My e-book “Tracing Chronic Fatigue Syndrome to mtDNA” will be free Wednesday and Thursday on Amazon

Hi Alvin,

Something I learned recently was that e-books don't have well defined page numbers. Because one person might read the book on a tablet, another on a phone, and another on a computer -- and all at different fonts -- e-books use a free flow format where pages cut at different places.

In fact, Amazon made me take out my page numbers before they would accept the manuscript. So any page numbers or place numbers are Amazons.

I hope that helps.

 

That is very interesting, though its no problem and i'm glad its not an error.
And congrats on writing a book, its something i have thought about doing for years but can't cognitively handle (i've tried) so congratulations.

 

Thank you!

 

Great questions @Trish . My brain stopped working a few hours ago, so I’ll do my best to answer now -- fully knowing my answer may sound like gibberish. I may have to come back and revisit my answer tomorrow morning when my brain comes back online. Here’s the best I can do at the moment.

My path for the book was tracing the low hanging fruit (family’s with ME/CFS back to mtDNA). The significant correlation between families with a history of ME/CFS+ and haplogroup subclades known for mitochondrial dysfunction is important for several reasons.

First, it backs-up the theory of hypometabolism and ME/CFS.

Second, mitochondrial dysfunction can be caused by mtDNA variants, nuclear variants, viruses, etc….. By realizing that some cases of ME/CFS are due to mitochondrial dysfunction caused by mtDNA variants, this opens the door wider for the researchers to look at other causes of mitochondrial dysfunction (including viruses) as also causing (or being a factor) in ME/CFS. Chapter 27, has a subsection titled “Damage from Viruses”. The fact that the Epstein Barr virus (and other viruses) can cause mitochondrial dysfunction is very telling. Especially, when these viruses are often mentioned by patients as the first time they experienced debilitating fatigue (beyond that experienced by the average person with these viruses).

Then to bring that all together with the threshold effect. From the article “Revealing the Complexity of Mitochondrial DNA-Related Disorders:
“Mutated mtDNA in a given tissue has to reach a minimum critical number before oxidative metabolism is impaired severely enough to cause dysfunction (threshold effect).”

It’s this idea of threshold effect that I find most interesting. The idea that there is a level of mitochondrial dysfunction that must be reached for symptoms. This can be caused by many things. Then there is the further idea that we can go back and forth over this threshold of being symptomatic (or even further along the spectrum into more severe symptoms).

Therefore, the study focusing on mtDNA was a first step. It’s much bigger than the families with multiple cases of ME/CFS. But what the families with multiple cases of ME/CFS do is bring an opening into studying ME/CFS from the perspective of mitochondrial dysfunction.

You raise another great question regarding where is the cutoff point between someone being diagnosed as having a mitochondrial disorder vs other things….And do the mito and ME doctors agree on this? …..

The mito experts today do not agree amongst themselves where the line is between mitochondrial disease and mitochondrial dysfunction. Trying to get the mito experts to agree on a definition and to describe where that line is – is near impossible. It’s part of being in the infancy of this field. Yet, they all work very hard and share their research. Dr. Naviaux already goes back and forth between both groups of experts (mito and ME). He appears at both OMF and UMDF conferences. Many of the experts from ME and mito know each other.

An initial step for the researchers will be to conduct a study similar to mine to look at the maternal haplogroup subclades of families with multiple cases of ME/CFS and see if they come up with the same finding.

You stated that “The book seems to suggest that mitoDNA might be relevant for everyone with ME.” The title “Tracing Chronic Fatigue Syndrome to mtDNA” was from the standpoint of my family and the families with multiple cases of ME/CFS. What that does is open the door for linking mitochondrial dysfunction and ME/CFS in at least some of the cases and that then opens the door further for researchers to look more thoroughly at mitochondrial dysfunction and ME/CFS from other perspectives.

In Figure 4 I tried to emphasize this with the illustration of “Many Factors Are Involved with ME/CFS”. That illustration shows that there are many important components, including nuclear genes and environmental factors. Figure 12 “Mitochondrial Metabolism” also was meant to show how various items can cause mitochondrial dysfunction and low energy fatigue. Figure 13 “Mitochondrial Dysfunction Causes and Potential Symptoms” was supposed to bring that point home.

Due to the amount of information I try to get across, I was hoping that point didn’t get lost. I’m sorry about that.

mtDNA could be relevant to everyone with ME/CFS and it may not be. It’s too early to know. I personally think it’s much more complex than that. What I hope I did is raise new questions and theories in the researchers minds. The more researchers think about ME/CFS, the better for all of us.

I hope I don’t cringe when I read the above tomorrow. I did my best to write in a straight line, but I’m sort of "done in" from the day.

@Trish I really appreciate that you read the book. All of your questions and observations are important. If you felt this, then you won’t be the only one. Thanks again!

 

hi @BeautifulDay, could you please tell us who you are, a scientist, a patient or both, and whether you have a university degree in the field relevant to your book?

 

Thank you @BeautifulDay.
Book safely downloaded.

 

@Trish. You’re welcome. It was my pleasure.

None of the tests are perfect.

The cheapest way to determine your maternal haplogroup is through 23andme’s ancestry test. It’s $69 right now. 23andme does not test for most of the snp’s. The positions they do test for can be seen either by downloading the raw data from 23andme or viewing it online at: https://you.23andme.com/tools/data/
They will have tested for many of the defining variants for haplogroups, but they don’t test for most private variants. Depending upon when a person tests with 23andme will determine which positions are tested. Summary:
- 23andme is cheaper,
- provides maternal haplogroup,
- tests some mtDNA positions.

For Whole Genome Sequencing (WGS) and Whole Exome Sequencing (WES), I tend to go with whatever company is cheapest at the time, has good reviews, has 30x (or more) coverage for WGS or 100x (or more) coverage for WES, and provides VCF, BAM, and FASTQ files. If you use Dante Labs, be sure to ask for them to send you the flash drive with the BAM and FASTQ. Dante allows you to download the VCF. A doctor or researcher might want the BAM or FASTQ files later on (in addition to the VCF), so mine as well get it now if it doesn’t cost any more. Many of these companies provide the VCF with mtDNA aligned to the old reference genome. If you find that is the case, then be sure to follow the steps in Chapter 52 to convert the mtDNA variants from reference genome hg19 to NC_012920. I believe Dante Labs is now providing a work around for this, but I haven’t seen it yet in action. Summary:
- this is more expensive so look for sales,
- these companies usually do not provide maternal haplogroup, so you may have to figure it out on your own with some work,
- there is a lot more data to work with, and
- this can be overwhelming for those who aren’t ready to dive into their own DNA analysis.

When ordered by physicians, our health insurance has covered 100% of the cost of GeneDx for WES for several of us. Be sure to request the flash drive with the data. Chapter 52 covers my experience with GeneDX in more detail and what to expect and ask for. Summary:
- cost will depend upon your health insurance,
- if your doctor requests a certain type of test from GeneDx then haplogroup is provided,
- there is a lot more data to work with, and
- this can be overwhelming for those who aren’t ready to dive into their own DNA analysis.

With regards to your questions: "And a question about consequences of knowing the results of such tests - does it provide evidence that can be used to target treatments such as dietary adjustments and is there any research on this? And does it help in getting doctors to believe the illness is real?"

Having the results has helped us with schools and sick days. It has also helped us to be taken seriously in doctors' offices. In the past when we went in with ME/CFS, we'd get the eye roll. However, go in with ME/CFS due to mitochondrial issues and it's taken very seriously. We no longer hear that reducing our stress or getting more sleep will help us feel better. That has been a very good thing. Patient blaming should never happen. It's hard to get anywhere when doctors don't take you seriously. It has also been helpful in some (not all) of our mito cocktails being paid for by our health insurance. Before this, none of our mito cocktails were paid for by insurance.

From Chapter 8:
"We are blessed to now have excellent nurses throughout our school district. However, just a few years ago when our youngest was in kindergarten, the school nurse at her elementary school told others that our daughter was a hypochondriac coming into the nurses office one day with a limp, another day with a headache, another day with a muscle cramp in a leg, another day with severe stomach issues, and still other days with severe fatigue.
Thank goodness we know from our mitochondrial doctor that having such a broad assortment of symptoms is not unusual in patients with mitochondrial issues. The specialists at the hospital found her severe constipation was due to her colon muscles not working properly, and her mitochondrial headaches were aggravated further by a Chiari malformation in her brain. They taught her how to use crutches on days when her foot doesn’t work properly and she’s received multiple instructions on how to pace herself throughout the day to conserve energy.
When the nurse that thought our daughter was a hypochondriac and who hounded me over every sick day retired, we were blessed with a kind, thoughtful, and well educated nurse at that school. She worked with us and our doctors to provide the best school environment for our daughter under the daily changing symptoms."

As to your question specifically on "does it provide evidence that can be used to target treatments such as dietary adjustments", I would say no.

 

@Trish

You can also get your Mito DNA Haplogroup tested through the National Geographic society and the results contribute to science and our understanding of deep migration patterns of people over time.

Family members of mine had this done about 15 years ago and the project is still ongoing.

https://genographic.nationalgeographic.com/about/

 

@Snwodrop, it seems that only US citizens can buy the National Geographic test kit. It says on your linked website:

And if you click on the 'buy now' button, only US delivery is available.

For those in the US who are interested: it is $59.95

 

I didn't know that. Thanks for pointing it out.
That's unfortunate.

 

Thanks @BeautifulDay for sharing with us the results of what must have been an awful lot of hard work. I do hope somebody picks up on it and incorporates it into a larger study.

Do you happen to know if any of the teams currently hunting for ME-predisposing snps are looking at snp combinations rather than just single snps? Whether that be haplogroup + additional private snp combinations as you're suggesting, or even just something along the lines of ME patients having a higher number of mutations – any type - affecting say mitochondrial function, so not necessarily the same mutations in each patient, just a higher total number of them per patient than you'd expect.

Have only skimmed your book, best I'm capable of at the moment, so can't comment in detail but was interested because I have reason to suspect both my mother and my paternal grandmother had ME. Unfortunately neither was ever diagnosed with anything and both took their health secrets to the grave with them, so will never know for sure.

I do know I'm an H myself so in some ways an 'opposite' to you. If I understand correctly, Js tend toward lower VO2max, lower ATP production and lower ROS production, whereas Hs tend to be higher in all of of those. What's fascinating is that it looks like both can lead to mitochondrial dysfunction, just in different ways. One of the papers you reference (24) suggests that while Hs may have better ATP production they may not be able to utilise that ATP properly (possibly due to an additional mutation that may not matter too much in non-Hs but does matter in Hs). So whether you don't make enough ATP or whether you don't utilise your ATP has a similar result: mitochondrial dysfunction. Reminds me of insulin in type 1 and type 2 diabetes: there are different ways of mucking up the same system.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3734310/

One last question: do you know of a quick and easy tool to convert mutations written as e.g. G15150A into dbsnp rs-numbers?

 

Very interesting. I have recently read "A Brief History of Everyone who Ever Lived" by Adam Rutherford and it is clear that the information we will get from genetics is indeed coming in a tsunami that will take years to unravel but give great insights.

My grandmother and cousin may well have ME but it is paternal, also ASD in family but again from a paternal grandmother. having said that, most genes which control mitochondria reside in the cell nucleus.

Coxsackie B. which I had at the start of my ME and which was implicated in the epidemics is a close relative of polio and is an RNA virus so mitochondrial involvement is very likely.

It should always have been obvious that a disease with the cardinal symptom of an abnormal response to exertion must be due to damage to the workings of the energy production systems.

I agree that many people think they are cured when they are just managing to live with what their damaged systems can manage. That is why ME should be considered lifelong in the same way as controlled diabetes.

 

Thank you @Ravn

There are many scientists who have expressed interest in hunting for ME predisposing variant combinations. How far along and what their parameters, focus, tools, etc.... is unknown. Ron Davis mentioned ongoing work and future studies in his recent OMF presentation. Nova Southern University is recruiting for an ME/CFS Gene Study:
https://www.nova.edu/nim/research/mecfs-genes.html

Wigglethemouse recently pointed me to Nancy Klimas’s Powerpoint presentation from 2017 titled “Targeted therapeutics in GWI: Status report on CoQ10 and Rituximab Trials”
https://www.va.gov/RAC-GWVI/meetings/aug2017/KlimasAUG2017.pdf
-Under the topic of lab measures: “Gene expression by NanoString: We will use a NanoString nCounter of 450 genes selected from our previous work with GWI and 15 internal reference genes.”
- Under the topic of PHASE III CLINICAL TRIAL BIOREPOSITORY, Future Analyses includes “gene expression”.

The Department of Veterans Affairs has been heavily researching the link of mitochondrial dysfunction and Gulf War Illness. Here is an example from 2015. https://www.research.va.gov/pubs/docs/GulfWar-AnnualSummary2015.pdf
One of the studies being funded is: DoD-239 Mitochondrial and Nuclear Genetics in Gulf War Illness.
UC San Diego Health is looking for study participants: https://www.golombresearchgroup.org/mitohaplo/

Per the study titled “Role of mitochondrial DNA damage and dysfunction in veterans with Gulf War Illness” found that:
“Mitochondrial dysfunction has previously been hypothesized as an explanation for symptoms underlying GWI, particularly in the contexts of environmental exposures during deployment (e.g., carbamates and organophosphates) [8, 9]. Emerging evidence supports this rationale as mitochondria are increasingly recognized as a target for environmental toxicants [10, 11]. In fact, mitochondria appear uniquely susceptible to toxicants as a result of: 1) accumulation of toxicants due to the high lipid content of the mitochondrial membranes, slight negative charge of the mitochondrial matrix, and presence of metal cation transporters; 2) ability to activate organic compounds via mitochondrial cytochrome P450s; 3) the presence of the reactive oxygen species generating electron transport chain; 4) reduced repair mechanisms for mitochondrial DNA (mtDNA) in comparison to the nuclear genome, and 5) the potential for toxicant exposure to increase the endogenous level of production of reactive oxygen species.”

Under "Discussion", the authors state:
“This study provides the first direct biological evidence of mtDNA damage in the blood of veterans with GWI. Greater mtDNA damage and mtDNAcn are consistent with mitochondrial dysfunction [21], which may contribute to symptoms of GWI as well as the persistence of this illness over time. Levels of nuclear DNA lesion frequency were also elevated in GWI, despite prior work demonstrating that damage is more severe and persists longer in mtDNA than nuclear DNA [20]. Given increases in both mtDNA lesion frequency and mtDNAcn, we interpret these findings as evidence that mitochondrial dysfunction is involved in the pathobiology of GWI.”
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5599026/

 

Well said. These little machines within us can have multiple places where dysfunction can occur, that have similar results. There can be multiple issues including dysfunction in ATP production and at the other end usage issues such as a problem with uptake of ATP by an organ(s)/system(s).

Overshooting the metabolism can cause other issues. Take ALS for example. In this 2008 study titled "High metabolic level in patients with familial amyotrophic lateral sclerosis", the authors stated that:
"An abnormally elevated level of resting energy expenditure (REE, measured by indirect calorimetry) has been reported in a subset of patients with sporadic amyotrophic lateral sclerosis (SALS). Hypermetabolism (measured REE/calculated REE (cREE)≥1.1, or 110%) has also been observed in transgenic mice harbouring ALS-causing mutations in the SOD1 gene. ..... In conclusion, hypermetabolism appears to be a common feature of subjects with FALS (familial amyotrophic lateral sclerosis), suggesting that this impairment of energy homeostasis may be genetically driven. The high metabolic level of FALS patients should be taken into account for their nutritional management (need for a high-energy diet to prevent malnutrition).
https://www.tandfonline.com/doi/abs/10.1080/17482960802295192?journalCode=iafd19

 

There is no one tool I use. Generally, I'll first do a quick Google search of "G15150A" and then "15150G>A". Generally this will bring up what I need before I head into any deep dive. However, Google knows what sites I look at most (my favorite go to's) and the results of my Google searches may be different than yours.

The NCBI NIH site is likely going to be one of the top results for me and will have the link where an rs# could be found. For example, in my Google Search, up popped:
https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?do_not_redirect&rs=rs207460000