Projects

Indirect genetic effects within families during early life

Early life is hugely important in all animals, and changes that happen during the first part of life can have consequences throughout life, from the number of offspring mice go on to have as adults, through to developing a psychiatric disorder in humans.

Mothers and siblings provide a large part of the early life environment, and this allows indirect genetic effects to occur. Indirect genetic effects are when a gene in one individual causes a change in a trait in another individual. The most well-studied example of this are maternal genetic effects: for example, a gene in a mouse mother may increase the amount of maternal care she gives, and this could help her pup grow quicker. We designed cross-fostering experiments to examine all directions of these indirect genetic effects within a mouse family: a) mothers’ genes influence on foster-pups b) pups’ genes influence on their foster-mother, and c) foster-siblings’ genes influence on each other.

We were able to find quantitative trait loci (QTL; regions of the genome which influence the trait of interest) which have indirect genetic effects: that is, we found genes in one individual which altered the behaviour of a second individual. This showed that indirect genetic effects can have a large influence on early life and that these effects can be in unexpected directions, e.g. genes in one sibling can increase the amount of care another sibling gets.

Cross-species genetic analyses of complex traits and disease

Most genes found in humans also have an equivalent (homologous) gene in mice, and these homologous genes often play the same role in both species. This is because we are both descended from a common ancestor, and many biological systems have been maintained. This is what allows animal models to be used in wide areas of research, and it can also help us to identify genes controlling specific traits of interest.

Finding specific genes which affect specific traits in humans is difficult for a number of reasons, two of which are that any individual gene may only have a small effect and that there are many environmental (i.e. non-genetic) factors which affect us. In animal models, such as mice, we can counteract both of these problems, as, for example, mice can be kept in very tightly controlled environmental conditions. Therefore, by combining data that has already been collected by other groups, I have been able to identify novel genes underlying traits in both mouse and human.

Using this approach, I have found genes which influence the size of the hippocampus (an important brain region for memory) in both mouse and humans, and four genes which influence likelihood to develop bipolar disorder in humans and related traits in mice.

Mouse model of environmental exposures leading to Gulf War Illness

Gulf War Illness (GWI) is a medically unexplained, chronic condition characterised by persistent sickness behaviour, and immune reactions in the brain. An estimated 25-32% of the over 700,000 veterans of the First Gulf War can be diagnosed with GWI. Typically, sickness behaviour resolves itself after the causative infection or injury, but patients with GWI continue to show debilitating symptoms 25 years after the conflict, and this suggests that epigenetic changes may have occurred.

It has been suggested that the high physical and psychological stress of combat may have primed the immune system to over-react to the low level of the nerve gas sarin, which many veterans were exposed to during the war. Recent research in a mouse model has shown that pre-treatment with the stress hormone corticosterone (CORT) causes an increase in immune response after exposure to diisopropyl fluorophosphate (DFP), a sarin surrogate.

We examined gene expression and regulation in this mouse model of GWI. Our results show transcriptional, histone modification (H3K27ac) and DNA methylation changes in genes related to the immune and neuronal system, potentially relevant to neuroinflammatory and cognitive symptoms of GWI. Further evidence suggests altered proportions of myelinating oligodendrocytes in the frontal cortex, perhaps connected to white matter deficits seen in GWI sufferers.

Our findings may reflect the early changes which occurred in GWI veterans, and we observe alterations in several pathways altered in GWI sufferers. These close links to changes seen in veterans with GWI indicates that this model reflects the environmental exposures related to GWI, and may provide a model for biomarker development and testing future treatments.

We are currently looking how these changes may be able to have long lasting effects, and if these changes are reflected in the blood of the mice. We hope to be able to compare the changes we seen in mice with those with see in GWI patients, allowing us to test potential treatments.

Sequencing the BXD family, a cohort for experimental systems genetics and precision medicine

The BXD mouse genetic reference population is the most deeply phenotyped mammalian model system, with ~6000 phenotypes in GeneNetwork.org (GN), the repository for BXD family data. GN enables analysis of complex interactions among gene variants, phenotypes at different biological levels, environmental factors, and many cofactors and confounders that will influence quantitative phenotypes. The BXD family now consists of 152 inbred lines, each of which is a unique mosaic of alleles from the C57BL/6J and DBA2/J inbred founders, and segregate for ~5 million common sequence variants. Using the current genotype data from arrays and RNA-seq, it is possible to achieve mapping precision of under ±2.0 Mb over most of the genome. In this study we have sequenced the entire BXD family and the two parental strains.

We have carried out 40X sequencing using a 10x Chromium linked-read barcoding strategy. This deep sequencing of ~40 kb DNA fragments has several uses including: identification of structural variants that cannot be detected reliably using short read shotgun sequencing; identification of variants unique to each ‘epochs’ of BXD, derived in the last four decades; identification of truly rare spontaneous mutations, and production of the first ‘infinite marker maps’ of this family, allowing even higher precision mapping of phenotypes.
At present we have confirmed ~4.5 million variants that differ between C57BL/6J and DBA2/J parents. We have aligned sequences for >50 samples and identified haplotype blocks with greater precision than had been possible with microarray-based genotyping. Several candidates have been identified for a phenome-wide association study.

This family is an excellent resource for testing networks of causal and mechanistic relations among clinical phenotypes and millions of molecular and organismal traits, including metabolic syndrome, infection, addiction, neurodegeneration, and longevity. Full sequencing will only increase its usefulness as a platform for experimental precision medicine.

Future research interests

The above projects are unified by my interest in behaviour, and how genes and environment can interact (GxE) to modify complex traits. Further, this can be expanded to gene-gene interactions (epistasis), and environment-environment interactions (e.g. how high-quality maternal care could counteract a stressful early life environment), and how these can all combine together. New techniques producing large volumes of data, and the willingness to share this data, is finally allowing us to explore these complex, multifactorial problems.

Collaborations

My research so far has given me the opportunity to collaborate with a number of excellent researchers throughout the world. Much of my Ph.D. work has been using the BXD recombinant mouse lines, with Prof. Rob Williams. My cross-species work was in collaboration with the ENIGMA Network, especially Prof. Derrek Hibar, Prof. Jason Stein and Dr. Sarah Medland. I have also used data from the Psychiatric Genomics Consortium. My project on GWI at UTSC is in collaboration with several groups, including those of Dr James O’Callaghan and Prof. Gordon Broderick. Other collaborators have included Dr Rupert W Overall and  Prof. Alexandra Badea. I’m always happy to speak to new collaborators.