMB investigators

July 2018

Congratulations to Joanne Santini and Andrew Martin on their promotions to Professor of Microbiology and Professor of Bioinformatics and Computational Biology respectively in the Research Department of Structural and Molecular Biology at UCL.

Posted by ubcg49z in Achievements

Professor Andres Ramos receives new MRC programme grant

July 2018

Congratulations to Professor Andres Ramos on being awarded an MRC Programme grant for the project: ‘Molecular mechanisms regulating mRNA transport and local translation in neurons‘.

The research will investigate the crucial role played by RNA binding proteins in the regulation of the transport and translation of mRNAs in dendritic and axonal locations. The regulation of mRNA translation in space and time creates distinct local biochemical environments in the cell, which are essential in mediating inter-neuronal communication and establishing neuronal networks.

This MRC programme is a collaboration between groups at ISMB, the UCL Sainsbury Wellcome Centre, the Francis Crick Institute, the UCL Institute of Neurology and the Albert Einstein College of Medicine in New York. The grant will run from 2018 to 2023.

Posted by ubcg49z in Achievements