Cell Biology of Genome Maintenance

Mechanisms that counteract DNA damage are important to help maintain cellular homeostasis by suppressing mutagenic events and genome rearrangements that may lead to disease, particularly cancer. Among the most severe forms of genome rearrangements are chromosome translocations. These form by the illegitimate joining of chromosome breaks and often play key roles in the initial steps of tumorigenesis. Despite their prevalence and importance, our understanding of how translocations form is still rudimentary and many questions remain. 

Which are the molecular features that define recurrent chromosome breakpoints? How do the broken chromosome ends find each other within the nuclear space? Which are the DNA repair mechanisms that mediate chromosome fusion and which are the factors that favour interchromosomal fusion (translocation) over intrachromosomal repair? Using a combination of molecular biology techniques, genetics and high-throughput imaging and sequencing approaches, we aim to shed light on the basic molecular mechanisms underlying the formation of oncogenic chromosome translocations.

Chromatin dynamics & translocation biogenesis

There are contradicting ideas regarding how individual double-strand breaks (DSBs) find each other within the mammalian nuclear space and illegitimately repair to form translocations. To address this issue, we have established the first cell-based experimental system to visualise the formation of translocations in real time by tracking individual DSBs within the 3D nuclear space (Roukos et al., 2013). Using this established system and novel CRISPR/Cas9-based tools, we are interested in dissecting the molecular and cellular mechanisms that contribute to chromatin motion, double-strand break synapsis and illegitimate joining and in assessing their contribution to translocation biogenesis.  

Identifying mechanisms of recurrent oncogenic translocations 

Modelling the formation of recurrent cancer-initiating translocations requires a versatile approach. We have now established a methodology that uses fluorescence in situ hybridisation (FISH) to probe the position of individual chromosome ends of potential translocation partners in interphase cells in 3D (Figure 1). Using high-throughput microscopy and image analysis pipelines we have developed, we are able to probe and quantify individual cells with intra-chromosomal separation and rare cancer-initiating translocations with high sensitivity. We are currently using these tools in combination with molecular techniques and sequencing approaches to: 1) understand which are the molecular features that define breakpoint sites on recurrent translocation partners, 2) assess whether the chromatin environment predisposes to chromosome breakage and translocation formation, 3) identify molecular players of the DNA damage response and novel factors that mediate synapsis of chromosome breaks and their illegitimate fusion.

Figure showing Roukos group's method of visualising chromosome translocations
Figure 1. A methodology to quantify rare translocation events with single cell-resolution. A. Fluorescence in situ hybridisation (FISH) probes mark the position of chromosome ends on potential translocation partners. Intra-chromosomal breakage is detected by the physical separation of different fluorescent probes (green and red, marked by white arrow, middle) and translocations by the additional co-localisation of the chromosome end of the potential translocation partner (blue and green probe, white arrow, right). B. High-throughput confocal microscopy is used to acquire images in 3D and automated image analysis is used to detect chromosome locations marked by FISH probes. Distance measurements in 3D identify cells with spatial co-localisation or separation of chromosome ends based on distance thresholds of known pairs.

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