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Australian scientists make breakthrough in Chronic Fatigue Syndrome testing

Messages
15,786
None of the findings are statistically significant when correcting for multiple comparisons.
This letter was already briefly discussed at http://forums.phoenixrising.me/inde...-muscarinic-receptor-gene-polymorphism.43027/

Basically, the way they calculated percentages to find statistical differences is completely meaningless. Instead of looking at allele prevalence in each group (patients and controls), they listed the prevalence for each group as a percentage of the prevalence in the combined group. That's why the two values in each row always add up to 100%.

This is a problem because the ME group has 100 patients and the control group only has 90. So of course the ME group is going to have a bigger share of the genotypes listed.

I'm amazed they were even able to publish this as a letter. And I can't see how anything useful can result from this.
 

Sea

Senior Member
Messages
1,286
Location
NSW Australia
I must admit I am very confused. Neither the press release nor the blurb on Griffith Uni's page nor the transcript of the radio interview actually mention what the finding is or which paper it is referring to.

I've seen discussions over the last few days with people assuming it is the snps paper @Valentijn referenced above and others assuming it is this one

A Preliminary Comparative Assessment of the Role of CD8+ T Cells in
Chronic Fatigue Syndrome/Myalgic Encephalomyelitis and Multiple
Sclerosis
Ekua W. Brenu, Simon Broadley, Thao Nguyen, Samantha Johnston, Sandra
Ramos, Don Staines, and Sonya Marshall-Gradisnik
http://www.hindawi.com/journals/jir/2016/9064529/abs/

I haven't seen enough info out there to be able to tell if it's either of these or something else.

2 comments I've seen attributed to Don Staines:
1. "We've found a specific marker on white blood cells" (from the radio transcript I think)
2. "We've found a unique marker" (I can't remember where I read this one)

The snps study certainly can't be called a 'unique' marker and I don't know that it has anything to do with white blood cells either.

I wish the researchers would clarify what they're talking about. Surely that can be done without revealing anything confidential
 

alicec

Senior Member
Messages
1,572
Location
Australia
Which would make a little more sense than a study of SNPs in mitochondria

What study of SNPs in mitochondria?

The SNP study was of TRP melastatin M3 ion channels and muscarinic ACh M3 receptors.

The quote from Don Staines in the radio interview did sound more like it was referring to this SNP study rather than the CD8 T cell study.

"We're looking at changes in very specific parts of gene that then translate to certain receptors or proteins in the body that have key roles in metabolism, neuronal function, cardiovascular function and so on"

But it is all very vague, very preliminary, the SNP study is meaningless, the T cell study tiny - so nothing to get excited about yet.
 

alex3619

Senior Member
Messages
13,810
Location
Logan, Queensland, Australia
No snp, by itself, would be diagnostic. It might indicate a risk factor. However a change in how one or more genes are expressed, including protein changes, that could be important.

If a snp were causally associated with CFS, rather than risk for CFS, then most of us would have CFS (or ME) from birth.

So such a snp would have to be combined with one or more other factors to be used diagnostically.
 

user9876

Senior Member
Messages
4,556
It could be unpublished work. If they were to have found something good they may patent before publishing (I think in the US you get a years grace between publishing and patenting but not in the rest of the world).

They have recently filed this patent (filed 10th Aug 1015 but published Feb 2016)
https://www.google.co.uk/patents/WO2016023077A1?cl=en&dq=sonya marshall-gradisnik

Abstract

In one embodiment the invention relates to the use of differentially expressed microRNAs (miRNAs) as biological markers for identifying subjects that have Chronic Fatigue Syndrome (CFS) and/or Myalgic Encephalomyelitis (ME) [systemic exertion intolerance disease (SEID)], or are at risk of developing CFS and/or ME. In another embodiment, the invention relates to probes, tools, reagents, kits and assays for screening subjects for CFS and/or ME and/or managing CFS and/or ME and/or managing CFS and/or ME.


First claim is below which seems incredibly wide. Patent lawyers sometimes say try very general and it can be reduced later if the patent office complain. They have a huge number of claims as well.
1. At least one miRNA for use as a biological marker for Chronic Fatigue Syndrome (CFS) and/or Myalgic Encephalomyelitis (ME), or at least one miRNA biological marker for use in identifying or diagnosing a subject having CFS and/or ME, or at least one miRNA biological marker for use in identifying or diagnosing a subject at risk of developing CFS and/or ME, or at least one miRNA biological marker for use in managing a subject having or at risk of developing CFS and/or ME, or at least one miRNA when used as a biological marker for CFS and/or ME, or at least one miRNA biological marker when used in identifying, diagnosing and/or managing a subject having or at risk of developing CFS and/or ME.

I don't understand what micro RNA are but looking at wikipedia they could be some kind of role in controlling gene expression
https://en.wikipedia.org/wiki/MicroRNA
A micro RNA (abbreviated miRNA) is a small non-coding RNA molecule (containing about 22 nucleotides) found in plants, animals and some viruses, that functions in RNA silencing and post-transcriptional regulation of gene expression.[1][2]
 
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Bob

Senior Member
Messages
16,455
Location
England (south coast)
They have recently filed this patent (filed 10th Aug 1015 but published Feb 2016)
https://www.google.co.uk/patents/WO2016023077A1?cl=en&dq=sonya marshall-gradisnik
Good find!

(Edit: this is a better link for the patent because it displays the tables properly.)

Extracts from patent:
The present inventors have now discovered and characterised miRNAs that are differentially expressed in subjects having CFS and/or ME as compared with healthy subjects.
The present inventors believe themselves to be the first to identify miRNAs, particularly circulating or extracellular miRNAs that are differentially expressed in subjects having CFS and/or ME. The inventors have found that these miRNAs, particularly from biofluid such as plasma, (but also from serum, urine, sputum and cerebrospinal fluid), can serve as novel reproducible biological markers for CFS/ME screening, prevalence, diagnosis, monitoring and/or prognosis.
Although, there is currently no definitive source identified for extracellular miRNAs - i.e. a definitive source leading to miRNAs locating within biofluids - blood cells in particular reticulocytes, myeloid cells, lymphoid cells, platelets, cells from the liver, lungs and kidneys or lysed cells may release miRNAs into the circulation [31,32,33]. Similarly, miRNAs may be discharged into biofluid/plasma following tissue damage, for example, following acute myocardial infarction [34].
The at least one miRNA can be a SNP, including a SNP in pre-miRNA or miRNA flanks.
In view of the fact that one or more miRNA biological markers for CFS and/or ME have been discovered and characterised, this enables management of a subject that has been identified as having CFS and/or ME, and identifying whether a subject having CFS and/or ME is likely to respond to, or is responding to, management of that illness.
In some embodiments, the methods of the different forms of the invention can comprise the step of using a reference or control in the form of a reference gene. The reference gene can be any suitable stably expressed gene but is preferably hsa-miR-16-5p or RNU6B.
The method of any one of paragraphs 74 to 79, wherein said miRNA is hsa- miR127-3p, hsa-miR-142-5p or hsa-miR-143-3p.
Of the 19 differentially expressed miRNAs 16 were considered low in abundance due to a base mean count of less than 1,000 reads, their detection was found to be unreliable for confirmative RT-qPCR. However, they remain excellent candidates as miRNA biological markers for CFS/ME. The remaining three miRNAs (hsa-miR127-3p, hsa-miR-142-5p and hsa- miR-143-3p) were all up-regulated in CFS/ME compared to non-fatigued controls.
To date, screening for CFS/ME has been based on well-established case definitions [3,30]. Profiling of biofluid/circulating miRNA levels serves to enhance the molecular diagnosis of CFS/ME. Using Illumina HTS, 19 miRNAs were identified that were differentially expressed in CFS/ME patients. Of these, only three were confirmed to be highly abundant in the CFS/ME patients in comparison to the controls. These results suggest that miR-127-3p, miR-142-5p and miR-143-3p may be implicated in the pathogenesis of CFS/ME.
[00456] MiR-142-5p is important for T cell development where it targets SLAM associate protein (SAP). Inhibition of miR-142-5p may increase the expression of CD84, IL-10, SAP and IgG production [41]. CD84 is an important T cell regulatory marker as it regulates cytokine production, function, adhesion and interaction with B cells [42]. The levels of IL-10 have been shown to be equivocal in CFS/ME patients. The cause of an increase in miR-142-5p is unknown, however, it is possible that this may be related to heightened Treg suppression and additional autoimmune responses.

[00457] MiR-143-3p targets IgG Fey receptor 1 and also CD64 reducing lung inflammation. It is a tumour suppressor gene and is highly down regulated in colorectal cancer [43]. It inhibits the oncogene KRAS [44]. Overexpression of miR-143-3p in most cancer cells stagnates the growth of tumours and cancer cells [45] as it may act to reduce BCL2 mRNA thereby preventing tumour or cancer cell proliferation and promoting apoptosis [46]. miR-143-3p has been identified as a neutrophil specific miRNA [47]. Importantly, its expression is upregulated in cases of heightened erythropoiesis such as in polycythemia [48]. In CFS/ME increased levels of neutrophil apoptosis occurs in some patients [49,50,51], and this potentially ensues from high levels of miR-143-3p.

[00458] MiR-127-3p interferes with ERK signalling, a tumour suppressor and upregulations have been shown to increase apoptosis [52]. Importantly, it targets BCL6 a transcription factor which increases p53 expression [53]. BCL6 inhibits the production of IL-10 therefore by dampening BCL6 as a consequence of miR-127 upregulation may result in significant increases in IL-10 [54]. In CFS/ME equivocal levels of IL-10 have been reported and an over expression of miR-127-3p may explain to some extent some of these patterns. BCL6 is an important transcription factor required for germinal centre B cell and follicular helper T cell development [55,56,57]. Irregularities in the expression of BCL6 may result in aberrant inflammatory responses and the development of various lymphomas [58].
Plasma miRNAs show great promise as potential non-invasive biological markers, but at present the precise and accurate measurement is challenging. A number of factors including cellular contamination, haemolysis and low quantity can result in significant bias that does not reflect the original biological state of the sample. Current circulating miRNA research indicates that haemolysis may influence the availability of miRNAs in circulation [33].

Haemolysis may be evaluated in archival data by examining the delta Cq of miR-451 and miR- 23a [33]. In healthy individuals, 194 miRNAs may be detected in both haemolysed and non- haemolysed blood samples, where 40.2% may be upregulated following haemolysis, 13% may be down regulated and 28.9% are unaffected by haemolysis [62,63]. As described herein, three candidate miRNAs, miR-127-3p, miR-143-3p and miR-142-5p are among the miRNA genes unaffected by haemolysis in healthy individuals [62] .
Example 2 (i.e. Study 2):
[00477] As per Example 1 , hsa-miR-16-5p was the preferred reference gene. To determine whether hsa-miR-127-3p, hsa-miR-J42-5p, hsa-miR-143-3p are specific to CFS/ME patients, RT-qPCR was undertaken in a new and larger cohort of CFS/ME patients (n-49). RT-qPCR results for hsa-miR-127-3p, hsa-miR-l42-5p, hsa-miR-143-3p were consistent with previous findings in Example 1. However hsa-miR~142-5p was not statistically significant. See Figure 4, wherein CFS/ME patients are labelled 'CPS' and non-fatigued (healthy) controls are labelled 'HE' .

[00478] Discussion

[00479] The results from this validation study demonstrate that hsa-miR-l27-3p, hsa-miR- 142-5p, hsa-miR-143-3p are upregulated in the plasma samples of patients with CFS/ME as described in Example L thus confirming biological marker suitability.
Example 3 (i.e. Study 3):
No significant results using spinal fluid rather than blood plasma.
 
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A.B.

Senior Member
Messages
3,780
Table 5: MiRNAs differentially expressed between CFS/ME and non-fatigued controls
index.php
 

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nandixon

Senior Member
Messages
1,092
It could be unpublished work. If they were to have found something good they may patent before publishing (I think in the US you get a years grace between publishing and patenting but not in the rest of the world).

They have recently filed this patent (filed 10th Aug 1015 but published Feb 2016)
https://www.google.co.uk/patents/WO2016023077A1?cl=en&dq=sonya marshall-gradisnik
You had also previously (in 2014) started a thread for a published study that is closely related to the patent application you found:

High-Throughput Sequencing of Plasma MicroRNA in CFS/ME
 
Messages
15,786
You had also previously (in 2014) started a thread for a published study that is closely related to the patent application you found:

High-Throughput Sequencing of Plasma MicroRNA in CFS/ME
So it looks like it was based on a pretty small study with no correcting for multiple comparisons. And presumably hasn't been replicated in a larger group.

This is why patents never excite me. People literally patent everything, with little or no cause to think the patent will ever be useful.
 

Owl42

Psychedelic bird
Messages
53
Location
Mexico
Hey guys, is this the publication you've been waiting for? I just got through it and came here to look for your opinion on it. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3120691/

It remembers me of this other research on SFC biomarkers that is being done now in my country http://forums.phoenixrising.me/inde...led-immune-biomarker-study.42781/#post-692283

What do you think? I see it as very promising for the best treatment I've been given are immunomodulators that actually enchanced NKcell activation.