Availability of Environmental Data in some PD Cohorts

Accessing and Understanding Data
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Hello everyone!

Today, I wish to highlight the significance of environmental data in PD research. Often, our focus is drawn towards genetic and clinical aspects, but it’s crucial to acknowledge the role that environmental factors also play. As we all know, a variety of environmental factors can play an important role, either as protective or risk factors in the development of the disease and, possibly, in its progression.

This is a current hot topic in PD research. While several authors argue that a range of environmental factors are contributing to a significant increase in the incidence and prevalence of PD, which cannot be fully explained by population aging alone, thus supporting the concept of a PD pandemic (The Emerging Evidence of the Parkinson Pandemic - PubMed), others, although acknowledging the significant and known environmental influence in this scenario, argue that the intensity of these factors is not so great (What is the Parkinson Pandemic? - Movement Disorders). This opens up space for many reflections and studies that truly want to answer this question.

To illustrate this, I present a comparison across four PD research databases: PPMI (through its substudy: PPMI FOUND), Fox Insight, PDBP, and GP2. This simple spreadsheet was constructed by visiting each respective study’s platform and questionnaires utilized. If any information is imprecise, please notify me!

PPMI FOUND
(n = 684)		 Fox Insight
(n = 54,604)		 PDBP
(n = 5,034)		 GP2
(n = 24,935)
Air Quality / Pollutants No No No No
Alcohol Yes Yes No Yes
Anti-Inflammatory Medication Yes Yes No Yes
Caffeine Yes Yes No Yes
Calcium Channel Blocker Yes Yes No No
Head Injury or Concussion Yes Yes No Yes
Occuputaion Yes Yes No Yes
Female Reproductive Health Yes Yes No No
Pesticides at Work Yes Yes No Yes
Pesticides in Non-Work Settings Yes Yes No Yes
Physical Activity Yes Yes No No
Residental History Yes Yes No Yes
Smoking and Tobacco Yes Yes No Yes
Toxicants Yes Yes No No

Note: Although Fox Insight cohort numbers are huge, several patients did not respond to all of the aforementioned questionnaires.

I think that analyzing these data in conjunction with genetic and clinical information can reveal complex gene-environment interactions, aiding in identifying risk groups and tailoring treatments. I also envision that one great study would be to both calculate PD risk using polygenic risk scores and environmental factors in one single analysis. I think this would enhance our knowledge deeply and aid us in better understanding what is missing in the understanding of complex PD development. If you know of any publication that has already done this, please tell me!

My aim with this post is to further edit it as new suggestions are presented. I thought of including the UK Biobank here, however, as I do not have a lot of expertise with this dataset, I haven’t done so.

Thanks for the attention!

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Thank you for sharing! Very interesting!

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Hi @danieltds , thanks for sharing! Would note that the environmental exposure questionnaires from Fox Insight were administered only one-time (rather than longitudinally) and remained open from October 2017-March 2019, but response rates varied from ~2000-8000 depending on which environmental exposure survey is being considered.

In any event, think this table could be useful and I wonder if a series of tables like this based on subjects of interest would be a helpful resource? Not sure it will fit the data wrangling guide, but perhaps @malosco @ehutchins can weigh in later this week.

In terms of publications:

  1. Joanne Trinh (an MJFF collaborator in Christine Klein’s lab in Luebeck has recently published on PRS/environmental exposure (particularly regarding LRRK2/g2019s): Interaction of Mitochondrial Polygenic Score and Lifestyle Factors in LRRK2 p.Gly2019Ser Parkinsonism.

  2. Alastair Noice and many GP2 collaborators also look to have published on this topic regarding specifically UK Biobank data: Parkinson’s disease determinants, prediction and gene–environment interactions in the UK Biobank.

MJFF has long been interested in environmental exposure PD (see: paraquat-related research in particular), so definitely interest in our end too if you are looking at further research in this field.

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Thanks a lot for the additionnal information regarding Fox Insight! I checked 2 to 3 of those group of variables in the FoxDEN and saw something similar as you posted regarding the quantity of available data, but as I did not commit to all those specific information, I decided to not detail it any further, so thank you!

Regarding the shared articles: thanks also! I did not knew about the first and but I read the second one some time ago. I think they are more or less aligned with what I aimed to know, however, I wanted something in the mix of the genetic heritability as published in the largest GWAS to date (https://pubmed.ncbi.nlm.nih.gov/31701892/) and on the concept of an environemental Population Attributable Fraction (such as presented in Population fraction of Parkinson’s disease attributable to preventable risk factors - PMC)

In summary, I think an article stating that they could explain 30% of PD from genetic factor and like 20-25% from enviornmental factors or something in these lines would be interesting (from which 2% are from pesticides, 3% from head impact etc)

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Hi Daniel, Hi Josh,

Thank you for bringing this important point up. We have given extensive efforts in mining the available environmental data. Yes, there are gaps and more needs to be done to fill it. If you want details please give me a shout. Daniel, Your idea on the percentages of heritability vs environment is very nice.
We have some preprints and longitudinal data analysis planned ahead.

Here is my research group information:

We are affiliated with the institute of neurogenetics in Lübeck but are an independent group.

Keep me posted.
Joanne

P.S. I am new to this platform, hope I’m using this correctly :slight_smile:

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Thanks for commenting @joanne.trinh! Tagging @danieltds to ensure he sees your reply :slight_smile:

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Hello Joanne! It is a pleasure to meet you and to know of your interest in this topic!

It’s great to hear from someone with a shared interest in multimodal data integration in PD research. I read your research group areas of research and liked it a lot! Like you, I also think that aggregatting as much type of different data types and domains is of utmost importance for new discoveries in PD. I’m a medical doctor from Brazil, currently pursuing my PhD. My research involves PD subtyping, integrating neuroimaging, transcriptomics, and genomics to understand their clinical and biomarker correlations. Nonetheless, my interest in the relation of environmental factors to PD is very high.

Nice to see more people affiliated with the institute of neurogenetics in Lübeck! I’m currently collaborating with Zih-Hua from the GP2 monogenic hub and have previously co-authored an article with Dr. Christine Klein. It seems Lübeck is trully a reference on neurogenetics!

I’m quite excited about the analysis idea I’ve proposed, but like many researchers, I’m currently juggling multiple commitments and unable to take on additional projects., but I will give some attention to it if can (if someone hasn’t explored it yet). As a clinician, this type of data is really relevant to patients and policy making.

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