Wednesday, 16 December 2015

A fish that spins

I am scientist working on Parkinson’s disease, a form of neurodegeneration that still has no cure. Many people use cells, mice or flies to further understand disease, but my team and I use an alternative model organism, the zebrafish. Its advantages are that unlike mice, it is transparent, so we can monitor cells in real time. It is also genetically closer to humans than other model organisms such as flies, and it is also very cost effective to house. Although we don’t know the cause of most cases of Parkinson’s disease, we know that about 5% of patients carry a single defect in a gene known as Glucocerebrosidase (GBA). What is really interesting is that when you have two faulty copies of the GBA gene it leads to a rare neurodegenerative disorder known as Gaucher’s disease. 

Gaucher’s disease, in its extreme forms, can result in neurodegeneration and death in infancy. But its symptoms are very variable and can include a wide variety of symptoms including epilepsy, blood cell problems, osteoporosis, and enlarged organs to name a few. The pathology is mainly driven by immune cells that swell up with substrates normally broken down by GBA. These swollen cells known as “Gaucher cells” accumulate in different parts of the body such as the liver, causing it to swell in size quite dramatically. 

To further understand Gaucher’s disease and how these gene defects can cause these symptoms, we made a zebrafish with a faulty GBA gene, using a new technology known as “gene editing”. This made a large deletion in the GBA gene of the zebrafish. By studying the effects of a defective GBA gene, we are hoping to further understand both Gaucher’s disease and Parkinson’s disease. 

The lack of GBA1 in Gaucher's fish (top) causes them to develop a curved spine compared to controls who produce normal amounts for GBA1 (bottom).

he zebrafish carrying the defective GBA gene were very striking; they initially developed normally, but by the time they reached maturity at 3 months of age, they started to spin very fast in circles as can be seen in the video below. Such a behaviour was very surprising to us, as we had never encountered it before in any other zebrafish model.

Gaucher’s disease mainly affects the immune system so to investigate its effects further, we bred our Gaucher’s fish with special fish that have glowing immune cells and selected offspring that have both a faulty GBA gene and fluorescing immune cells. Due to the zebrafish’s transparency, we could then monitor how these immune cells were affected by the lack of a functional GBA gene. 

The lack of GBA1 leads to inflammation in the brain: brain sections of Gaucher's fish (left) show an increase in macrophages and microglia (green) compared
to healthy counterparts (right).

This led to the discovery that our fish were already showing signs of inflammation as the immune cells were affected very early on in development at 5 days of age. By the time the fish started to spin, we found these rogue immune cells had taken over vast areas of the liver and brain. This inflammation, we believe, is being triggered by increased levels of a special inflammatory master regulator gene called Mir155. We are currently investigating the biology of this gene further to see, if it will be a suitable drug target to treat Gaucher’s disease. 

Our Gaucher’s fish was an extremely exciting mutant to study and characterise. But like all scientific adventures it was a large team effort. Our lab was fortunate to collaborate with many gifted scientists all around the world.

Keatinge, M; Bui, H; Menke, A; Chen, YC; Sokol, AM; Bai, Q; Ellett, F; Da Costa, M; Burke, D; Gegg, M; Trollope, L; Payne, T; McTighe, A; Mortiboys, H; de Jager, S; Nuthall, H; Kuo, MS; Fleming, A; Schapira, AHV; Renshaw, SA; Highley, JR; Chacinska, A; Panula, P; Burton, EA; O'Neill, MJ and Bandmann, O. Glucocerebrosidase 1 deficient Danio rerio mirror key pathological aspects of human Gaucher disease and provide evidence of early microglial activation preceding alpha-synuclein-independent neuronal cell death. Hum. Mol. Genet. 2015, 1-13; September 16 doi: 10.1093/hmg/ddv369

 By Dr Marcus Keatinge

Marcus is a post-doctoral researcher in Professor Oliver Bandmann's group working on Parkinson's disease and related disorders. To find our more about his research, follow him on ResearchGate. 

Wednesday, 2 December 2015

How does studying rare genetic diseases help Parkinson's research?

My name is Alisdair and I am a “Clinical Academic”. This means I spend part of my week as a Consultant in the NHS and the remainder doing research at SITraN. In both aspects of my job I work to understand the genetic causes of diseases affecting the brain in adults and children.

Part of my research involves studying rare genetic diseases which affect the brain, with the aim of increasing our understanding of common brain disorders. A project I am undertaking will investigate whether a condition called DiGeorge syndrome is associated with an increased chance of developing Parkinson’s disease. 

DiGeorge syndrome affects around 1/3000 people and is caused by a small missing piece of chromosome number 22. A single research study suggested that people with DiGeorge syndrome are more likely than people in the general population to develop Parkinson’s disease. To see if this link is true, I am recruiting adults with DiGeorge syndrome from all over Britain and assessing them for symptoms of Parkinson’s disease. We are aiming to recruit around 100 participants. If people with DiGeorge syndrome have an increased chance of developing Parkinson’s disease then this will have important implications for their health. 

If DiGeorge syndrome does predispose to Parkinson’s disease then studying this condition could help us understand better the causes of Parkinson’s disease. The piece of chromosome 22 which is missing in people with DiGeorge syndrome contains several important genes (instructions) for mitochondria. staff. "Blausen gallery 2014". Wikiversity Journal of Medicine.
wjm/2014.010. ISSN 20018762. - Own work. Licensed under CC BY 3.0 via Commons

The mitochondria are the batteries which provide the energy supply to our bodies. For many years it has been known that reduced functioning of mitochondria happens in several brain diseases including Parkinson’s disease. By studying the function of mitochondria in blood samples from people with DiGeorge syndrome we may be able to better understand the role of mitochondria in causing Parkinson’s disease. 

In my experience, the perceived lack of relevance of a rare disease to population health can make it difficult to secure funding. But I believe that these conditions offer unique opportunities to understand the causes of diseases which are common in Britain and so have relevance to population health in general. 

By Alisdair McNeill

Alisdair is a Senior Clinical Research Fellow in Neuroscience & Clinical Genetics research at @INSIGNEO & SITraN groups and a Honorary Consultant in Clinical Genetics at the Sheffield Children's Hospital. You can follow Alisdair on Twitter @am_sheffgenet and on Researchgate.

Wednesday, 18 November 2015

Celebrating our 5th anniversary

A research institute dedicated to motor neuron disease (MND)

Building a research institute dedicated to finding treatments for motor ne
uron disease (MND) was a fantastic challenge and would not have been possible with all our supporters who still make a big difference to our research every day. The last five years have been very exciting and have seen SITraN rise to one of the world–leading centres for research into MND

Experts from all over the world have joined us in the fight against this devastating disease and, as neurodegenerative diseases share common mechanisms that cause nerve cells to die, we study not only MND but also have teams working on Alzheimer’s, Parkinson’s and related disorders to find further clues to advance our understanding. Breakthroughs made in one disease area can thus benefit the research into other related diseases and particularly our research into MND.

SITraN - a research institute dedicated to finding treatments for
motor neuron disease (MND) and related disorders
Major Challenges of MND research

MND research faces major challenges; firstly, neurons and particularly motor neurons can’t be easily studied in people or modelled in the lab and, secondly, in 9 out of 10 MND cases the cause of the disease is not yet known – this knowledge, however, is crucial to developing treatments. A major part of our research therefore still focusses on understanding the disease mechanisms at work that cause motor neurons to deteriorate and die. Today, up to 20 genes have been associated with MND, the major ones are SOD1, C9ORF72, TDP43 and FUS. We model and study these inherited mutations in the lab to find clues on how to target the disease.

Understanding disease mechanisms is the key
to new treatments

Developing models to study MND

We have specialised in generating a cell and animal models of MND, including neuronal cell lines, zebrafish and mouse models and have - based on our discovery of certain pathways and targets in the disease process - developed ways in which to assess the effectiveness of drugs in these models. Riluzole, the only drug currently available for MND patients, is used as the standard against which to measure any new treatment. We are also working with skin cells donated by patients which we can reprogram into stem cells and then turn into motor neurons or other brain cells such as glial cells. This new and exciting technology allows us now to study disease processes using human cell models growing them in the lab in 2D or 3D cultures. 

Co-culture of nerve cells (green) and star-shaped
helper cells (astrocytes in red)

Pre-clinical drug development

We have invested in an industrial style high-throughput drug screening facility to be able to screen libraries of drugs in SITraN and to determine whether any of the drugs which have already proven safe in humans have beneficial effects in MND. This repurposing strategy could save many years of research and hundreds of millions of pounds compared to drug development from scratch. Our drug screens have already successfully produced a promising candidate for MND (S-Apomorphine), as well as a promising drug for Parkinson’s disease (UDCA). Both drugs are now being further tested at SITraN to see if they have strong enough effects in a range of our disease models to be taken forward to clinical trials. 

High-throughput drug screening at SITraN

Another pillar of our therapy development at SITraN is our gene therapy programme. We are developing gene-based therapies for spinal muscular atrophy (SMA), a childhood form of MND, and for inherited forms of MND such as SOD1 and C9ORF72 MND. Here, the faulty gene is known and can potentially be replaced or silenced which will be as close to a cure as we can get.
SMA gene therapy: restoring the missing SMN protein
(red) to the cell

Advances into personalised medicine

MND is a very complex disease. We know today that more than ten cellular pathways can be affected in motor neurons from people with MND. In order to better manage the disease, predictions are that we might either need a cocktail of drugs to target several of the disease processes, or find the major switch to target all or most of them at once. It is likely that we will need to develop drugs according to certain variants of MND following a personalised medicine approach
and finding the best treatments for each of the sub-groups of patients

  Different types of MND might need different
treatment approaches

New Centre for Genome Translation

In order to tackle the variability in MND, we have invested in cutting edge DNA sequencing equipment that will allow us to sequence the genomes of MND patients and compare their genes to healthy individuals in order to find the disease causing genes and pathways and target them accordingly. Computational Biologist Professor Winston Hide has joined us from Harvard University in 2014 and has established a Centre for Genome Translation at SITraN along with a new Masters course to train future researchers in this field. With funding and support from the world-leading US biotech company Biogen and our partners from Project MineE, we will hopefully be able to solve the mystery of the disease causes and processes in MND in the near future. 

New Centre for Genome Translation: Making sense of our genomes

Improving lives of people with MND

While we are waiting for more effective drugs to be available, we also have a comprehensive clinical research programme which aims to improve the care of people with MND here and now. We initiate and lead UK multi-centre studies to evaluate clinical interventions in MND; results for diaphragm pacing (DiPALS) and gastrostomy feeding (Progas) in MND have been published this year in the prestigious journal Lancet Neurology. Among the new technologies developed and trialled at SITraN is a customisable neck collar specifically designed for MND patients to alleviate the problems with posture, communication and eating caused by weak neck muscles. The innovative collar developed in a collaboration between SITraN, NIHR, Devices4Dignity, Sheffield Hallam University
and Sheffield Teaching Hospitals with support from the MND Association has just received a UK patent this month.

An innovative neck collar for people with MND

New technologies for people with MND
We have also developed a new web resource for people living with non-invasive ventilation and a telehealth system (TiM) for people with MND that allows the specialist care team to monitor MND patients at home and ensures that patients have access to specialist care when and as they need it and not just at their 2-monthly clinic appointments. Crucial input and support for our research comes from our Sheffield MND research advisory group, the first and only public and patient involvement (PPI) group for MND in the UK whose members are actively shaping research at SITraN to ensure the greatest benefit for people with MND.

MyNIV - a web resource with infos, practical tips and videos 
for people using non-invasive ventilation in MND

Diagnosing MND earlier

Early diagnosis is another priority in the fight against MND. By the time MND symptoms occur, more than half of the motor neurons have already deteriorated. From the onset of symptoms until finally a diagnosis of MND is made usually another year has gone by. It is crucial therefore that we find biomarkers that allow us to recognise the disease early and to determine at an early stage whether neuroprotective treatments are having beneficial effects. As part of our diagnostic tools discovery programme we are investigating blood and cerebrospinal fluid samples to find critical markers for MND, as well as using advanced neuroimaging techniques to see how muscle composition can be used to monitor the course of MND. 

The Muscle Energy Study

5 years on....

...we have put all the components, expertise and cutting-edge technologies here at SITraN in place to tackle MND from multiple fronts. Moreover, we collaborate with the MND research community worldwide to make sure that our joint efforts will deliver tangible benefits for people with MND.

We hope that the next five years will be equally successful and see a number of promising therapy developments in MND and that SITraN will play a big part in this. We are immensely grateful to our research funders and loyal supporters who made SITraN a reality and keep us focused on our goal - to defeat this devastating disease!

By the SITraN team

Follow all our news on our website, Twitter @neuroshef or on Facebook.
For video recordings of events and lectures check out our YouTube channel.

Wednesday, 11 November 2015

The brain: An essential gift to neuroscience

Have you ever considered donating your brain for research or do you know someone who has? And are you wondering what happens to a donated brain?

The human
brain is difficult to study in living people, therefore much of the research into neurodegenerative diseases such as motor neuron disease (MND), Parkinson’s and Alzheimer's disease relies on studying donated brain tissue - or animal or cell models which can only resemble what happens in living humans. Brain tissue helps us to understand what happens in the brain as a result of disease and is essential to develop new and better treatments.

I can’t stress enough how important it is for us scientists that people help us by donating their brains to research. Sadly, due to lack of awareness, brains from healthy donors which are needed as control tissue are particularly scarce.

Examining brain tissue is a big part of my own research and I’d like to give you some insights into how a donated brain is prepared and used for research:


When a brain is donated to research it needs to be treated immediately; generally, one half of it will be frozen and stored at -80°C, and the other half will be fixed in formalin for at least two weeks, which preserves everything in the brain. These two methods make the brain useful for future investigations, and both of them will conserve the brain for many years.

The conserved brain tissue is stored in a brain bank, a central repository that allows researchers from around the world to request and use tissue for their investigations. For most studies only a very small amount of tissue is needed, so each donated brain can benefit a large number of research studies.


The formalin-fixed brains are then examined by a professional neuropathologist. A neuropathologist is a medical doctor who prepares and examines the donated brains in order to diagnose neurological conditions. Extremely sharp knives are used to slice and dissect the brain in a particular order and to observe certain features which are key in the diagnosis of brain diseases. The brain can then either be classified as healthy, or it can be allocated to a disease group according to the diagnosis.


To take a closer look at the brain under the microscope, brain samples need to be sectioned, i.e. cut into very thin almost transparent slices. As fixed tissue is too soft to be sectioned straight away, we need to harden it to make it easier. To picture this, think of the difference between cutting a chicken breast before and after cooking it: it is way easier to do it afterwards, because it has been hardened! The usual way to harden the brain is by embedding smaller bits of it in a paraffin wax. The tissue will be dehydrated and then immersed in warm paraffin wax. After that, we let the wax harden at room temperature to obtain a solidified brain block. 


Once the brain tissue is hard, it can be easily sectioned using a specialised machine called “microtome” like the one shown below. 

The microtome cuts 5 micrometre thick slices off the brain block. For you to picture how thin these slices are, 5 micrometres is a half of the width of a cotton fibre. 

These extremely thin sections are then mounted on a transparent glass slide like the ones below.



As you can see, the section is colourless just after being cut. This is what almost any kind of tissue will look like after being sectioned this thin. For us to look at anything under the microscope, we need to stain the brain with different dyes which will show specific features that we researchers are interested in. Examples of these features are protein aggregates in MND, or loss of myelin in a variety of neurological diseases. 

On the right is a microscopic picture of a stained brain cortex section. That section has been stained to show the myelin sheaths of the neuronal axons, which appear in brown, forming bundles of fibres. Every single small blue circle is a cell’s nucleus, and blood vessels (which span the brain to supply it) usually appear as big hollow structures. 

Once the brain slides are stained, we can compare healthy brains with those from people who suffered a brain disease, in order to try to find the main characteristics and the possible causes of the disease. 

I hope you found this story of what happens to a person’s brain after the donation very interesting and useful. Most advances in our understanding of brain diseases have come through people who volunteer to take part in research through brain donation programmes.

We scientists are very grateful for these donations as they help us fight some of the most terrible diseases such as Alzheimer's, Parkinson’s and motor neuron disease, and I hope that someday we will find a cure thanks to these donors that will benefit their children and grandchildren so we can give something back.

By Alejandro Lorente Pons

I am a PhD student in SITraN and I am investigating brain cells called oligodendrocytes and how they contribute to C9ORF72 MND. You can follow me on Researchgate and on Twitter @ALorentePons.