Tagged: Lrrk2

BioRxiv – open access preprints

si-bioRxiv

For the vast majority of the general population, science is consumed via mass media head lines and carefully edited summaries of the research.

The result of this simplified end product is an ignorance of the process that researchers need to deal with in order to get their research in the public domain.

As part of our efforts to educate the general public about the scientific research of Parkinson’s disease, it is necessary to also make them aware of that process, the issues associated with it, and how it is changing over time.

In todays post, we will look at how new research reports are being made available to the public domain before they are published.


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Getting research into the public domain. Source: STAT

Every morning here at the SoPD, we look at what new research has entered the public domain over night and try to highlight some of the Parkinson’s disease relevant bits on our Twitter account (@ScienceofPD).

To the frustration of many of our followers, however, much of that research sits behind the pay-to-view walls of big publishing houses. One is allowed to read the abstract of the research report in most cases, but not the full report.

Given that charity money and tax payer dollars are paying for much of the research being conducted, and for the publication fee (approx. $1500 per report on average) to get the report into the journal, there is little debate as to the lack of public good in such a system. To make matter worse, many of the scientists doing the research can not access the published research reports, because their universities and research institutes can not afford the hefty access fees for all of the journals.

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Source: Libguides

To be fair, the large publishing houses have recognised that this is not a sustainable business model, and they have put forward the development of open-access web-based science journals, such as Nature communications, Scientific reports, and Cell reports. But the fees for publishing in these journals can in some cases be higher than the closed access publications.

This is crazy. What can we do about it?

Well, there have been efforts for some time to improve the situation.

Projects like the Public Library of Science (or PLOS) have been very popular and are now becoming a real force on the scientific publishing landscape (they recently celebrated their 10 year anniversary and during that time they have published more than 165,000 research articles). But they too have costs associated with maintaining their service and publications fees can still be significant.

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Is there an easier way of making this research available?

So this is Prof Paul Ginsparg.

Ginsparg_at_Cornell_University

Source: Wikipedia

Looks like the mad scientist type right? Don’t be fooled. He’s awesome! Prof Ginsparg is a professor of Physics and Computing & Information Science at Cornell University.

Back in 1991, he started a repository of pre-print publications in the field of physics. The repository was named arXiv.org, and it allowed physics researchers to share and comment on each others research reports before they were actually published.

The site slowly became an overnight sensation.

The number of manuscripts deposited at arXiv passed the half-million mark on October 3, 2008, the million manuscript mark by the end of 2014 (with a submission rate of more than 8,000 manuscripts per month). The site currently has 1,257,315 manuscripts that are freely available to access. A future nobel prize winning bit of research is probably in there!

Now, by their very nature, and in a very general sense, biomedical researchers are a jealous bunch.

For many years they looked on with envy at the hive of activity going on at arXiv and wished that they had something like it themselves. And now they do! In November 2013, Cold Spring Harbor Laboratory in New York launched BioRxiv.

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Source: BioRxiv

And the website is very quickly becoming a popular destination: by April 21, 2017, >10,000 manuscript had been posted, at a current rate of over 800 manuscripts per month (Source).

Recently they got a huge nod of financial support from the Chan Zuckerberg Initiative – a foundation set up by Facebook founder Mark Zuckerberg and his wife Priscilla Chan to “advance human potential and promote equality in areas such as health, education, scientific research and energy” (Wikipedia).

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Source: ChangZuckerberg

In April of this year, the Chan Zuckerberg Initiative announced a partnership with Cold Spring Harbor Laboratory to help support the site (Click here to see the press release).

So what is bioRxiv?

bioRxiv is a free OPEN ACCESS service that allows researchers to submit draft copies of scientific papers — called preprints — for their colleagues to read and comment on before they are actually published in peer-reviewed scientific journals.

Here are two videos explaining the idea:

Sounds great right?

To demonstrate how the bioRxiv process works, we have selected an interesting manuscript from the database that we would like to review here on the SoPD.

This is the article:

HEMMER

Title: In Vivo Phenotyping Of Parkinson-Specific Stem Cells Reveals Increased a-Synuclein Levels But No Spreading
Authors: Hemmer K, Smits LM, Bolognin S, Schwamborn JC
Database: BioRxiv
DOI: https://doi.org/10.1101/140178
PMID: N/A                   (You can access the manuscript by clicking here)

In this study (which was posted on bioRxiv on the 19th May, 2017), the researchers have acquired skin cells from an 81 year old female with Parkinson’s disease who carries a mutation (G2019S) in the LRRK2 gene.

Mutations in the Leucine-rich repeat kinase 2 (or Lrrk2) gene are associated with an increased risk of developing Parkinson’s disease. The most common mutation of LRRK2 gene is G2019S, which is present in 5–6% of all familial cases of Parkinson’s disease, and is also present in 1–2% of all sporadic cases. We have previously discussed Lrrk2 (Click here to read that post).

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The structure of Lrrk2 and where various mutations lie. Source: Intech

The skin cells were transformed using a bit of biological magic in induced pluripotent stem (or IPS) cells. We have previously discussed IPS cells and how they are created (Click here to read that post). By changing a subjects skin cell into a stem cell, researchers can grow the cell into any type of cell and then investigate a particular disease on a very individualised basis (the future of personalised medicine don’t you know).

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IPS cell options available to Parkinson’s disease. Source: Nature

Using this IPS cell with a mutation in the LRRK2 gene, the researchers behind todays manuscript next grew the cells in culture and encouraged the cells to become dopamine producing cells (these are some of the most vulnerable cells in Parkinson’s disease). The investigators had previously shown that neurons grown in culture from cells with the G2019S mutation in the LRRK2 gene have elevated levels of of the Parkinson’s disease protein alpha Synuclein (Click here to read that OPEN ACCESS paper).

In this present study, the investigators wanted to know if these cells would also have elevated levels of alpha synuclein when transplanted into the brain. Their results indicate that the cells did. Next, the investigators wanted to use this transplantation model to see if the high levels of alpha synuclein in the transplanted cells would lead to the protein being passed to neighbouring cells.

Why did they want to do that?

One of the current theories regarding the mechanisms underlying the progressive spread of Parkinson’s disease is that the protein alpha synuclein is lead culprit. Under normal conditions, alpha synuclein usually floats around as an individual protein (or monomer), but sometime it starts to cluster (or aggregate) with other monomers of alpha synuclein and these form what we call oligomers. These oligomers are believed to be a toxic form of alpha synuclein that is being passed from cell to cell. And it ‘seeds’ the disease in each cell it is passed on to (Click here for a very good OPEN ACCESS review of this topic).

Mechanism of syunuclein propagation and fibrillization

The passing of alpha synuclein between brain cells. Source: Nature

There have been postmortem analysis studies of the brains from people with Parkinson’s who have had cell transplantation therapy back in the 1990s. The analysis shows that some of the transplanted cells have evidence of toxic alpha synuclein in them – some of those cells have Lewy bodies in them, suggesting that the disease has been passed on to the healthy introduced cells from the diseased brain (Click here for the OPEN ACCESS research report about this).

In the current bioRxiv study, the investigators wanted to ask the reverse question:

Can unhealthy, toxic alpha synuclein producing cells cause the disease to spread into a healthy brain?

So after transplanted the Lrrk2 mutant cells into the brains of mice, they waited 11 weeks to see if the alpha synuclein would be passed on to the surrounding brain. According to their results, the unhealthy alpha synuclein did not transfer. They found no increase in levels of alpha synuclein in the cells surrounding the transplanted cells. The researchers concluded that within the parameters of their experiment, Parkinson’s disease-associated alpha synuclein spreading was not detected.

Interesting. When will this manuscript be published in a scientific journal?

We have no idea.

One sad truth of the old system of publication is: it may never be.

And this illustrates one of the beautiful features of bioRxiv.

This manuscript is probably going through the peer-review process at a particular scientific journal at the moment in order for it to be properly published. It is a process that will take several months. Independent reviewers will provide a critique of the work and either agree that it is ready for publication, suggest improvements that should be made before it can be published, or reject it outright due to possible flaws or general lack of impact (depending on the calibre of the journal – the big journals seem to only want sexy science). It is a brutal procedure and some manuscripts never actually survive it to get published, thus depriving the world of what should be freely available research results.

And this is where bioRxiv provides us with a useful forum to present scientific biological research that may never reach publication. Perhaps the researchers never actually intended to publish their findings, and just wanted to let the world know that someone had attempted the experiment and these are the results they got (there is a terrible bias in the world of research publishing to only publish positive results).

The point is: with bioRxiv we can have free access to the research before it is published and we do not have to wait for the slow peer-review process.

And there is definitely some public good in that.

EDITORS NOTE HERE: We are not suggesting for a second that the peer-review process should be done away with. The peer-review process is an essential and necessary aspect of scientific research, which helps to limit fraud and inaccuracies in the science being conducted.

What does it all mean?

This post may be boring for some of our regular readers, but it is important for everyone to understand that there are powerful forces at work in the background of scientific research that will determine the future of how information is disseminated to both the research community and general population. It is useful to be aware of these changes.

We hope that some of our readers will be bold/adventurous and have a look at some of what is on offer in the BioRxiv database. Maybe not now, but in the future. It will hopefully become a tremendous resource.

And we certainly encourage fellow researchers to use it (most of the big journals now accept preprint manuscripts being made available on sites like bioRxiv – click here to see a list of the journals that accept this practise) and some journals also allow authors to submit their manuscript directly to a journal’s submission system through bioRxiv via the bioRxiv to Journals (B2J) initiative (Click here for a list of the journals accepting this practise).

The times they are a changing…


The banner for today’s post was sourced from ScienceMag

The Melanoma drug from MODAG

Melanoma

A build up of a protein called alpha synuclein inside neurons is one of the characteristic feature of the Parkinsonian brain. This protein is believed to be partly responsible for the loss of dopamine neurons in this condition.

A similar build up of alpha synuclein is also seen in the deadly skin cancer, Melanoma… but those cells don’t die (?!?)… in fact, they just keep on dividing.

Why is there this critical difference?

In today’s post we look at an interesting new study that may have solved this mystery.


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A melanoma. Source: Huffington Post

Parkinson’s disease has a very strange relationship with the skin cancer melanoma.

As we have stated in previous posts (Click here, herehere and here to read those posts) people with Parkinson’s disease are 2-8 times more likely to develop melanoma than people without Parkinson’s (And this finding has been replicated a few times: Olsen et al, 2005; Olsen et al, 2006; Driver et al 2007; Gao et al 2009; Lo et al 2010; Bertoni et al 2010;Schwid et al 2010; Ferreira et al, 2010Inzelberg et al, 2011; Liu et al 2011; Kareus et al 2012; Wirdefeldt et al 2014; Catalá-López et al 2014; Constantinescu et al 2014; Ong et al 2014).

The truly baffling detail in this story, however, is that this relationship is reciprocal – if you have melanoma you are almost 3 times more likely to develop Parkinson’s disease than someone without melanoma (Source: Baade et al 2007; Gao et al 2009).

What is melanoma exactly?

Melanoma is a type of skin cancer.

It develops from the pigment-containing cells known as melanocytes. Melanocytes are melanin-producing cells located in the bottom layer (the stratum basale) of the skin’s outer layer (or epidermis).

Blausen_0632_Melanocyte

The location of melanocytes in the skin. Source: Wikipedia

Melanocytes produce melanin, which is a pigment found in the skin, eyes, and hair. It is also found in the brain in certain types of cells, such as dopamine neurons (where it is referred to as neuromelanin).

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Neuromelanin (brown) in dopamine neurons. Source: Schatz

Melanomas are usually caused by DNA damage resulting from exposure to ultraviolet radiation. Ultraviolet radiation from tanning beds increases the risk of melanoma (Source), as does excessive air travel (Source), or simply spending to much time sun bathing.

Approximately 2.2% of men and women will be diagnosed with melanoma at some point during their lives (Source). In women, melanomas most commonly occur on the legs, while in men they are most common on the back. Melanoma makes up 5% of all cancers (Source).

Generally, melanomas is one of the safer cancers, as it can usually be detected early by visual inspection. This cancer is made dangerous, however, by its ability to metastasise (or spread to other organs in the body).

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The stages of melanoma. Source: Pathophys

Are there any genetic associations between Parkinson’s disease and melanoma?

No.

When the common genetics mutations that increase the risk of both conditions were previously analysed, it was apparent that none of the known Parkinson’s mutations make someone more susceptible to melanoma, and likewise none of the melanoma-associated genetic mutations make a person vulnerable to Parkinson’s disease (Meng et al 2012;Dong et al 2014; Elincx-Benizri et al 2014).

In fact, researchers have only found very weak genetic connections between two conditions (Click here to read our previous post on this). It’s a real mystery.

Are there any other connections between Parkinson’s disease and melanoma?

Yes.

Another shared feature of both Parkinson’s disease and melanoma is the build up of a protein called alpha synuclein. Alpha synuclein is believed to be one of the villains in Parkinson’s disease – building up inside a cell, becoming toxic, and eventually killing that cell.

But recently researchers noticed that melanoma also has a build up of alpha synuclein, but those cells don’t die:

Melan2

Title: Parkinson’s disease-related protein, alpha-synuclein, in malignant melanoma
Authors: Matsuo Y, Kamitani T.
Journal: PLoS One. 2010 May 5;5(5):e10481.
PMID: 20463956               (This article is OPEN ACCESS if you would like to read it)

In this study, researchers from Japan found that alpha synuclein was detected in 86% of the primary and 85% of the metastatic melanoma. Understand that the protein is not detectable in the non-melanoma cancer cells.

So what is it doing in melanoma cells?

Recently, researchers from Germany believe that they have found the answer to this question:

Melanoma

Title: Treatment with diphenyl-pyrazole compound anle138b/c reveals that α-synuclein protects melanoma cells from autophagic cell death
Authors: Turriani E, Lázaro DF, Ryazanov S, Leonov A, Giese A, Schön M, Schön MP, Griesinger C, Outeiro TF, Arndt-Jovin DJ, Becker D
Journal: Proc Natl Acad Sci U S A. 2017 Jun 5. pii: 201700200. doi: 10.1073/pnas.1700200114
PMID: 28584093

In their study, the German researchers looked at levels of alpha synuclein in melanoma cells. They took the melanoma cells that produced the most alpha synuclein and treated those cells with a chemical that inhibits the toxic form of alpha synuclein (which results from the accumulation of the protein).

What they observed next was fascinating: the cell morphology (or physically) changed, leading to massive melanoma cell death. The investigators found that this cell death was caused by instability of mitochondria and a major dysfunction in the autophagy process.

Mitochondria, you may recall, are the power house of each cell. They keep the lights on. Without them, the lights go out and the cell dies.

Mitochondria

Mitochondria and their location in the cell. Source: NCBI

Autophagy is the garbage disposal/recycling process within each cell, which is an absolutely essential function. Without autophagy, old proteins and mitochondria will pile up making the cell sick and eventually it dies. Through the process of autophagy, the cell can break down the old protein, clearing the way for fresh new proteins to do their job.

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The process of autophagy. Source: Wormbook

Waste material inside a cell is collected in membranes that form sacs (called vesicles). These vesicles then bind to another sac (called a lysosome) which contains enzymes that will breakdown and degrade the waste material. The degraded waste material can then be recycled or disposed of by spitting it out of the cell.

What the German research have found is that the high levels of alpha synuclein keep the mitochondria stable and the autophagy process working at a level that helps to keeps the cancer cell alive.

Next, they replicated this cell culture research in mice with melanoma tumors. When the mice were treated with the chemical that inhibits the toxic form of alpha synuclein, the cancer cancer became malformed and the autophagy process was blocked.

The researchers concluded that “alpha synuclein, which in PD exerts severe toxic functions, promotes and thereby is highly beneficial to the survival of melanoma in its advanced stages”.

So what does all of this mean for Parkinson’s disease?

Well, this is where the story gets really interesting.

You may be pleased to know that the chemical (called Anle138b) which was used to inhibit the toxic form of alpha synuclein in the melanoma cells, also works in models of Parkinson’s disease:

Wagner

Title: Anle138b: a novel oligomer modulator for disease-modifying therapy of neurodegenerative diseases such as prion and Parkinson’s disease.
Authors: Wagner J, Ryazanov S, Leonov A, Levin J, Shi S, Schmidt F, Prix C, Pan-Montojo F, Bertsch U, Mitteregger-Kretzschmar G, Geissen M, Eiden M, Leidel F, Hirschberger T, Deeg AA, Krauth JJ, Zinth W, Tavan P, Pilger J, Zweckstetter M, Frank T, Bähr M, Weishaupt JH, Uhr M, Urlaub H, Teichmann U, Samwer M, Bötzel K, Groschup M, Kretzschmar H, Griesinger C, Giese A.
Journal: Acta Neuropathol. 2013 Jun;125(6):795-813
PMID: 23604588              (This article is OPEN ACCESS if you would like to read it)

In this first study the researchers discovered Anle138b by conducted a large screening study to identify for molecules that could inhibit the toxic form of alpha synuclein.

They next tested Anle138b in both cell culture and rodent models of Parkinson’s disease and found it to be neuroprotective and very good at inhibiting the toxic form of alpha synuclein. And the treatment looks to be very effective. In the image below you can see dark staining of toxic alpha synuclein in the left panel from the brain of an untreated mouse, but very little staining in the right panel from an Anle138b treated mouse.

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Toxic form of alpha synuclein (dark staining). Source: Max-Planck

Importantly, Anle138b does not interfere with normal behaviour of alpha synuclein in the mice (such as production of the protein, correct functioning, and eventual degradation/disposal of the protein), but it does act as an inhibitor of alpha synuclein clustering or aggregation (the toxic form of the protein). In addition, the investigators found no toxic effects of Anle138b in any of their experiments even after long-term high-dose treatment (more than one year).

And in a follow up study, the drug was effective even if it was given after the disease model had started:

Olig2

Title: The oligomer modulator anle138b inhibits disease progression in a Parkinson mouse model even with treatment started after disease onset
Authors: Levin J, Schmidt F, Boehm C, Prix C, Bötzel K, Ryazanov S, Leonov A, Griesinger C, Giese A.
Journal: Acta Neuropathol. 2014 May;127(5):779-80.
PMID: 24615514                (This article is OPEN ACCESS if you would like to read it)

During the first study, the researchers had started Anle138b treatment in the mouse model of Parkinson’s disease at a very young age. In this study, however, the investigators began treatment only as the symptoms were starting to show, and Anle138b was found to significantly improve the overall survival of the mice.

One particularly interesting aspect of Anle138b function in the brain is that it does not appear to change the level of the autophagy suggesting that the biological effects of treatment with Anle138b is cell-type–specific (Click here to read more about this). In cancer cells, it is having a different effect to that in brain cells. These differences in effect may also relate to disease conditions though, as Anle138b was not neuroprotective in a mouse model of Multiple System Atrophy (MSA; Click here to read more about this).

Is Anle138b being tested in the clinic?

Not yet.

Ludwig-Maximilians-Universität München and the Max Planck Institute for Biophysical Chemistry (Göttingen) have spun off a company called MODAG GmbH that is looking to advance Anle138b to the clinic (Click here for the press release). The Michael J Fox Foundation are helping to fund more preclinical development of this treatment (Click here to read more about this).

We will be watching their progress with interest.

What does it all mean?

Summing up: There are many mysteries surrounding Parkinson’s disease, but some researchers from Germany may have just solved one of them and at the same time developed a potentially useful new treatment.

They have discovered that the Parkinson’s associated protein, alpha synuclein, which is produced in large amounts in the skin cancer melanoma, is actually playing an important role in keeping those cancer cells alive. By finding a molecule that can block the build up of alpha synuclein, they have not only found a treatment for melanoma, but also potentially one for Parkinson’s disease.

And given that both diseases are closely associated, this could be seen as a great step forward. Two birds with one stone as the saying goes.


The banner for today’s post was sourced from Wikipedia

Sheffield: flies, fish and a Tigar

total-produce-ltd-sheffield1

When people in England think of the city of Sheffield, quite often images of a great industrial past will come to mind.

They usually don’t think of the flies, fish and (yes) a Tigar (no, not a typo!) that are influencing Parkinson’s disease research in the city.

In today’s post we will look at how the re-invention of a city could have a major impact on Parkinson’s disease.


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The industrial heritage of Sheffield. Source: SIMT

It is no under statement to say that the history of Sheffield – a city in South Yorkshire, England –  is forged in steel.

In his 1724 book, “A tour thro’ the whole island of Great Britain, the author Daniel Defoe wrote of Sheffield:

“Here they make all sorts of cutlery-ware, but especially that of edged-tools, knives, razors, axes, &. and nails; and here the only mill of the sort, which was in use in England for some time was set up, for turning their grindstones, though now ’tis grown more common”

Sheffield has a long history of metal work, thanks largely to its geology: The city is surrounded by fast-flowing rivers and hills containing many of the essential raw materials such as coal and iron ore.

And given this fortunate circumstance and an industrious culture, the city of Sheffield particularly prospered during the industrial revolution of the mid-late 1800s (as is evident from the population growth during that period).

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The population of Sheffield over time. Source: Wikipedia

But traditional manufacturing in Sheffield (along with many other areas in the UK) declined during the 20th century and the city has been forced to re-invent itself in the early 21st century. And this time, rather than taking advantage of their physical assets, the city is focusing on its mental resources.

Great. Interesting stuff. Really. But what does this have to do with flies, fish and Parkinson’s disease???

Indeed. Let’s get down to business.

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The Sheffield Institute for Translational Neuroscience (SITraN) was officially opened in 2010 by Her Majesty The Queen. It is the first European Institute purpose-built and dedicated to basic and clinical research into Motor Neuron Disease as well as related neurodegenerative disorders such as Parkinson’s and Alzheimer’s disease.

Since its opening, the institute has published some pretty impressive research, particularly in the field of Parkinson’s disease.

And here is where we get to the flies:

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Pink flies. Source: Wallpapersinhq

We have previously discussed “Pink” flies and their critical role in Parkinson’s research (Click here to read that post).

Today we are going to talk about Lrrk2 flies.

What is Lrrk2?

This is Sergey Brin.

sergey_brin

He’s a dude.

One of the founders of the search engine company “Google”. Having changed the world, he is now turning his attention to other projects.

One of those other projects is close to our hearts: Parkinson’s disease.

In 1996, Sergey’s mother started experiencing numbness in her hands. Initially it was believed to be RSI (Repetitive strain injury). But then her left leg started to drag. In 1999, following a series of tests, Sergey’s mother was diagnosed with Parkinson’s disease. It was not the first time the family had been affected by the condition: Sergey’s late aunt had also had Parkinson’s disease.

Both Sergey and his mother have had their DNA scanned for mutations that increase the risk of Parkinson’s disease. And they discovered that they were both carrying a mutation on the 12th chromosome, in a gene called PARK8 – one of the Parkinson’s disease associated genes. Autosomal dominant mutations (meaning if you have just one copy of the mutated gene) in the PARK8 gene dramatically increase one’s risk of developing Parkinson’s disease.

PARK8 provides the instructions for making an enzyme called Leucine-rich repeat kinase 2 (or Lrrk2).

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The structure of Lrrk2. Source: Wikipedia

Also known as ‘Dardarin (from the Basque word “dardara” which means trembling), Lrrk2 has many functions within a cell – from helping to move things around inside the cell to helping to keep the power on (involved with mitochondrial function).

Fig-2-LRRK2-involvement-in-cellular-mechanisms-Several-data-posit-that-LRRK2-through

Source: Researchgate

NOTE: Curiously, mutations in the PARK8 gene are also associated with Crohn’s disease (Click here and here for more on this) – though the mutation is in a different location for PD.

Now, not everyone with this particular mutation will go on to develop Parkinson’s disease, and Sergey has decided that his chances are 50:50. But he does not appear to be taking any chances though. Being one of the founders of a large company like Google, has left Sergey with considerable resources at his disposal. And he has chosen to focus some of those resources on Lrrk2 research (call it an insurance  policy). He has done this via considerable donations to groups like the Michael J Fox foundation.

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Actor Michael J Fox was diagnosed at age 30. Source: MJFox foundation

So just as Pink flies derive their name from mutations in the Parkinson’s associated Pink1 gene, Lrrk2 flies have mutations in the Lrrk2 gene.

So what have the researchers at Sheffield done with the Lrrk2 flies?

In 2013, the Sheffield researchers published an interesting research report:

brain

Title: Ursocholanic acid rescues mitochondrial function in common forms of familial Parkinson’s disease
Authors: Mortiboys H, Aasly J, Bandmann O.
Journal: Brain. 2013 Oct;136(Pt 10):3038-50.
PMID: 24000005

In this study, the investigators took 2000 drugs (including 1040 licensed drugs and 580 naturally occurring compounds) and conducted a massive screen to identify drugs that could rescue mitochondrial dysfunction in PARK2 (Pink1) mutant cells.

Mitochondria are the power house of each cell. They keep the lights on. Without them, the lights go out and the cell dies.

Mitochondria

Mitochondria and their location in the cell. Source: NCBI

In certain genetic forms of Parkinson’s disease (such as those associated with mutations in the PARK2 gene), the mitochondria in cells becomes dysfunctional and may not be disposed of properly (Click here to read our previous post related to this).

In their huge screen of 2000 drugs, the researchers in Sheffield identified 15 drugs that could rescue the mitochondria dysfunction in the PARK2 skins cells. Of those 15 compounds, two were chosen for further functional studies. They were:

  • Ursocholanic acid
  • Dehydro(11,12)ursolic acid lactone

Neither ursocholanic acid nor dehydro(11,12)ursolic acid lactone are FDA-licensed drugs. We have little if any information regarding their use in humans. Given this situation, the researchers turned their attention to the chemically related bile acid ‘ursodeoxycholic acid’, which has been in clinical use for more than 30 years.

What is Ursodeoxycholic Acid?

Ursodeoxycholic Acid (or UDCA) is a drug that is used to to improve bile flow and reduce gallstone formation. In the USA it is also known as ‘ursodiol’.

800px-Ursodiol

Ursodiol. Source: Wikimedia

Bile is a fluid that is made and released by your liver, and it stored in the gallbladder. Its function is to help us with digestion. UDCA occurs naturally in bile – it is basically a bile acid and can therefore be useful in dissolving gallstones. UDCA has been licensed for the treatment of patients since 1980. UDCA also reduces cholesterol absorption.

So what did the Sheffield researchers find with UDCA?

The researchers tested UDCA on mitochondrial function in PARK2 skin cells, and they found that the drug rescued the cells. They then tested UDCA on skin cells from people with Parkinson’s disease who had mutations in the PARK8 (Lrrk2) gene (G2019S).

The researchers had previously found impaired mitochondrial function and morphology in skin cells taken from people with PARK8 associated Parkinson’s disease (Click here to read more about this), and other groups had reported similar findings (Click here for more on this).

And when they treated the Lrrk2 cells with UDCA, guess what happened?

UDCA was able to rescue the mitochondrial effect in those cells as well!

Obviously these results excited the Sheffield scientists and they set up a collaboration with researchers at York University and from Norway, to look at the potential of UDCA in rescuing the fate of Lrrk2 flies. The results of that study were published two years ago:

Oliver

Title: UDCA exerts beneficial effect on mitochondrial dysfunction in Lrrk2 (G2019S) carriers and in vivo.
Authors: Mortiboys H, Furmston R, Bronstad G, Aasly J, Elliott C, Bandmann O.
Journal: Neurology. 2015 Sep 8;85(10):846-52.
PMID: 26253449        (This article is OPEN ACCESS if you would like to read it).

The researchers tested UDCA on flies (or drosophila) with specific Lrrk2 mutations (G2019S) display a progressive loss of photoreceptor cell function in their eyes. The mitochondria in the photoreceptor are swollen and disorganised. When the investigators treated the flies with UDCA, they found approximately 70% rescue of the photoreceptor cells function.

The researchers in Sheffield concluded that UDCA has a marked rescue effect on cells from a Parkinson’s disease-associated gene mutation model, and they proposed that “mitochondrial rescue agents may be a promising novel strategy for disease-modifying therapy in Lrrk2-related PD, either given alone or in combination with Lrrk2 kinase inhibitors” (for more information about the Lrrk2 inhibitors they refer, click here).

And the good news regarding this line of research: other research groups have also observed similar beneficial effects with UDCA in models of Parkinson’s disease:

Low1

Title: Ursodeoxycholic acid suppresses mitochondria-dependent programmed cell death induced by sodium nitroprusside in SH-SY5Y cells.
Authors: Chun HS, Low WC.
Journal: Toxicology. 2012 Feb 26;292(2-3):105-12.
PMID: 22178905

This research group also demonstrated that UDCA could reduce cell death in a cellular model of Parkinson’s disease.

And this study was followed by another one from a different research group, which involved testing UDCA in animals:

Salem1

Title: Ursodeoxycholic Acid Ameliorates Apoptotic Cascade in the Rotenone Model of Parkinson’s Disease: Modulation of Mitochondrial Perturbations.
Authors: Abdelkader NF, Safar MM, Salem HA.
Title: Mol Neurobiol. 2016 Mar;53(2):810-7.
PMID: 25502462

These researchers found UDCA rescued a rodent model of Parkinson’s disease (involving the neurotoxin rotenone). UDCA not only improved mitochondrial performance in the rats, but also demonstrated anti-inflammatory and anti-cell death properties.

Given all this research, the Sheffield researchers are now keen to test UDCA in clinical trials for Parkinson’s disease.

Has anyone tested UDCA in the clinic for Parkinson’s disease?

Not that we are aware of, but two groups are interested in attempting it.

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Firstly, the University of Minnesota – Clinical and Translational Science Institute has registered a trial (Click here to read more about this). This trial will not, however, be testing efficacy of the drug on Parkinson’s symptoms. It will focus on measuring UDCA levels in individuals after four weeks of repeated high doses of oral UDCA (50mg/kg/day), and determining the bioenergetic profile and ATPase activity in those participants. Basically, they want to see if UDCA is safe and active in people with Parkinson’s disease.

The CurePD trust (in the UK) is also currently seeking to run a clinical trial for UDCA (Click here for more on this). The group are currently organising the funding for that trial.

url-3


EDITOR’S NOTE HERE: Before we move on, the team at the SoPD would like to say that while UDCA is a clinically available drug, it is still experimental for Parkinson’s disease. There is no indication yet that it has beneficial effects in people with Parkinson’s disease. In addition, UDCA is also is known to have side effects, which include flu symptoms, nausea, diarrhea, and back pain. And individuals have been known to have allergic reactions to UDCA treatment (Click here and here for more on the side effects of UDCA). Thus we must impress caution on anyone planning to experiment with this drug. Before attempting any kind of change in a current treatment regime, PLEASE discuss your plans with a medically qualified physician who is familiar with your case history.


Ok, so that was the flies research, what about the fish? And the… uh, tigar?

Yes. The fish are called Zebrafish (or Danio rerio).

They are a tropical freshwater fish that is widely used in biological research.

Zebrafisch

Biology researchers love these little guys because their genome has been fully sequenced and they has well characterised and testable behaviours. In addition, their development is very rapid (3 months), and its embryos are large and transparent.

And the researchers at Sheffield are using these fish to study Parkinson’s disease.

How did they do that?

tiger

Title: TigarB causes mitochondrial dysfunction and neuronal loss in Pink1 deficiency
Authors: Flinn LJ, Keatinge M, Bretaud S, Mortiboys H, Matsui H, De Felice E, Woodroof HI, Brown L, McTighe A, Soellner R, Allen CE, Heath PR, Milo M, Muqit MM, Reichert AS, Köster RW, Ingham PW, Bandmann O.
Journal: Ann Neurol. 2013 Dec;74(6):837-47.
PMID:
24027110        (This article is OPEN ACCESS if you would like to read it)

Firstly, the group at Sheffield generated zebrafish that had a mutation in the Parkinson’s associated gene ‘PARK6’. This gene provides the plans for the production of a protein called Pink1 (we have previously discussed Pink1 – click here to read more on this).

In normal healthy cells, the Pink1 protein is absorbed by mitochondria and eventually degraded as it is not used. In unhealthy cells, however, this process becomes inhibited and Pink1 starts to accumulate on the outer surface of the mitochondria. Sitting on the surface, it starts grabbing another Parkinson’s associated protein called Parkin. This pairing is a signal to the cell that this particular mitochondria is not healthy and needs to be removed.

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Pink1 and Parkin in normal (right) and unhealthy (left) situations. Source: Hindawi

The process by which mitochondria are removed is called mitophagy. Mitophagy is part of the autophagy process, which is an absolutely essential function in a cell. Without autophagy, old proteins and mitochondria will pile up making the cell sick and eventually it dies. Through the process of autophagy, the cell can break down the old protein, clearing the way for fresh new proteins to do their job.

Think of autophagy as the waste disposal/recycling process of the cell.

Print

The process of autophagy. Source: Wormbook

Waste material inside a cell is collected in membranes that form sacs (called vesicles). These vesicles then bind to another sac (called a lysosome) which contains enzymes that will breakdown and degrade the waste material. The degraded waste material can then be recycled or disposed of by spitting it out of the cell.

In the case of a PARK6 mutations, Pink1 protein can not function properly with Parkin and the autophagy process breaks down. As a result, the old or unhealthy mitochondria start to pile up in the cell, resulting in the cell getting sick and dying.

Now back to the Zebrafish.

When the Sheffield researchers mutated PARK6 in the zebrafish, they noticed that the fish had a very early and persistent loss of dopamine neurons in their brains. These fish also had enlarged, unhealthy mitochondria and reduced mitochondrial activity.

Given this result, the investigators next wanted to identify which genes have increased or decreased levels of activity as a result of this genetic manipulation. They identified 108 genes that were higher in the PARK6 mutant, and 146 genes had lower activity.

One gene in particular had activity levels 12 times higher in the PARK6 mutant fish than the normal zebrafish.

The name of that gene? TP53-Induced Glycolysis And Apoptosis Regulator (or Tigar).

What is Tigar?

Tigar is a gene that provides the instructions for making a protein that is activated by p53 (also known as TP53).

What does that mean?

p53 is a protein that has three major functions: controlling cell division, DNA repair, and apoptosis (or cell death). p53 performs these functions as a transcriptional activator (that is a protein that binds to DNA and helps produce RNA (the process of transcription) – see our previous post explaining this).

800px-P53

p53 protein structure, bound to DNA (in gold). Source: Wikipedia

In regulating the cell division, p53 prevents cells from dividing too much and in this role it is known as a tumour suppression – it suppresses the emergence of cancerous tumours. Genetic mutations in the p53 gene result in run away cell division, and (surprise!) as many as 50% of all human tumours contain mutations in the p53 gene.

Apop

Cancer vs no cancer. Source: Khan Academy

In DNA repair, p53 is sometimes called “the guardian of the genome” as it prevents mutations and helps to conserve stability in the genome. This function also serves to prevent the development of cancer, by helping to repair potentially cancer causing mutations….and in this role it is known as a tumour suppression. Obviously, if there is a mutation in the p53 gene, less DNA repair will occur – increasing the risk of cancer occurring.

And finally, in cell death, p53 plays a critical role in telling a cell when to die. And (continuing with the cancer theme), if there is a mutation in the p53 gene, fewer cells will be told to die – increasing the risk of cancer occurring. And in this role p53 is known as a tumour suppression.

In normal cells, the levels of p53 protein are usually low. When a cell suffers DNA damage and stress, there is often an increase in the amount of p53 protein. If this increases past a particular threshold, then the cell will be instructed to die.

If you haven’t guessed yet, p53 is a major player inside most cell, and it controls the activity of a lot of genes.

And one of those genes is Tigar.

But what does Tigar actually do?

So we have explained the “TP53-Induced” part of the “TP53-Induced Glycolysis And Apoptosis Regulator” name, let’s now focus on the “Glycolysis And Apoptosis Regulator”

Tigar is an interesting protein because it is an enzyme that primarily functions as a regulator of the breaking down of glucose (“Glycolysis” involves the conversion of glucose into a chemical called pyruvate). In addition to this role, however, Tigar acts in preventing cell death (or apoptosis).

Increased levels of Tigar protects cells from oxidative-stress induced apoptosis, by decreasing the levels of free radicals. In this way, it promotes anti-oxidant activities.

But hang on a second, anti-oxidant activity should be good for the cell right? Why are the dopamine cells are dying if Tigar levels are increasing in the PARK6 mutants?

Fantastic question!

The answer: TIGAR is also a negative regulator of a process called mitophagy. As we discussed above, mitophagy is the process of removing mitochondria by autophagy. Increases in the levels of TIGAR blocks mitophagy in a cell, and results in an increased number of swollen and unhealthy mitochondria in those cells (Click here to read more about this). These swollen mitochondria are comparable to the enlarged mitochondria identified the PARK6 zebrafish by the Sheffield researchers.

And the researchers believe that this may be the cause of the cell death in the PARK6 zebrafish – the double impact of PARK6 and Tigar induced problems with mitophagy.

NOTE: Problems with mitophagy is believed to be an important mechanism in the development of early-onset Parkinson’s disease (Click here for a recent review on this)

Ok, and what did the Sheffield researchers do next?

Given that there was such a huge increase in Tigar levels in the PARK6 zebrafish, the investigators decided to reduce Tigar levels in the PARK6 zebrafish to see what impact this would have on the fish (and their mitochondria).

Remarkably, reductions of Tigar levels resulted in complete rescue of the dopamine neurons in the PARK6 fish. It also increased mitochondrial activity in those cells, and reduced the activation of the microglia cells, which can also play a role in the removal of sick cells in the brain.

The researchers concluded that the results demonstrate that TIGAR is “a promising novel target for disease‐modifying therapy in Pink1‐related Parkinson’s disease”.

And what are the researchers planning to do next with Tigar?

Prof Oliver Bandmann, the senior scientist who ran the study, has said that they “need to finish studying TIGAR levels in the brains of people with Parkinson’s and want to better understand how this protein is involved in maintaining the cell batteries – called ‘mitochondria'” (Source).

Our guess is that the group will also be conducting studies looking at Tigar reduction in rodent models of Parkinson’s disease to determine if this is a viable target in mammals. If Tigar reduction in rodents is found to be effective, the researchers will probably turn their attention to drug screening studies to identify currently available drugs that can reduce the activity of Tigar. Such a drug would provide us with yet another potential treatment for Parkinson’s disease.

We’ll be keeping an eye out for these pieces of research.

This is all very interesting. What does the future hold for Parkinson’s research in Sheffield?

Well, in a word: Keapstone.

Que?

In March, the University of Sheffield and Parkinson’s UK have launched a new £1 million virtual biotech company called “Keapstone Therapeutics” (see the press release by clicking here).

parkinsons_virtual_biotech_graphic

Source: Parkinson’s UK

The goal of the company – the first of its kind – is to combine world-leading research from the University with funding and expertise from the charity to help develop revolutionary drugs for Parkinson’s disease.

What is virtual about it? The biotech won’t be building its own labs, employing a team of specialist laboratory scientists, or buying any high-tech equipment (which would all be incredibly expensive). Rather they will form partnerships with groups that do specific tasks the best.

Here is a video of Dr Author Roach (director of Research at Parkinson’s UK) explaining the idea behind this endeavour:

By seeking a collaboration with Sheffield in the creation of a spin-out biotech company, Parkinson’s UK is not only acknowledging Sheffield’s track record, but also making an investment in their future research. While we cannot be entirely sure of what the long-term future holds for Parkinson’s research in Sheffield, we do know that Keapstone will be an important aspect of it in the immediate future.

Could this be a model for the future of Parkinson’s disease research? Only time will tell. We will have a closer look at Keapstone Therapeutics in an upcoming post.

Click here to learn more about the virtual biotech project.

So what does it all mean?

In 2017, we here at the SoPD have decided to begin highlighting some of the Parkinson’s disease research centres as an addition feature on the blog. We have not been approached by the research group in Sheffield or the University itself, and our selection of this city as our first case study was based purely on the fact that we really like what is happening there with regards to Parkinson’s research!

The research group in Sheffield has undertaken multiple lines of research which could potentially providing us with several novel treatment options for Parkinson’s disease. These lines of research have focused not only on clinically available drugs, but also identifying novel targets. We like what they are doing and will keep a close eye on progress there.

And over the next year we will select additional centres of Parkinson’s research based on the same criteria (us liking what they are doing). Our next case study will be the Van Andel Research Institute in Grand Rapids, Michigan (we would hate to be accused of having a UK bias).


EDITORIAL NOTE:  Under absolutely no circumstances should anyone reading the material on this website consider it medical advice. The information provided here is for educational purposes only. Before considering or attempting any change in your treatment regime, PLEASE consult with your doctor or neurologist. While some of the drugs discussed on this website are clinically available, they may have serious side effects. We urge caution and professional consultation before altering any treatment regime. SoPD can not be held responsible for any actions taken based on the information provided here. 


The banner for today’s post was sourced from TotalProduceLocal

NRF2 and Parkinson’s disease

nrf2-effects-on-cells

Over the Christmas festive period an interesting study was published in the journal Proceedings of the National Academy of Sciences (PNAS). It was about a protein called Nuclear Factor Erythroid 2-Related Factor 2 (Nrf2) that has some impressive properties that could be good for Parkinson’s disease.

In today’s post we will review the results of the study and discuss what they mean for Parkinson’s disease.


free-radical-n0864buocgw24nkj0fwain64rsquzlav3pxwjiibho

We are going to be talking about free radicals. Source: PRIMOH2

Antioxidants are one of those subjects that is often discussed, but not well understood. So before we review the study that was published last week, let’s first have a look at what we mean when we talk about antioxidants.

What is an antioxidant?

An antioxidant is simply a molecule that prevents the oxidation of other molecules.

OK, but what does that mean?

Well, the cells in your body are made of molecules. Molecules are combinations atoms of one or more elements joined by chemical bonds. Atoms consist of a nucleus, neutrons, protons and electrons.

Oxidation is simply the loss of electrons from a molecule, which in turn destabilises the molecule.

Think of iron rusting. Rust is the oxidation of iron – in the presence of oxygen and water, iron molecules will lose electrons over time. Given enough time, this results in the complete break down of objects made of iron.

1112dp_01rust_bustingrusty_bottom_of_door

Rust, the oxidation of metal. Source: TravelwithKevinandRuth

The exact same thing happens in biology. Molecules in your body go through a similar process of oxidation – losing electrons and becoming unstable. This chemical reaction leads to the production of what we call free radicals, which can then go on to damage cells.

What is a free radical?

A free radical is an unstable molecule – unstable because it is missing electrons. They react quickly with other molecules, trying to capture the needed electron to re-gain stability. Free radicals will literally attack the nearest stable molecule, stealing an electron. This leads to the “attacked” molecule becoming a free radical itself, and thus a chain reaction is started. Inside a living cell this can cause terrible damage, ultimately killing the cell.

Antioxidants are thus the good guys in this situation. They are molecules that neutralize free radicals by donating one of their own electrons. The antioxidant don’t become free radicals by donating an electron because by their very nature they are stable with or without that extra electron.

imgres

How free radicals and antioxidants work. Source: h2miraclewater

Interesting, but what does all this have to do with this new gene Nrf2?

Well, Nrf2 is a ‘transcription factor’ with some interesting properties.

What is a transcription factor?

So you remember your high school science class when some adult at the front of the class was talking about biology 101 – DNA gives rise to RNA, RNA gives rise to protein.

maxresdefault

The basic of biology. Source: Youtube

Ultimately this is a circular cycle, because the protein that is produced using RNA is required at all levels of this process. Some of the protein is required for making RNA from DNA, while other proteins are required for making protein from the RNA instructions.

A transcription factor is a protein that is involved in the process of converting (or transcribing) DNA into RNA.

Now, a transcription factor can be an ‘activator’ of transcription – that is initiating or helping the process of generating RNA from DNA.

6567f50d30ad3ac65aff1e815caf202b3abd7111

An example of a transciptional activator. Source: Khan Academy

Or it can be a repressor of transcription – blocking the machinery (required for generating RNA) from doing it’s work.

6286f2dbd5e353145bef785aecb273d25176ff23

An example of a transciptional repressor. Source: Khan Academy

Nrf2 is an activator of transcription. When it binds to DNA to aids in the production of RNA, which then results in specific proteins being produced.

And this is where Nrf2 gets interesting.

You see, Nrf2 binds to antioxidant response elements (ARE).

What are ARE?

Antioxidant response elements (ARE) are regions of DNA is commonly found in the regulatory region of genes encoding various antioxidant and cytoprotective enzymes.

The regulatory region of genes is the section of DNA where transcription is initiated for each gene. They are pieces of DNA that a transcription factor like Nrf2 binds to and activates the production of RNA.

ARE are particularly interesting because these regions reside in the regulatory regions of genes that encode naturally occurring antioxidant and protective proteins. And given that antioxidants and protective proteins are generally considered a good thing for sick/dying cells, you can see why Nrf2 is an interesting protein to investigate.

By binding to ARE, Nrf2 is directly encouraging the production of naturally occurring antioxidant and protective proteins. And this is why a lot of people are excited by Nrf2 and call it the ‘next big thing’.

So what did the new research study report?

Well, this is where the story gets really interesting.

The researchers in the new study found that Nrf2 has some additional features that may be completely unrelated to the antioxidant properties:

nrf2

Title: Nrf2 mitigates LRRK2- and α-synuclein-induced neurodegeneration by modulating proteostasis.
Authors: Skibinski G, Hwang V, Ando DM, Daub A, Lee AK, Ravisankar A, Modan S, Finucane MM, Shaby BA, Finkbeiner S.
Journal: Proc Natl Acad Sci U S A. 2016 Dec 27. pii: 201522872.
PMID: 28028237

The researchers wanted to determine what effect introducing exaggerated amounts of Nrf2 into cell culture models of Parkinson’s disease would have on the behaviour and survival of the cells. There were two types of cell culture models of Parkinson’s disease used in the study: one produced a lot of the Parkinson’s associated protein alpha synuclein (normal un-mutated) and the other cell culture model involved two mutations in the Lrrk2 gene (we have previously discussed Lrrk2 – click here to read that post).

The researchers had previously demonstrated that both of these cell culture models of Parkinson’s disease exhibited increased levels of cell death when compared with normal cells. In the current study, when the researchers artificially exaggerated the amounts of  Nrf2 in both sets of cell cultures, they found that not only did Nrf2 reduce Lrrk2 and alpha-synuclein toxicity in cell culture, but it also influenced alpha-synuclein protein regulation, by increasing the degradation of the protein. This means that Nrf2 increased the disposal of the unnecessary excess of alpha synuclein.

In addition, Nrf2 also promoted the collection of free-floating mutant Lrrk2 and bundling it up into dense ‘inclusion bodies’ – dense clusters which are similar to the Lewy bodies of Parkinson’s disease but inclusion bodies are not associated with cell death. The scientists concluded that excessive levels of Nrf2 help to make the cells healthier and that this could represent a new target for future therapies of Parkinson’s disease. The researchers acknowledge that the ARE-related features of Nrf2 may be also playing a beneficial role in the cells, but this is the first time the alpha synuclein and Lrrk2 features have been identified.

Sounds great. Are there any catches?

Yes, a very interesting one.

The response of Nrf2 is time-dependent. The researchers found that over stimulation with Nrf2 leads to natural compensation from cells that eventually limits the activity of Nrf2. In other words, too much of a good thing loses it’s affect over time. Biology is one giant balancing act and sometimes when one factor is artificially introduced, cells will compensate regardless of whether it’s a good thing or not.

The researchers suggested that this issue could potentially be over come by periodic use of Nrf2, rather than simply chronic (or continuous) use of the protein. This still needs to be determined, however, in follow up experiments.

What does it all mean?

This new study provides us with new data relating to a protein that has been seen as holding great promise in the treatment of neurodegenerative conditions (not just Parkinson’s disease). The new research, however, demonstrates some interesting characteristic of Nrf2 specific to two Parkinson’s disease related genes.

Nrf2 has been considered a drug target for some time and agents targeting this protein have been patented and are under investigation (Click here to read more on this). We will be keeping an eye out for these compounds and we’ll report here the results of any research being conducted on them.


Interesting side note here:

We have previously discussed the treatments for Parkinson’s disease that were prescribed in India over 2000 years ago (Click here for that post). Outlined in the ancient texts, called the ‘Ayurveda’ (/aɪ.ərˈveɪdə/; Sanskrit for “the science of life” or “Life-knowledge”) was the use of the seeds of Mucuna pruriens in treating conditions of tremor. The seeds of this tropical legume we now know have extremely high levels of L-dopa in them (L-dopa being the standard therapy for Parkinson’s disease in modern medicine).

Here’s the interesting bit:

A second popular Ayurvedic treatment that is popular for Parkinson’s disease is Curcumin.

turmeric

Tumeric. Source: Cerebrum

Curcumin is an active component of turmeric (Curcuma longa), a dietary spice used in Indian cuisine and medicine. Curcumin exhibits antioxidant, anti-inflammatory and anti-cancer properties, crosses the blood-brain barrier and there are numerous studies that indicate neuroprotective properties in various models of neurological disorders.

Curcumin has also been shown to activate Nrf2 (Click here , here and here for more on this).

It has also been shown to prevent the aggregation of alpha synuclein (click here for more on this).

We are always amazed at the curious little connection with ancient remedies that can be found in modern research and medical practice, and we thought we’d share this one here.


EDITORIAL NOTE: The content provided by the Science of Parkinson’s website is for information purposes only. It is provided by research scientists, not medical practitioners. Any actions taken – based on what has been read on the website – are the sole responsibility of the reader. The information provided on this website should under no circumstances be considered medical advice, and any actions taken by readers should firstly be discussed with a qualified healthcare professional.


The banner for today’s post was sourced from NRF2 science

An update on the connection between Melanoma and Parkinson’s disease

We have previously discussed the strange connection between Melanoma and Parkinson’s disease (click here to read that post).

Melanoma

That post included the curious observations that:

  • People with Parkinson’s disease are 2-8 times more likely to develop melanoma than people without Parkinson’s.
  • People with melanoma are almost 3 times more likely to develop Parkinson’s disease than someone without melanoma.

And we have no idea why (there is no shared genetic predisposition for the two conditions).

Research published this week, however, may begin to explain part of the connection:

Melanoma-title

Title: Parkinson disease (PARK) genes are somatically mutated in cutaneous melanoma.
Authors: Inzelberg R, Samuels Y, Azizi E, Qutob N, Inzelberg L, Domany E, Schechtman E, Friedman E.
Journal: Neurol Genet. 2016 Apr 13;2(3):e70.
PMID: 27123489     (This research article is OPEN ACCESS if you would like to read it)

In this study, the scientists looked at somatic mutations in cells from 246 tissue samples of melanoma.

What are somatic mutations?

Somatic mutations are genetic alteration that have been acquired by a cell that can then be passed to the progeny of that mutated cell (via cell division). These somatic mutations are different from ‘germline’ mutations, which are inherited genetic alterations that are present in the sperm and egg that were used in making each of us.

germlinesomatic1

Somatic vs Germline mutations. Source: AutismScienceFoundation

In the 246 samples analysed, the researchers found 315,914 somatic mutations in 18,758 genes. Yes, that is a lot, but what was very interesting was their discovery of somatic mutations in many of the PARK genes.

What are PARK genes?

There are a number (approx. 20) genes that are now recognised as conferring vulnerability to developing Parkinson’s disease. These genes are referred to as PARK genes. They include the gene that makes the protein Alpha synuclein ( SNCA ) and many others with interesting names (like PINK1 and LRRK2). Approximately 15% of cases of Parkinson’s are believed to occur because of a mutation in one (or more) of the  PARK genes. As a result there is a lot of research being conducted on the PARK genes.

Were all of PARK genes mutated in the Melanoma samples?

Somatic mutation in 14 of the 15 PARK genes (that the researchers analysed) were present in the melanoma samples. This means that after the skin cells turned into melanoma cancer cells, they acquired mutations in some of the PARK genes. Overall, 48% of the analysed samples had a mutation in at least 1 PARK gene, and 25% had mutations in multiple PARK genes (2–8 mutated genes). One PARK gene in particular, PARK 8, was more significantly present in the melanoma cells than the others. PARK8 is also known as Leucine-rich repeat kinase 2 or LRRK2 (we have previously discussed Lrrk2 – click here to read that post). Three additional PARK genes (PARK2, PARK18, and PARK20) were also significantly present, but not as significant as Lrrk2.

So what does it all mean?

The researchers speculate in the discussion of their report about what the findings could mean, but it is interesting to note that many of the PARK genes are susceptible to acquiring mutations (particularly  Lrrk2). And this is important to consider when thinking about our development as individual human beings – even though you may not born with a particular mutation for Parkinson’s disease (you haven’t inherited it from our parents), somewhere along the developmental pathway (from egg fusing with sperm to full grown adult) you could acquire some of these mutations which would make you vulnerable to Parkinson’s disease.And here we should note that skin and brain share the same developmental source (called the ectoderm). A mutation in a PARK gene could occur during your development and you would never know.

We thought this was a very interesting study – certainly worthy of reporting here.

Something lrrk-ing in the water…

 

Before you read any further, I feel it only fair to warn the squeamish amongst you that todays post is going to deal with the topic of urine. I myself have a little ‘three-nager’ who is potty training at the moment, so I am rather intimately familiar with the stuff. But consider yourselves fair warned.


 

Warning out of the way, let’s begin:

What is urine?

Urine is a liquid excression from our body, consisting of water, salts and a substance called urea. It is made in the kidneys, temporarily stored in the bladder, and eventually released through the urethra. Pretty simple right.

On a good day approximately 90-95%  of your urine will be water. Within the remaining 5%, however, there is a lot of solids that have been removed from the blood system by the kidneys. Those solids may be considered waste by our bodies, but they can tell us a lot about what is happening inside us.

Last week some researchers from the University of Alabama and Columbia University (NY) published a study that analysed some of those solids – looking at one enzyme in particular – being excreted in urine. They wanted to determine whether there were any differences between normal healthy individuals and people with Parkinson’s disease.

Their results are really interesting:

 

Urine-title

Title: Urinary LRRK2 phosphorylation predicts parkinsonian phenotypes in G2019S LRRK2 carriers.
Authors: Fraser KB, Moehle MS, Alcalay RN, West AB; LRRK2 Cohort Consortium.
Journal: Neurology. 2016 Feb 10.
PMID: 26865512

We have previously discussed Lrrk2 (and you can find that post here). It is a gene that is particularly interesting with regards to Parkinson’s disease because mutations in that gene are associated with susceptibility to the condition.

The Lrrk2 gene gives rise to an enzyme that has different functions in our cells. The researchers in the current study extracted the lrrk2 enzyme from the solid waste of urine and started analysing the “phosphorylation status of the enzyme”.

Ok, um,…what is Phosphorylation?

Phosphorylation is the process by which a phosphoryl group is added to a molecule.

And what is a phosphoryl group?!?

Oh, never you mind. Just remember that phosphorylation is basically the way in which many enzymes – like Lrrk2 – are turned on (and off when they are dephosphorylated). Through phosphorylation the function/activity of an enzyme is changed. They can go from dormant to active through this process. And this addition of the phosphoryl group to the molecule can occur at different places on that molecule, affecting the resulting activity in different ways.

So what did the researchers find?

The scientists found that people with Parkinson’s disease who also have a particular mutation in the Lrrk2 gene (that mutation is called p.G2019S) had almost 5 times more phosphorylation at a particular part of the Lrrk2 enzyme than normal healthy control subjects. Interestingly, those levels were also 4.5 times higher than those of people with PD, but who did not have the Lrrk2 mutation.

This means that the researchers have found a potential biomarker of the Lrrk2 mutation (independent of Parkinson’s disease itself). This finding could offers us a means of determining people with the Lrrk2 mutation – who may be susceptible to Parkinson’s disease – with a simple urine test.

But the researchers also noticed that among all of the study participants who have the Lrrk2 mutation,those who also had Parkinson’s disease had levels of phosphorylation twice as high as those who did not have Parkinson’s disease. Thus the overall results suggest that regardless of mutation status, higher levels of Lrrk2 phosphorylation are associated with a greater risk or the presence of Parkinson’s disease.

Lrrk-Urine1

A diagram graph illustrating the findings of the Lrrk2 study. Source: Neurology

What does this mean?

Firstly, we need to point out that the study was conducted on a small population of men (two studies actually – the first had 14 subjects, and the second had 62 subjects). The results need to be independently replicated in larger groups (ideally also containing some female participants).

The results are very exciting, however, as they may point towards potential therapeutic pathways. It could also provide a means of monitoring clinical trials – a feature that the University of Alabama researchers are currently testing in another clinical trial. They are investigating if a LRRK2 inhibitor drug, called Sunitinib, results in lower leaves of phosphorylated Lrrk2 in the urine.

The research is also encouraging with regards to the search for biomarkers in Parkinson’s disease – a quest that has struggled somewhat until recently. Novel biomarkers provide useful tools in our fight against this terrible disease.

New research – new targets of Lrrk2

 

This is Sergey Brin.

sergey_brin

He’s a dude.

Having brought us ‘Google’, he is now turning his attention to other projects.

One of these other projects is close to our hearts: Parkinson’s disease.


 

In 1996, Sergey’s mother started experiencing numbness in her hands. Initially it was believed to be RSI, but then her left leg started to drag. In 1999, following a series of tests, Sergey’s mother was diagnosed with Parkinson’s disease. It was not the first time the family had been affected by the condition: Sergey’s late aunt had also had Parkinson’s disease.

Both Sergey and his mother have had their genome scanned for mutations that increase the risk of Parkinson’s disease. And both of them discovered that they were carrying a mutation on the 12th chromosome, in a gene called Leucine-rich repeat kinase 2 or Lrrk2.

Not everyone with this particular mutation will go on to develop Parkinson’s disease, but Sergey has decided that his chances are 50:50. Being one of the founders of a large company like Google, however, has left Sergey with resources at his disposal. And he has chosen to focus some of those resources on Lrrk2 research (call it an insurance  policy).

Today, the fruits of some of that research has been published and the results are really interesting:

Elife-Lrrk2-title

Title: Phosphoproteomics reveals that Parkinson’s disease kinase LRRK2 regulates a subset of Rab GTPases
Authors: Martin Steger, Francesca Tonelli, Genta Ito, Paul Davies, Matthias Trost, Melanie Vetter, Stefanie Wachter, Esben Lorentzen, Graham Duddy, Stephen Wilson, Marco AS Baptista, Brian K Fiske, Matthew J Fell, John A Morrow, Alastair D Reith, Dario R Alessi, Matthias Mann
Journal: Elife 2016;10.7554/eLife.12813
PMID: 26824392  (This report is openly available for reading on the Elife website)

So what is Lrrk2?

Also known as dardarin (Basque for ‘trembling‘), Lrrk2 is a gene in our DNA that is responsible for making an enzyme. That Lrrk2 enzyme is involved in many different aspects of cell biology. From cellular remodeling and moving (‘trafficking’) various proteins around in the cell, to protein degradation and stabilization, Lrrk2 has numerous roles.

Discovered in 2004, Lrrk2 was quickly associated with Parkinson’s disease because mutations in this gene are amongst the most common in ‘familial Parkinson’s‘ (where an inherited genetic mutation is present in the sufferer; accounting for about 10-20% of all cases of Parkinson’s disease). The most common mutation of LRRK2 gene is G2019S, which is present in 5–6% of all familial cases of Parkinson’s disease, and is also present in 1–2% of all sporadic cases.

Curiously, mutations in Lrrk2 are also associated with increased risk of Crohn’s disease and cancer.

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The structure of Lrrk2 and where various mutations lie. Source: Intech

Given the association with Parkinson’s disease, there have been attempts to develop inhibitors of Lrrk2 as a means of treating the condition. These efforts, however, have been hampered by a poor agreement as to which proteins are interacting with Lrrk2.

The goal of the current study was to identify the key proteins that Lrrk2 acts upon.

What did they discover?

Using various techniques to accomplish their task, the scientists began with 30,000 possible targets and gradually whittled that number down to a small group of Lrrk2 targets.

Most importantly, they found that Lrrk2 is deactivating certain proteins that are called ‘Rabs’. The Rab family are heavily involved with trafficking (and that’s not the mafia drug variety!). Trafficking in cells in moving proteins around within the cell itself. And Lrrk2 was found to deactivate 4 Rab family members (3, 8, 10 and 12).

This is a very important result as not only does it provide us with novel Lrrk2 targets, but it also offers us an excellent tool with which we can determine if Lrrk2 inhibitors are actually working  – a functioning Lrrk2 inhibitor will lower the activity of Rab 3, 8 10 & 12 and this can be measured.

The results represent a major leap forward in our understanding of Lrrk2 and a significant return on investment for one Mr Sergey Brin.