Today’s post involves massive multidimensional datasets, machine learning, and being able to predict the future.
Researchers are the National Institute on Aging and the University of Illinois at Urbana–Champaign have analysed longitudinal clinical data from the Parkinson’s Progression Marker Initiative (PPMI) and they have found three distinct disease subtypes with highly predictable progression rates.
NOTE: Reading about disease progression may be distressing for some readers, but please understand that this type of research is critical to helping us better understand Parkinson’s.
In today’s post, we will look at what the researchers found and discuss what this result could mean for the Parkinson’s community.
Today I am going to break one of the unwritten rules of science communication (again) .
Until a research report has been through the peer-review process you probably should not be discussing the results in the public domain.
But in this particular case, the research is really interesting. And it has been made available on the OPEN ACCESS preprint depository website called BioRxiv.
So what does the new research investigate?
In an effort to better understand Parkinson’s, researchers have repeatedly analysed data from large epidemiological studies in order to gain insight into factors that could have a possible causal influence in the development of the condition.
This week a manuscript was made available on the preprint website BioRxiv that provided us with a large database of information about aspects of life that are associated with increased incidence of Parkinson’s.
Some new associations have been made… and some of them are intriguing, while others are simply baffling!
In today’s post, we will have a look at what has been learnt from epidemiological research on Parkinson’s, and then discuss the new research and what it could mean for Parkinson’s.
What are the differentiators? Source: Umweltbundesamt
What makes me different from you?
Other than my ridiculous height and the freakishly good looks, that is. What influential factors have resulted in the two of us being so different?
Yes, there is the genetics component playing a role, sure. 7,500 generations of homo sapien has resulted in a fair bit of genetic variation across the species (think red hair vs brown hair, dark skin vs light skin, tall Scandinavians vs African pygmies, etc). And then there are aspects like developmental noise and epigenetics (factors that cause modifications in gene activity rather than altering the genetic code itself).
And over-riding all of this, is a bunch of other stuff that we generally refer to simply as ‘life’. Habits and routines, likes and dislikes, war and famine, etc. The products of how we interact with the environment, and how it interacts with us.
But which of all these factors plays a role in determining our ultimate outcome?
It is a fascinating question. One that absorbs a large area of medical research, particularly with regards to factors that could be influential in causing a specific chronic conditions.
What does this have to do with Parkinson’s?
One of the cardinal features of the Parkinsonian brain are dense, circular clusters of protein that we call ‘Lewy bodies’.
But what exactly are these Lewy bodies?
How do they form?
And what function do they serve?
More importantly: Are they part of the problem – helping to cause of Parkinson’s? Or are they a desperate attempt by a sick cell to save itself?
In today’s post, we will have a look at new research that makes a very close inspection of Lewy bodies and finds some interesting new details that might tell us something about Parkinson’s.
Neuropathologists conducting a gross examination of a brain. Source: NBC
A definitive diagnosis of Parkinson’s disease can only be made at the postmortem stage with an examination of the brain. Until that moment, all cases of Parkinson’s disease are ‘suspected’.
When a neuropathologist makes an examination of the brain of a person who passed away with the clinical features of Parkinson’s, there are two characteristic hallmarks that they will be looking for in order to provide a final diagnosis of the condition:
1. The loss of specific populations of cells in the brain, such as the dopamine producing neurons in a region called the substantia nigra, which lies in an area called the midbrain (at the base of the brain/top of the brain stem).
The dark pigmented dopamine neurons in the substantia nigra are reduced in the Parkinson’s disease brain (right). Source:Memorangapp
2. Dense, circular clusters (or aggregates) of protein within cells, which are called Lewy bodies.
A cartoon of a neuron, with the Lewy body indicated within the cell body. Source: Alzheimer’s news
What is a Lewy body?
A Lewy body is referred to as a cellular inclusion (that is, ‘a thing that is included within a whole’), as they are almost always found inside the cell body. They generally measure between 5–25 microns in diameter (5 microns is 0.005 mm) thus they are tiny, but when compared to the neuron within which they reside they are rather large (neurons usually measures 40-100 microns in diameter).
A photo of a Lewy body inside of a neuron. Source: Neuropathology-web
How do Lewy bodies form? And what is their function?
The short answer to these questions is:
The longer answer is: Our understanding of how Lewy bodies are formed – and their actual role in neurodegenerative conditions like Parkinson’s – is extremely limited. No one has ever observed one forming. Lewy bodies are very difficult to generate in the lab under experimental conditions. And as for their function, this is the source of much guess work and serious debate (we’ll come back to this topic later in this post).
Ok, but what are Lewy bodies actually made of?
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.
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.
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.
Is there an easier way of making this research available?
So this is Prof Paul Ginsparg.
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.
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).
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:
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
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).
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).
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).
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