What do we do?
The
lab is located on the fourth floor of the Strathclyde Institute of
Pharmacy and Biomedical Sciences (SIPBS) Hamnett Wing. There are
currently three main research areas:
- The
development of 'Gene Trapping' as a method to search for genes
involved in any process that can be studied and meaasured in laboratory
cells. A
useful way to think about gene trapping is that it is like
studying an entire human population in a dish. We are all genetically
unique humans,
with distinct combinations of genetic variation that have been shuffled
and passed down from our ancestors. That's why individuals have very
different genetic susceptibilities to disorders such as cancer,
Alzheimers and diabetes - or sometimes different responses to
therapeutic medication. It's important to uncover the genes and their
variants that are behind these differences as this will lead to better
drugs tailored to the individual patient. Classically, Human
Genetics is the route to identify such connections. However, this
requires collecting DNA samples from many individuals, and
then using expensive and time-consuming methodologies to look for
variants that are associated with the illness or biological
phenomenon under study. Even after such effort, the links are complex
and often of small effect. Sometimes, the complexity of the genetic
differences between individuals can prove a barrier to gene
identification: rare gene mutations in a person diagnosed with an
illness can be likened to a room full of murderers - you know one of
them 'did it', but it's hard to prove which one. Here's where Gene
Trapping offers an alternative (and much cheaper) route. A human laboratory cell line is
mutated by introducing a special stretch of DNA. If this drops into the
middle of a gene, by chance, then that gene will be switched off in
that cell. Because we use many thousands of cells in this process, by
the end we have created a 'library' of cells - each with its own gene
mutation. This library can be thought of as similar to the genetically
diverse human population. Now we can ask any biological question of
that library. For example: 'which mutant cells in the library fail to
respond to this particular drug?', 'which mutant cells can't complete
this biological process?', or 'which cells are resistant to infection
by this microbe?'. At the end of the screen, we have isolated a set of cells
containing mutations in genes that must be functionally
important in that process - and simple molecular techniques can be used
to reveal the gene identities. Note that I put the word 'functionally'
in bold - why? Many genetic techniques such as microarrays and some
human genetic approaches are based on 'association' and cannot separate
cause and effect. An analogy to illustrate the problems with
association might be that the common cold is
associated with winter. Or watching a film at the cinema is
associated with popcorn stuck between your teeth. At one level these
observations are sort of true, but not really mechanistically
informative - and prone to misinterpretation. You might try to wear a
woolly hat to prevent contaging a cold.
Imagine if you don't understand what a cinema is (we frequently don't
understand biological systems). You might conclude that the cinema is
where you go to cure popcorn in your teeth - a cause and effect
confusion.
Gene traps, by contrast, are functional because you look for a real
response to an action (the mutation). They are like hitting
yourself over the head with a hammer. It hurts, and there's
no ambiguity about the cause. I'm painting a very rosy picture of gene
traps. They are not perfect. Here are some issues: they only model
one kind of mutation (gene loss-of-function) whereas, in real life,
there are several; they are used in laboratory cell lines that can
sometimes act very differently to cells growing in a living body; gene
traps can sometimes cause 'dirty' or 'non-canonical' mutations where it
becomes harder to pin down their effects to a specific gene; and
lastly, not all genes can be mutated in this way. Nevertheless, I
believe they can make a useful contribution to many biological
questions (especially so, if married to Human Genetics data). Click here to view a much more detailed description of precisely what we are doing with gene trapping.
- A collaboration with Dr David Watson on the identification of metabolomic biomarkers associated wtih mental illness.
Metabolomics is one of the more recently defined 'omics' disciplines.
It relates to the identification of the complete profile of small
chemical entities (not DNA, RNA or proteins - they have their own
'omics') that exist in our cells, organs and circulatory system.
Examples of these molecules include the lipids (fats), amino acids,
carbohydrates (sugars), hormones, and co-factors. One of our goals
is to identify metabolite 'biomarkers'
that might be clinically useful to help diagnose mental illnesses such
as schizophrenia, bipolar disorder, and depression. In the past, we
identified which metabolites changed in the brain of mice that modelled
a form of schizophrenia observed in patients who had a mutation in the NPAS3 gene. This told us that energy production from glucose
was affected - and we also observed a significant increase in markers
of inflammation (unpublished). We have now completed a new study into
the relationship between the brain metabolite changes seen in
schizophrenia, depression, bipolar disorder and diabetes - in
comparison to healthy brains. The scientific literature has already
revealed that there may be common genetic threads between the different
psychiatric disorders, and our NPAS3 study highlighted the metabolic
deficits in schizophrenia. The results of this latest study have just
been submitted for publication but back up this idea of shared
biological underpinnings and response to these devastating conditions.
- A
collaboration with Dr Hilary Carswell, Dr Katharine 'Chris' Carter and a local
SME, Pharmacells, on the characterisation of a totally new mammalian
cell type with some interesting properties. This work will be published in the future.
- The study of epigenetic DNA changes associated with ageing.
Shakhawan Mawlood is a PhD student working with me and Lynn Dennany in
Forensic Science. Shakhawan is working on DNA methylation levels on
normal chromosomes (autosomes) as well as that occuring in
mitochondrial DNA. The object is to determine which sites have
methylation levels that change with age.