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Tackling ME/CFS in New Zealand by the Principles of Precision Medicine

Bob

Senior Member
Messages
16,455
Location
England (south coast)
Below are the details of a report in the new 2016 conference version of Invest in ME's journal. The report starts on page 46.

The report details an interesting biomedical study, being carried out in New Zealand, involving proteomics, cytokines and miRNAs. It sounds fascinating.

Invest in ME - The Journal of IiMER 2016
http://www.investinme.org/Documents/Journals/Journal of IiME Vol 10 Issue 1.pdf

Tackling ME/CFS in New Zealand by the Principles of Precision Medicine

Warren P. Tate, Eiren C. Sweetman, Alex J. K. Noble, Christina D. Edgar, Grace Bateman, Angus Mackay, Margaret M. Ryan, Lynette D. Hodges & Rosamund Vallings.

Extract from the report:
In line with these concepts, we are now in the data collection stage for two small pilot studies, each with 10 patients, recruited in two separate regions of New Zealand. They are matched by age/gender with healthy controls, with one of the studies having a comparative cohort of multiple sclerosis (MS) patients, as an example of a ‘fatigue illness’ distinct from ME/CFS. Our goal is to examine and correlate changes in plasma cytokines and miRNAs, with the cellular transcriptome, and the proteome in purified immune cells. In the second study we are planning to link these molecular analyses to an exercise regime that measures physiological parameters before and after exercise. These two pilot studies in turn are preliminary to a planned larger study with 40 carefully evaluated patients from Dr Vallings health practice.

To understand the disease mechanism of ME/CFS in our NZ cohort at a molecular level, a comprehensive analysis has been undertaken in an initial pilot study group. Peripheral blood samples were taken from the study participants and plasma, lymphocytes and neutrophils extracted. From the plasma and lymphocyte immune cells total RNA (including small RNAs) was isolated using a mirVana™ PARIS™ RNA and Native Protein Purification Kit. Total protein was also obtained from the lymphocyte and neutrophil cells for western and proteome analysis. So far we have obtained and analysed data on both cytokines and microRNAs from plasma in one of our pilot studies, and are awaiting the results of analyses on the transcriptome encompassing coding, small and large noncoding RNAs, and initiating a study of the proteome.
Acknowledgements: We are grateful for support from ANZMES the national ME/CFS group of New Zealand, Lottery Health Fund of New Zealand, H S and J C Anderson Charitable Trust, a private bequest.
The study is supported by ANZMES. The Associated New Zealand ME Society Inc, Auckland, New Zealand. http://www.anzmes.org.nz



Forum discussion thread for the journal:
http://forums.phoenixrising.me/inde...journal-of-iimer-2016-conference-no-11.45036/


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Hutan

Senior Member
Messages
1,099
Location
New Zealand
For those of you not familiar with Prof Warren Tate and interested to find out more, this video is good. His daughter has ME/CFS.


Edit: Just watching it again, it's interesting to note that (20?) years ago he tried to get funding for a study on mitochondria in ME/CFS - but the medical profession and funding bodies just weren't interested in ME/CFS.
 
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Cohen2

Senior Member
Messages
119
Location
New Zealand
I am lucky enough to now be a patient in Prof Tate and his team's ongoing Me/cfs study after meeting him at a talk he gave. He was updating the local support group on the progress that had been made in the study. Unfortunately I've forgotten the details but they have found differences between controls and M E patients. I will try to get the details to update the forum.

The next stage of the study is using a Seahorse machine to look at Bioenergetic Health index in live blood cells (a measure of energy production). He and his colleagues still can't get funding from the government.

He is also in contact with Ron Davis, who showed an interest in the study at the International conference. I believe they will be sharing findings etc. I'm stoked to be part of this.

@Hutan, you may be interested in this
 

Snowdrop

Rebel without a biscuit
Messages
2,933
I am lucky enough to now be a patient in Prof Tate and his team's ongoing Me/cfs study after meeting him at a talk he gave.

I'm wondering if there may be some non disclosure issues around being in the study if they want to publish the data down the road.

Glad to hear that there is some good research going on in NZ too.
 

Cohen2

Senior Member
Messages
119
Location
New Zealand
I'm wondering if there may be some non disclosure issues around being in the study if they want to publish the data down the road.

Glad to hear that there is some good research going on in NZ too.

they've been open with their findings so far. Or would the issue be me saying I'm in it?
 

Snowdrop

Rebel without a biscuit
Messages
2,933
they've been open with their findings so far. Or would the issue be me saying I'm in it?

I don't know. There have been questions regarding sharing info on other threads about ongoing research but maybe different issues.
 

Hutan

Senior Member
Messages
1,099
Location
New Zealand
I am lucky enough to now be a patient in Prof Tate and his team's ongoing Me/cfs study after meeting him at a talk he gave. He was updating the local support group on the progress that had been made in the study. Unfortunately I've forgotten the details but they have found differences between controls and M E patients. I will try to get the details to update the forum.

Thanks for this, I look forward to hearing more about what Prof Tate spoke about.

Do you have a contact email or phone number for the study? I'd travel to Dunedin to participate if it's possible.
 

Cohen2

Senior Member
Messages
119
Location
New Zealand
Thanks for this, I look forward to hearing more about what Prof Tate spoke about.

Do you have a contact email or phone number for the study? I'd travel to Dunedin to participate if it's possible.

I think they have all participants they need/ can afford.
 

Cohen2

Senior Member
Messages
119
Location
New Zealand
Heres some slides from a talk Prof Tate gave in November on his and his collegues research. He has given me permission to post them. They may be hard to follow as they were used to aid his talk.

upload_2017-1-11_21-36-1.png

upload_2017-1-11_21-36-27.png

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upload_2017-1-11_21-37-44.png

upload_2017-1-11_21-38-22.png


upload_2017-1-11_21-39-22.png


Sorry that one slide is impossible to read
 

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user9876

Senior Member
Messages
4,556
I'm concerned that they talk about their model predictions but I assume their model was trained on the data so they are effectively reporting how well they can train a classifier to separate out their dataset.

This in itself is interesting but to claim performance figures or a classifier (or predictor as they call it) conventionally you need to use three data sets. A training set used to train the model or set of models. A test set used whilst looking at different model parameters and generally optimizing what works and a third verification set from which results are quoted once the models have been chosen and optimized.

The data does look interesting but very small sample size.
 

Mel9

Senior Member
Messages
995
Location
NSW Australia

Snow Leopard

Hibernating
Messages
5,902
Location
South Australia
The cytokine results are uninteresting, but I am interested in seeing the rest of the results, particularly the gene expression results.

Those mRNAs are different to what have been reported in previous studies, but there isn't always overlap between the candidates in such research.
 

Cohen2

Senior Member
Messages
119
Location
New Zealand
I'm concerned that they talk about their model predictions but I assume their model was trained on the data so they are effectively reporting how well they can train a classifier to separate out their dataset.

This in itself is interesting but to claim performance figures or a classifier (or predictor as they call it) conventionally you need to use three data sets. A training set used to train the model or set of models. A test set used whilst looking at different model parameters and generally optimizing what works and a third verification set from which results are quoted once the models have been chosen and optimized.

The data does look interesting but very small sample size.

They do plan on increasing the sample size but will need more funding