Changes in the transcriptome of circulating immune cells of a NZ cohort with ME/CFS (2019) Sweetman et al

[RoseE]

I saw this posted on the "ME/CFS-Evolving Science" facebook page...

Changes in the transcriptome of circulating immune cells of a New Zealand cohort with myalgic encephalomyelitis/chronic fatigue syndrome
Eiren Sweetman, Margaret Ryan, Christina Edgar, Angus MacKay, Rosamund Vallings, Warren Tate (NZ)

International Journal of Immunopathology and Pharmacology Volume: 33 Article first published online: January 11, 2019; Issue published: January 1, 2019

https://doi.org/10.1177/2058738418820402

"Our exploratory approach has enabled us to obtain a rich differentially expressed gene dataset to identify changed biology in ME/CFS. We have identified the circadian rhythm dysregulation pathway as a new possible underlying cause of the unrefreshing sleep, fatigue and metabolic abnormalities seen in ME/CFS. Furthermore, impaired mitochondrial function and resulting oxidative stress, coupled with chronic immune-inflammatory signalling, provides a compelling explanation for the fatigue, cognitive dysfunction and post-exertion malaise experienced in ME/CFS.

Therefore, this study is a further step towards gaining an understanding of the disease process and identifying putative biomarkers to support clinical diagnosis. The biological pathways identified offer a rational explanation of the complex and often multi-systemic nature of ME/CFS."

 

[obeat]

@Keela Too @adambeyoncelowe . Do not let NICE wimp out on sleep hygiene. The problem is that we can't " self-correct" our sleep

 

[Andy]

Full abstract, although link in the original post above gives access to full paper.

Abstract
Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a poorly understood disease affecting 0.2%–2% of the global population. To gain insight into the pathophysiology of ME/CFS in New Zealand, we examined the transcriptomes of peripheral blood mononuclear cells by RNA-seq analysis in a small well-characterized patient group (10 patients), with age/gender-matched healthy controls (10 control subjects).

Twenty-seven gene transcripts were increased 1.5- to sixfold and six decreased three- to sixfold in the patient group (P < 0.01). The top enhanced gene transcripts, IL8, NFΚBIA and TNFAIP3, are functionally related to inflammation, and significant changes were validated for IL8 and NFΚBIA by quantitative polymerase chain reaction (qPCR). Functional network analysis of the altered gene transcripts (P < 0.01) detected interactions between the products related to inflammation, circadian clock function, metabolic dysregulation, cellular stress responses and mitochondrial function. Ingenuity pathway analysis (P < 0.05) provided further insights into the dysfunctional physiology, highlighting stress and inflammation pathways. This analysis provides novel insights into the molecular changes in ME/CFS and contributes to the understanding of the pathophysiological mechanisms of the disease.

 

[obeat]

One of the grant application for NIH center was a sleep related project, although I can't remember what type of study it was.

 

[mariovitali]

@ScottTriGuy @JaimeS


"The Devil is in the detail "

From the same paper, supplemental material :






Link : https://journals.sagepub.com/doi/su...8820402/suppl_file/Supplementary_Material.pdf

Also mentions on PPAR signaling :

The TNFR2 signalling pathway (Supplementary Table S4) regulates TNFα activity by antagonizing TNFα-induced apoptosis, especially in highly activated T cells. LPS-stimulated mitogen activated protein kinase (MAPK) (Supplementary Table S4) drives the inflammatory response in macrophage immune cells. Peroxisome Proliferator-Activated Receptors (PPAR) signalling was also identified as affected (Supplementary Table S4). PPAR signalling molecules regulate metabolic processes in heart muscle tissue, inflammation and oxidative stress and facilitate interactions between circadian, metabolic (lipid metabolism) and cardiovascular pathways

 

[rvallee]

I saw this posted on the "ME/CFS-Evolving Science" facebook page...

Changes in the transcriptome of circulating immune cells of a New Zealand cohort with myalgic encephalomyelitis/chronic fatigue syndrome
Eiren Sweetman, Margaret Ryan, Christina Edgar, Angus MacKay, Rosamund Vallings, Warren Tate (NZ)

International Journal of Immunopathology and Pharmacology Volume: 33 Article first published online: January 11, 2019; Issue published: January 1, 2019

https://doi.org/10.1177/2058738418820402

"Our exploratory approach has enabled us to obtain a rich differentially expressed gene dataset to identify changed biology in ME/CFS. We have identified the circadian rhythm dysregulation pathway as a new possible underlying cause of the unrefreshing sleep, fatigue and metabolic abnormalities seen in ME/CFS. Furthermore, impaired mitochondrial function and resulting oxidative stress, coupled with chronic immune-inflammatory signalling, provides a compelling explanation for the fatigue, cognitive dysfunction and post-exertion malaise experienced in ME/CFS.

Therefore, this study is a further step towards gaining an understanding of the disease process and identifying putative biomarkers to support clinical diagnosis. The biological pathways identified offer a rational explanation of the complex and often multi-systemic nature of ME/CFS."

I'm not sure there's anything particular about our sleep. It's "unrefreshing" not because of anything in particular, it's just that nothing is. For sure some have disturbed sleep patterns but that may just be coincidence, it's a common problem. When nothing gives you back energy, it's just normal that sleep would fail at that too.

 

[mariovitali]

I'm not sure there's anything particular about our sleep. It's "unrefreshing" not because of anything in particular, it's just that nothing is. For sure some have disturbed sleep patterns but that may just be coincidence, it's a common problem. When nothing gives you back energy, it's just normal that sleep would fail at that too.

In my case, it was part of ME/CFS. I had many issues with my sleep and the amazing thing is that as i was beginning to feel better, so was my sleep getting deeper, i was able to recall dreams (something that hasn't happened for years) and also the duration of the sleep was gradually being increased. At the worst point of my problems i was getting around 4.5-5 hours sleep per day

 

[ScottTriGuy]

We have identified the circadian rhythm dysregulation pathway as a new possible underlying cause of the unrefreshing sleep, fatigue and metabolic abnormalities seen in ME

@Alvin

 

[Perrier]

I'm not sure there's anything particular about our sleep. It's "unrefreshing" not because of anything in particular, it's just that nothing is. For sure some have disturbed sleep patterns but that may just be coincidence, it's a common problem. When nothing gives you back energy, it's just normal that sleep would fail at that too.

Dear Rvallee
Our family member had good normal sleep. Obviously, before an exam there might be anxiety, but sleep was good. Once the ME hit overnight, the sleep also tanked, and tanked so badly meds were required and still it is not good.

 

[Amw66]

In my case, it was part of ME/CFS. I had many issues with my sleep and the amazing thing is that as i was beginning to feel better, so was my sleep getting deeper, i was able to recall dreams (something that hasn't happened for years) and also the duration of the sleep was gradually being increased. At the worst point of my problems i was getting around 4.5-5 hours sleep per day

That' s around what i get without ME with around 2-3 breaks in it. ...I have never been a good sleeper .

 

[Hutan]

To the best of our knowledge, this is the first RNA-seq that has analysed PBMCs of ME/CFS patients. This technology was, however, used in a recent whole blood study analysing adolescent ME/CFS participants by gene set enrichment.4 Our analysis was consistent with their findings, suggesting impairment of B cell differentiation and survival, enhanced innate antiviral responses and inflammation.

It's good to see this study; it feels as though it could contain some clues.

I need to read it again, and then a few more times, and even then I won't understand everything.

In the meantime, I do wonder about the graph:

Figure 1. (a) Mean fold-change in expression between ME/CFS and controls of IL8, NFKBIA and TNFAIP3after RT-qPCR assays (±SEM). (b) Scatter plot of normalized triplicate RT-qPCR assay Ct values for each gene in the ME/CFS (n = 10) and control (n = 10) cohorts. The mean Ct value for each gene in the cohorts is also shown (orange line). The Ct value is the PCR amplification cycle at which the gene transcript exceeded the individually calculated baseline threshold level for that gene.

(note the numbers on the y axis. Ct value: smaller numbers indicate fewer PCR amplification cycles required to produce enough gene transcript to exceed a baseline threshold. So smaller numbers indicate that there is more of the relevant RNA.)

The distribution of data points doesn't look that different in PwME and controls - there's a lot of overlap. These are small samples. It would be interesting to know if the people with high levels of IL8 gene transcripts are also the ones with high gene transcripts for NFKBIA and TNFAIP3, and, if so, if there was anything different about those PwME from the significant number of PwME who had levels comparable with the controls.

Edit: also there don't seem to be 10 data points for each [transcript type+cohort]. Why is that?

Also this:

Several elevated gene transcripts in the ME/CFS group encode core proteins that regulate the circadian clock (Supplementary Table S2), the central mechanism that drives our 24-h circadian rhythm. A disturbed circadian rhythm can be linked directly to many ME/CFS symptoms, such as pain, fatigue, sleep disturbance, flu-like symptoms, cognitive impairment, post-exertional malaise and dysfunction of metabolic and immune systems.6 These results suggest that disruption of the circadian rhythm is likely in ME/CFS and could be a plausible candidate for sustaining both the symptoms and severity of ME/CFS.

The authors seem to be suggesting a possible causal relationship between disruption of the circadian rhythm and ME/CFS. My son's sleep cycle is definitely delayed. But then, he is also a teenager, with friends that he often plays computer games with who live in a later time zone, and he usually doesn't need to get up early. Efforts to normalise his sleep pattern didn't change the illness.

I pretty much always wake up at the same time each morning, relatively early. My circadian rhythm is stable and normal unless I have been awake in the night with pain, which is not often. My son and I have similar symptoms. My personal experience doesn't support a direct causal relationship between delayed sleep and ME/CFS symptoms. I'd be concerned if this study was used to support the idea that more advice needs to be given to people with ME on sleep hygiene.

 

[NelliePledge]

As a mild/moderate person my pain level isn’t so high it’s that keeping me from getting to sleep. I consider I have delayed sleep pattern as part of PEM. At the start of PEM it is tired but wired then subsequent nights it goes to delayed sleep - doesn’t matter what time i get up or go to bed. Melatonin helps bring it forward to earlier in the night. Insomnia/sleep timing being out of whack is one of the symptoms I’ve had for a good few years before diagnosis. I somehow used to push through on no or a couple of hours sleep then crash out at weekends. I did ask for a referral for a sleep study but was told only for sleep apnea.......

 

[Alvin]

@Alvin

Thanks for pinging me on this one

I gotta read this when i have cognitive functioning
I'm gonna run it past my sleep neurologist when i see him next

 

[Ravn]

We have identified the circadian rhythm dysregulation pathway as a new possible underlying cause of the unrefreshing sleep, fatigue and metabolic abnormalities seen in ME/CFS.

It's worth checking out the reference given for the circadian issues. Have only scanned it so far; it's a very long article but looks interesting though not directly addressing ME.

Sounds like there are several different 'clocks' in our body, including in immune cells.

So it's not just about sleep-wake cycles but all sorts of other stuff, too, e.g. inflammation and immune reactions have a circadian rhythm so if something goes wrong there you could end up with a whole lot of issues that have little to do with sleep - but may have a something to answer for in ME.

ETA: The article in question is:
Comas, M, Gordon, CJ, Oliver, BG. (2017) A circadian based inflammatory response – Implications for respiratory disease and treatment. Sleep Science and Practice 1: 18.
https://sleep.biomedcentral.com/articles/10.1186/s41606-017-0019-2

ETA-2:
FWIW, my own sleep is ok-ish at baseline but goes completely haywire in PEM.

 

[Ravn]

From the paper:

The concepts of Precision Medicine with appropriate statistical analysis have been applied to this small clinically well-characterized patient cohort in this RNA-seq transcriptome analysis. This approach has been successfully applied to cohorts of rare diseases, where available patients are small in number.

This is intriguing. Does anyone know what “concepts of Precision Medicine with appropriate statistical analysis” means, exactly? And if it's any good at overcoming the limitations of minute sample sizes (which ME research seems to be full of)?

 

[Sunshine3]

Dear Rvallee
Our family member had good normal sleep. Obviously, before an exam there might be anxiety, but sleep was good. Once the ME hit overnight, the sleep also tanked, and tanked so badly meds were required and still it is not good.

My sleep is desperate since ME started, it was hypersomnia initially, now complete insomnia. I've tried so many meds. I need some kind of horse or elephant tranquilizer. The insomnia started early December and I can't get a handle on it. I crave Orange juice when I wake. It's so messed up.

 

[Mithriel]

I'm not sure there's anything particular about our sleep. It's "unrefreshing" not because of anything in particular, it's just that nothing is. For sure some have disturbed sleep patterns but that may just be coincidence, it's a common problem. When nothing gives you back energy, it's just normal that sleep would fail at that too.

I recently read this book "Why We Sleep" by Matthew Walker who runs sleep lab research. It impressed me because everything was objective, for instance when they did a study about appetite and sleep they weighed all the food people were given and how much they left, no questionnaires!

The most important findings in the book was that sleep is an active, complex process. As a biologist, over the years there have been findings that stunned me and were so obvious it made me wonder why I hadn't realised them before. Even earthworms and molluscs sleep. Something that is so conserved by evolution when it is energy intensive is vital to an organism.

I don't think our sleep is "disturbed" in the trivial sense it is often used but there is a real possibility that the basic neurological functioning of sleep is damaged for us and causing waking symptoms. So many of our biological systems are involved it would be strange if sleep was not. The IOM may have hit on something important by coincidence.

I would love if there was a large scale research project using sleep labs to investigate all aspects of the sleep process in ME.

 

[ukxmrv]

Not sure if it is relevant but I noticed in the supplementary notes that the majority of patients had 'glandular fever' as their onset

This may produce a group with similar characteristics in some ways but I haven't looked to see if there is any research on post-EBV immune signatures

 

[Mij]

I slept like a baby the first 11 years of illness. Then something changed, I started experiencing hypersomnia and then terrible insomnia for a few years, then back to sleeping ok again. I don't have problems sleeping when I have PEM.

Some pwME experience severe insomnia from day one. My dear friend took serious heavy medications to sleep for 18 yrs.

 

[leokitten]

Like others, at the beginning of ME I had hypersomnia followed by insomnia to this day caused by a strong wired-but-tired feeling at night.

I also very often get this intense abdominal/gut irritation feeling and itching in my psoriasis areas only during sleep time at night. It will constantly wake me up and cause my brain to suddenly become totally awake and not able to fall back asleep. The intense irritation feels like it travels up my enteric nervous system to my brain and wakes it up while exhausting me at the same time. This symptom will only start after initially falling asleep and goes away by early morning.

The abdominal/gut irritation is like nothing else I’ve ever experienced, it’s a horizontal line of irritation across my abdomen just above the bellybutton. It’s hard to tell what specific part of the gut it’s coming from. It also sometimes feels like I have an upset gut like I ate something wrong, but never results in diarrhea or anything like that.

I know these symptoms are likely are due to overexertion and part of PEM because when I aggressively rest these symptoms go away and only come back once I’ve overexerted again.

I started getting nighttime insomnia for the first time in my life about 1 to 1 1/2 years before getting sudden onset ME. I slept like a baby my entire life before that. I started getting the nightly psoriasis itching symptoms in my early 30s, though I’ve had psoriasis my entire adult life. ME has made it worse and I’m fairly certain there is a connection.

Because of all this, ME has made it nearly impossible to sleep properly and at a normal time. It’s one of the most debilitating and life-ruining parts of my ME. It generally pushes me to sleeping during the day and up at night, so it inverts my sleep cycle.

The symptoms are so powerful that medications that help with sleep don’t work after a while and I would have to increase the dosage. So I stopped using them on a regular basis because the only thing that works to promote regular sleep is to cut exertion.