Updated search criteria ...

The previous search criteria found an aggregate result of 2,617 articles, which is way too many to review. In this updated version by restricting neurodegeneration to the title, and the remaining search strings to the abstract the aggregated result is 323 articles which is much more manageable.

When the seven test journal articles were run against the results, 6 out of seven (86%) of the articles were found. The next step is to progressively review the resulting abstracts in the 323 articles to ensure they search criteria is working accurately.

"...on being inclusive ..."

It is easily understood that when reviewing the search results that we want to be focused on the main articles so the end result are manageable.

However I am puzzled by two things that I am having trouble reconciling:

1. You suggest a final target of around 100 articles. However, in the area of mitochondria there are many articles written every day and so the likelihood of getting around 80-100 articles will be tough and will require quite restrictive exclusion criteria I think.
2. With tight inclusion & exclusion criteria we will be knocking out a lot of documents that could contain some relevance to the research topic. Granted the whole article is not on the topic but there may be very significant sections. Why would we exclude such an article?

I am still wrapping my mind around how to combine each of the key words in my topic and to find something that registers as a systematic component.

In my topic discussion I have focused on using the search strategies discussed in my earlier posts and the relevant results to draft up as much of the methods section and results flow diagram as possible. If I then draft up a narrative around the temporal flow and the key connections this will allow us to focus more accurately on a draft rather than talking about a proposed theme in broad terms. With the draft we can see what its strengths and weaknesses are and then look to see how we extend it to define and incorporate the systematic section which hopefully can include something we can measure.

In terms of the measurement it would be ideal to have the preamble discuss how inflammation triggers the immune response and that microglia once activated can become chronic leading to significant mitochondrial damage and subsequently being associated with neuronal damage and cell apoptosis. One measure of this could be finding experimental results that looked at ATP production, bioenergetics and mitochondrial biogenesis.

Mitochondrial dysfunction due to matrix damage

Improving upon Neuroinflammation, Microglia and neurodegeneration ...

In the initial searches of both PubMed & Medline, using Neuroinflammation, Microglia and neurodegeneration as key words produced a large number of results, often too many to be sifted through in Covedence to choose the eventual systematic review articles to investigate more fully.

Two planned changes:

1. Mitochondria are at the heart of all neurodegenerative damage, so adding in either mitochondria or mitochondrial dysfunction or impairment to capture papers investigating the links between malfunctioning mitochondria and neurodegeneration
2. Adding in ATP as the resulting loss of cellular function and/or death is due to insufficient ATP being available. lack of ATP can be tracked to either mitochondrial impairment or insufficient ATP even though the mitochondria are fully functional, due to major trauma in the cell elsewhere causing the majority of ATP to be used to remedy this trauma leaving minimal ATP for other cellular use.

Preliminary testing of these search strings is showing large numbers of results when keywords is selected because this function tests for virtually all fields ie title, abstract headers. The next test to trim down the results and make the results more relevant is to potentially do a preliminary run using a key word and mapping this to the Mesh heading to select only those categories relevant to my research. 

Running this Mesh test resulted in roughly 250% more hits moving up from 632,900 to over 1,656,967 rather than less even though the search was restricted to those key categories of interest to my research.

The next test was to explode the Mesh headers chosen o see if we can make the target search more specific to drop the numbers further. 

Unfortunately, this further narrowing of the selection virtually doubled the selection from 1,656,967 items to over 2,435,049 items.

Microglial over activation and mitochondrial dysfunction

Searching on neurodegeneration, inflammation, blood based analysis for reserach on over-activation of microglia and mitochondrial dysfunction found no systematic reviews or simple litereature reviews.

"been there done that ..."

The initial idea for chapter one of my PhD was to do a Systematic Search on a topic that introduces the links between neuroinflammation and neurodegeneration. The immune response was a focus turning up across many of the articles read, with cytokines being investigated by many researchers, so this seemed a good place to start the summary.

Unfortunately there were already numerous review articles on the involvement of cytokines with inflammation and neurodegeneration, ruling this topic out as a possible systematic review.
Next I decided to investigate what triggered the immune system, and settles on macrophages, as they had both a signalling pathway role and performed phagocytosis on endotoxins, but again this topic had been done. So again I stepped back earlier to investigate the immune response and looked at the role of microglial, specifically the their role when there was an over-activation of the microglial. Over activation seemed to the showing up as a detrimental impact on dopaminergic neuronal cells causing a higher than normal level of apoptosis. Unfortunately this topic had also been summarised.

In each of the above topics, there was only one systematic review with all the other topics having had literature reviews done on them. The problem with these reviews was that there were not all that many with the majority being a number of years old and some quite poorly written. It was almost as if these researchers were not interested in their own original research, but wanted to get their publication count up and doing a review of someone else's work was just "low hanging fruit'. Thus the number of reviews in these areas was becoming a real stumbling block to getting started on my PhD because I could not find a unique area to summarise, that also set the scene for the types of experiments that would support my research into inflammation and neurodegeneration.

The next area I looked at was the impact on cellular energy requirements when neuroinflammation and the immune response over activated microglia damaging the mitochondria and causing apoptosis due to the cells not being able to sustain their energy requirements. Searching on this topic found no systematic reviews or literature reviews, which was a great start but a problem in that there may be very few studies to investigate. This means there is definitely a gap in the research but this same gap may make it hard to create a systematic review for publication.

However I have updated my PROSPERO application to reflect my findings with the new title being :

"The role of inflammation and microglial over activation in mitochondrial dysfunction and neurodegenerative progression: A Systematic Review"

Searching PROSPERO for Macrophages ...

In order to make sure there are no other Systematic Searches on the relationships between neuroinflammation, macrophages and neurodegeneration in progress, I ran a wide search in PROSPERO using all fields for each term which revealed only three articles and each not close to my area of interest.

Search stings used:

Resulting articles: 

Macrophages signal cytokine activation

One advantage of having to change topics slightly from a cytokine focus to Macrophages, is that the research is showing that macrophages seem to activate earlier than cytokines. Thus if the end goal is to find an early bio-marker for Parkinson's disease progression, the earlier the signal from neuroinflammation and neurodegeneration the better the chances of slowing or treating the damaging process.

Moving forward, I read a paper some time back by Perry (2004) "The influence of systemic inflammation on inflammation in the brain: implications for chronic neurodegenerative disease",  in which he made mention of the role of macrophages as a key messenger in sickness behaviour. Further reading on macrophages indicated that these were instrumental in the triggering of neurodegeneration. 

The importance of macrophages was reinforced in a more recent paper by Blaylock (2017), "Parkinson's disease: Microglial and macrophage induced immunoexcitotoxicity as a central mechanism of neurodegeneration". Research by Blaylock suggests that macrophages must be fully activated in order to signal and activate cytokines such as TNF-alpha and IL-1B. In addition, they need to operate in unison with other signalling pathways such as the glutamate receptors in order to trigger excitatory responses, and that it is the combination of both macrophages and excitatory responses that creates the heightened activity that leads to increased cell death and neurodegeneration.

Systematic Review Title ...

Initial thoughts were to look at inflammation, particularly neuroinflammation and the resulting immune response - mainly cytokines & interleukin and their impact on subsequent cell death and triggering of neurodegenerative diseases such as Parkinson's disease.

The results from some of my preliminary database searches turned up a recent Systematic review:

 "Aberrations in Peripheral Inflammatory Cytokine Levels in Parkinson Disease: A Systematic Review and Meta-analysis", 2016, Qin et al.

Given that the above systematic search is very close to the one I was working on, I need to change my focus towards other blood based signalling mechanisms involved in the immune response.

Action items :

• How many articles have looked at macrophages?
• What other pathways do macrophages activate (excluding cytokines)?
• Have any of those downstream arms of the pathways been implicated?
• Look at articles citing Perry for guidance

Macrophages

Data Management for file selection

Data Management

     Once each of the search strategies are run, the following methodology will be used to collect the results and save each as individual files:

1.    Each selected database will be searched on title and abstract using the defined Search Strategy & Structure criteria outlined above. The initial raw results will then be saved to an XML file.

2.    Next the initial results will be filtered for both the inclusion and exclusion criteria outlined above, and the results will be saved to an XML file. Each of these steps will be repeated for all databases to be searched.

3.    Initial results and filtered results for inclusions and exclusions i.e. number of journals found for each database search will be recorded in line with the PRISMA 2009 Systematic review flow diagram requirements.

4.    Each XML result file will be uploaded into Covidence to assist in identifying duplicate articles. The number of duplicates will be recorded in the PRISMA flow diagram to adjust the available articles for systematic review.

5.    The resulting “cleaned” Covidence reference database journal numbers will be recorded in the PRISMA flow diagram.

6.    An email link will then be sent to three independent research academics suitably skilled to review and select appropriate journal articles for review. To ensure there is no research or selection bias, the selection of a successful article will require two out of three votes to be included for the systematic review.

7.    The final selection of journal articles will be exported as an XML file from Covidence and retained along with the raw and filtered search results from each of the five databases to support any future requests for information on the search methodology.

8.    The Covidence XML export of the final selection of journals will then be uploaded into Endnote v9 and read in full with information collected and analyzed for summary and discussion in the systematic review.

Systematic Search Strings ...

Based on the key words aken from potential target journal articles, I have developed four search strings for Inflammation, Neurodegeneration, Parkinson's disease and Blood.

Search Strategy & Structure:

Key terms used in the search strategy are:

1.  Inflamm(*) using a wild card to capture terms such as inflammation, inflammatory, neuroinflammatory

2.  Neurodegen(*) OR brain* OR “white matter” OR CNS OR “nervous system” OR neuron(*) OR dopamine(*) OR apopto(*) OR mitochond(*) using a wild card to capture terms such as neurodegeneration and neurodegenerative topics

3.  Parkinson(*) using a wild card to capture terms such as Parkinson’s disease, Parkinson’s and Parkinsonism

4. Blood(*) OR plasma OR serum OR haemoglob(*) OR "white blood cells" OR "red blood cells" OR leukocyte(*) OR peripheral(*)

Creating Key Search Words ...

Started reading a few selected journals on neuroinflammation and nerodegeneration to investigate what key word the authors were using to find their references.

My Key Words so far - A work in progress ....

Key Words:

• Neuroinflammation, inflammatory,
• Neurodegeneration, Parkinson’s disease
• Bio-marker, blood, plasma, serum,
• Dopamine, serotonin,
• Substantia nigra pars compacta (SNpc), hippocampus, neurons
• Mitochondria, reactive oxygen species, oxidative stress, misfolding, mtRNA, mtDNA
• Immune response, astrocyte, microglia, macrophage, cytokine
• Proteomics, protein,
• Lewy bodies, alpha-synuclein, tau, tauopathy, toxicity, apoptosis
• Genomics, genes
• Dysfunction, mutation

Which journal is likely to publish my review ?

How do I identify a journal that is likely to publish my systematic review?

To analyse this question, I did a preliminary database search that referenced neuroinflammation, neurodegeneration and Parkinson's disease in their key words or abstract and retrieved around 85 peer reviewed journal articles.

Next, each of the articles were uploaded into EndNote 9 and a comma delimited text file was exported to my references folder, then opened in Excel. This test failed as the file formatting was very untidy and could not be easily read.

To rectify the poor EndNote 9 formatting issues, I Googled the problem and found a YouTube file on how to export neatly from EndNote 9 into Excel.

This process involved creating a new style which included Tabs to delimit the fields. The Endnote reference export worked well this time showing author, year, title and journal name.

As each of these 85 test articles was deemed to be relevant, the excel database was then filtered by journal and the number of papers published in each journal was counted.

The test results below show that no single journal is a preferred publisher in this area and that the top three journals to investigate are the Journal of Molecular Biology, Neurobiological disorders and The Lancet Neurology.


Journal count results - 30th July 2109

1.  Journal of Molecular Neurobiology : 5
2. Neurobiological Disorders : 4
3. Lancet Neurology : 4
4. Molecular Neurodegeneration : 2
5. Neuron : 2
6. Parkinsonism and related disorders : 2

the chicken or the egg?

Proposed Systematic Review questions:

Essentially the research question is focusing on whether neuroinflammation causes cell death and leads to neurodegeneration or whether, as a result of neurodegenerative progression, there is an elevated immune response which increases neuroinflammation and leads to increased neuronal cell death.

1. Does an elevated neuroinflammation level cause increased neuronal cell death, triggering neurodegenerative disease progression, such as Parkinson’s disease or does the progression of neurodegenerative diseases such as Parkinson’s disease cause an increase in mitochondrial, genomic and proteomic dysfunction, mutation and/or failure, leading to an increased immune response triggering elevated neuroinflammation causing increased neuronal cell death.
   
2. What are the key neuroinflammatory mechanisms associated with triggering neurodegenerative progression and neuronal apoptosis in Parkinson's Disease and is it possible to identify changes over time in order to establish a blood based early bio-marker suggesting a predisposition towards neurodegeneration?

Searching PROSPERO for similar research

In the PRISMA-2015 document, there is mention of registering our research idea and the type of systematic review we are going to undertake on PROSPERO. 

I thought I would go onto PROSPERO & see if anybody is already in our space and found that only one group (Mirian 2018 – attached) are currently close to out idea. Their objective is very similar to ours:

“Review question: What are the neuroinflammatory cellular mechanisms associated with the neurodegenerative process in Parkinson's Disease?

Main outcome(s): To observe cellular alterations, specifically, in microglia, mast cells and astrocytes through post mortem tissue of individuals with Parkinson's Disease. To compare the results with cellular characteristics of post mortem tissue of individuals without Parkinson's Disease.”

Whilst we may have a similar review question, and look to investigate similar variables i.e. microglia & astrocytes as part of the immune system response to neuroinflammation, I think there is still a big difference between the two studies. Their study will be based on post mortem tissue samples, which I feel is a reactive and slow study, whilst ours is a pro-active study which plans to use current whole blood & plasma samples from existing PD patients to compare normal controls against PD patients to establish some of the following:

1. Does neuroinflammation as a result of an immune response lead to neurodegeneration and trigger PD, OR does the presence of cellular/protein changes such as Lewy bodies present in neurodegenerative cases such as PD, cause an increased immune response leading to a heightened level of neuroinflammation ?
2. Correlation between controls & PD for protein mutations i.e. LRRK2 linked to the onset of PD using proteomic and statistical analysis
3. Corroboration of mutation and identification of aberrant genetic mutation and malfunction using genomic & statistical analysis
4. Levels of oxidative respiration dysfunction, mutation and/or failure in mitochondria implicated in PD and their associated areas in the brain
5. In each of the analyses above how are neuroinflammation response markers such as microglia, astrocytes and macrophages manifested and are 5their differences between a normal control and PD group?

Another key difference in their study, is that their patient is already dead so cannot be helped, ours are still alive and for those just entering the study as part of assisting us to set up a temporal database, any finding we make, may be able to be exploited to infer an early high correlation bio-marker that could assist in making early changes to their medication and clinical treatment, resulting in slowing the onset of further neurodegeneration, neuroinflammation and subsequent onset of PD symptoms.

Finally, If we can register our research gap to protect our idea and subsequent IP, it might be good to approach this team down the track to see if each of our results are pointing in the same direction i.e. are their post mortem results showing the terminal results we anticipate from our temporal proteomics and mitochondrial analysis from bloods?

Registering on PROSPERO: PROSPERO Home page:

Search for competing research

A search of the PROSPERO International prospective register of systematic reviews found only one close review to my proposed work.

Topic: Analysis of neuroinflammatory cell mechanisms associated with neurodegenerative
process in Parkinson's disease: a systematic review

Proposed by: Mirian David, Renaly Rodrigues, Carlúcia Franco, Clarissa Bezerra

Review question: What are the neuroinflammatory cellular mechanisms associated with the neurodegenerative process in Parkinson's Disease?

The main key difference is that Mirian et.al. are investigating how the immune response of astrocytes and microglia are showing up in post mortem brain slices, whilst we are proposing to look at changes and mutations in protein structures and mitochondria in neural cells using proteomics and Seahorse oxidative respiration analysis.

Document link:

PROSPERO Link for Analysis of neuroinflammatory cell mechanisms: A systematic Review

Planning a Systematic Review (PRISMA-P)

In preparation for doing a systematic review on my research topic to see what prior research has been done, how it might relate to my topic of neuroinflammation, neurodegeneration and the triggering of Parkinson's disease, I need to take a look at the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-analyses) guidelines.

Document DOI reference: 10.1136/bmj.g7647