Genetic risk prediction methods applied to CFS

Research abstract:

Background:

The current practice of using only a few strongly associated genetic markers in regression models results in generally low power in prediction or accounting for heritability of complex human traits.

Purpose:

We illustrate here a Bayesian joint estimation of single nucleotide polymorphism (SNP) effects principle to improve prediction of phenotype status from pathway-focused sets of SNPs. Chronic fatigue syndrome (CFS), a complex disease of unknown etiology with no laboratory methods for diagnosis, was chosen to demonstrate the power of this Bayesian method. For CFS, such a genetic predictive model in combination with clinical evidence might lead to an earlier diagnosis than one based solely on clinical findings.

Methods:

One of our goals is to model disease status using Bayesian statistics which perform variable selection and parameter estimation simultaneously and which can induce the sparseness and smoothness of the SNP effects. Smoothness of the SNP effects is obtained by explicit modeling of the covariance structure of the SNP effects.

Results:

The Bayesian model achieved perfect goodness of fit when tested within the sampled data. Tenfold cross-validation resulted in 80 % accuracy, one of the best so far for CFS in comparison to previous prediction models. Model reduction aspects were investigated in a computationally feasible manner. Additionally, genetic variation estimates provided by the model identified specific genetic markers for their biological role in the disease pathophysiology.

Conclusions:

This proof-of-principle study provides a powerful approach combining Bayesian methods, SNPs representing multiple pathways and rigorous case ascertainment for accurate genetic risk prediction modeling of complex diseases like CFS and other chronic diseases.

Prediction of complex human diseases from pathway-focused candidate markers by joint estimation of marker effects: case of chronic fatigue syndrome, by Madhuchhanda Bhattacharjee, Mangalathu S. Rajeevan and Mikko J. Sillanpaa in Human Genomics 2015, 9:8  Published: 11 June 2015

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Mitochondrial depletion & energy problems in CFS

Mitochondrial Depletion Could Underlie the Energy Problems in Chronic Fatigue Syndrome, comment by Cort Johnson, May 26, 2015

Very, very few chronic  fatigue syndrome studies have emerged from Germany, but the last two have been good ones. The one before this was the first to find evidence of EBV activation in ME/CFS, in years.

This one – a model exploring mitochondrial dynamics –  may help explain what’s causing the post-exertional problems, published in the Biophysical Chemistry journal, this study extended a well-known metabolic model explaining what happens to the mitochondria in the skeletal muscles during exercise.  The authors enhanced it by adding  some processes to it (lactate accumulations / purine degradation) known to occur in the mitochondria.

In silico analysis of exercise intolerance in myalgic encephalomyelitis/chronic fatigue syndrome. Nicor Lengert,  Barbara Drossel Institute for Condensed Matter Physics, Technische Universität.  Biophysical Chemistry 202 (2015) 21–31

The Study

The model covers two parts of the inner mitochondria – the cytosolic space and the mitochrondrial matrix. It does not cover interactions between the mitochondrial membrane and the rest of the mitochondria.

The model was rather….complex.

The production of the model was sparked by  a number of findings (reduced ATP production and peak oxygen uptake) suggesting problems with aerobic (oxygen related) energy production, were present in chronic fatigue syndrome.  Findings of increased acidification, reduced anaerobic threshold and prolonged pH recovery times suggested that anaerobic respiration – a less efficient and more toxic form of energy production – was attempting to compensate for a broken aerobic energy production system.

They noted that several factors that could affect mitochondrial activity. They included possible “mitochondrial deletions”, Epstein-Barr virus induced alterations of mitochondrial gene transcription, pro-inflammatory cytokines and increased levels of oxidative stress.

They ran two iterations of the model; one representing the reactions  in the mitochondria occurring in healthy controls, and one representing a person with probably severe ME/CFS, for whom mitochondrial capacity was reduced by about a third. Then they examined what happened during three exercise scenarios: 30 seconds of intensive exercise, an  hour of moderate exercise and an hour of moderate exercise spread across two days. Then they looked to see if the models fit what the studies suggest is happening in ME/CFS.

It turns out that they did.

Results
ATP reaches critically low concentrations during high intensity exercise in CFS simulations and the acidification in muscle tissue increases compared to control simulations. [Authors]

 Several studies suggest that the rates of ATP production/oxidative phosphorylation (mitochondrial capacity) are about 65% of normal in ME/CFS. This model suggests reduced mitochondrial capacity could be causing the ATP problems and the increased acidosis and lactate accumulations found in several studies.  (The increased acidosis is the problem, lactate is not.  Lactate is produced to protect the cell from acidification.)

Healthy people are able to maintain an ATP level during exercise that protects their mitochondria. The  models suggested, however, that the  minimum ATP levels maintained in ME/CFS patients during exercise, may be significantly lower – low enough perhaps to induce cell death.  This finding was buttressed by one of Sarah Myhill’s studies, which found greatly increased levels of a factor (cell-free DNA) that’s associated with increased cell death.

When the mitochondrial capacity of a cell is exhausted; i.e. when ATP demand outstrips supply the cell copes with this by digging into its reserves. Converting two ADP molecules to one ATP and one AMP molecule, frees up some energy (ATP), but does two negative things as well. First, it reduces the total adenine pool in the cell (adenine triphospate (ATP) and diphosphate (ADP)) and second it increases levels of inosine, hypoxanthine and finally uric acid.

The model suggested that the healthy controls in the model were able to exercise without purine nucleotide loss while the people with reduced mitochondrial dysfunction suffered from significant losses of purine nucleotides.

Acidosis Plays Key Role

Anaerobic respiration greatly increases the rate of acidosis.  Acidification is produced by the breakdown (hydrolysis) of ATP and is related, if I have it right, to increased rates of cell damage and subsequent purine nucleotide loss.  The model suggested that the increased acidosis in the “ME/CFS patients” increases lactate accumulations and lactate efflux from the cell by 10-15%. The situation in ME/CFS might be worse, however, than the model with its forty percent reduction in mitochondrial production suggested. The rates of acidosis and lactate accumulations found in ME/CFS studies were significantly higher than those produced by the model.

Prolonged Recovery Periods

The reduction in the adenine pool means the cell will need time in the post-exercise period to get back to normal.  After prolonged bouts of intense exercise even professional athletes need 72 hours to replenish the adenine pools in their muscle cells.  But what would short periods of exercise to please with reduce exercise capacity? The model predicted it would take 3-5 times longer for the ATP levels in the muscles of ME/CFS patients to return to normal after exercise than for healthy controls. The model predicted that short (30 seconds), intense exercise periods would be easier for “ME/CFS patients” to recover from.

The model predicted it would take 49 hours for ATP levels in the muscles to return to normal after a longer (30 minutes) but more moderate period of exercise.  It would take 32 hours for the ATP levels in the muscles of ME/CFS patients to return to normal after short but intense (30 secs.) periods of exercise. Adding another exercise bout before recovery could occur would add substantially more time to the recovery period.

The findings provide another possible reason (ATP depletion) for the post-exertional malaise seen in ME/CFS.  It could also explain why some people with ME/CFS cannot reproduce their levels of energy on the second day of a bicycle exercise test.

The model did not account for the possibility of increased cell death during exercise – something the researchers thought likely – that would extend recovery times further. Other factors, such as sympathetic nervous system and immune dysregulation and increased oxidative stress, not included in the model, may also come into play.

Recovery Reversal
..the model…. demonstrates that long moderate exercises are more exhaustive than short intensive exercises contrary to the results for healthy controls. Authors

The model suggested that mitochondrial depletion results in more difficulty with longer bouts of moderate exercise, than with shorter bouts of intense exercise. This pattern was opposite to that found in the controls. Healthy controls recover more quickly from longer moderate bouts of exercise (4.5 hours) than short, intense bouts of exercise (10.3 hours). The altered scenario fits well with recommendations by exercise physiologists for ME/CFS suggesting that exercise periods be short and interspersed with rest perios

Two Subsets?

Studies of mitochondrial respiration in the neutrophils in ME/CFS suggested two groups of mitochondrial deficient ME/CFS patients may be present. One group compensates for the mitochondrial deficiency by upregulating glycolysis and the other by increasing purine nucleotide degradation. This model in this paper suggests both are possible.

Treatment

The authors suggested that D-Ribose could help in the short term but worried about its “rapid glycation of proteins” – something they said was associated with some neurodegenerative diseases. They suggested measuring mitochondrial respiration co-factors (ubiquinol (CoQ10), NAD, L-carnitine and others) and supporting it with supplements.

Wrap Up

The new model produced in this study extends a less sophisticated model of mitochondrial metabolism. That fact that it was produced in response to findings in ME/CFS, is in itself interesting, and suggests how unusual the findings in ME/CFS exercise studies are. It should be emphasized that this is a model, and therefore does not necessarily demonstrate what’s happening in ME/CFS.

The model indicates that reduced mitochondrial production could, however, help explain the exercise findings, and post exertional malaise studies indicate it is present in ME/CFS. It buttresses the idea, emerging more strongly in ME/CFS in recent years, that the mitochondria may play an important role.

It did this by showing how, when put under load, reduced mitochondrial capacity feeds on components of the cells to make energy. This works in the short term, but in the longer term depletes the cells of vital energy making factors. This long term depletion – lasting for at  least a day, but possibly much longer – could help explain the post-exertional malaise and difficulty reproducing energy production, in the second day of a two day exercise test.

It indicated that shorter periods of exercise – even if they are more intense – should be easier to recover from, than longer periods of more moderate exercise. Because the model failed to predict the very high levels of lactate and acid production found  in some ME/CFS studies, it may be understating the depth of the mitochondrial depletion found. It does not say anything about what is causing the possible depletion of mitochondrial capacity.

The authors suggested the appropriate supplementation (CoQ10, NAD, L-carnitine) may be helpful.

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Diagnostic methods for ME/CFS: a review

Research abstract:

Background: The diagnosis of myalgic encephalomyelitis (ME)/chronic fatigue syndrome (CFS) is based on clinical criteria, yet there has been no consensus regarding which set of criteria best identifies patients with the condition. The Institute of Medicine has recently proposed a new case definition and diagnostic algorithm.

Purpose: To review methods to diagnose ME/CFS in adults and identify research gaps and needs for future research.

Data Sources: MEDLINE, PsycINFO, and Cochrane databases (January 1988 to September 2014); clinical trial registries; and reference lists.

Study Selection: English-language studies describing methods of diagnosis of ME/CFS and their accuracy.

Data Extraction: Data on participants, study design, analysis, follow-up, and results were extracted and confirmed. Study quality was dual-rated by using prespecified criteria, and discrepancies were resolved through consensus.

Data Synthesis: Forty-four studies met inclusion criteria. Eight case definitions have been used to define ME/CFS; a ninth, recently proposed by the Institute of Medicine, includes principal elements of previous definitions. Patients meeting criteria for ME represent a more symptomatic subset of the broader ME/CFS population. Scales rating self-reported symptoms differentiate patients with ME/CFS from healthy controls under study conditions but have not been evaluated in clinically undiagnosed patients to determine validity and generalizability.

Limitations: Studies were heterogeneous and were limited by size, number, applicability, and methodological quality. Most methods were tested in highly selected patient populations.

Conclusion: Nine sets of clinical criteria are available to define ME/CFS, yet none of the current diagnostic methods have been adequately tested to identify patients with ME/CFS when diagnostic uncertainty exists. More definitive studies in broader populations are needed to address these research gaps.

Primary Funding Source: Agency for Healthcare Research and Quality. (PROSPERO: CRD42014009779)

The terms myalgic encephalomyelitis (ME) and chronic fatigue syndrome (CFS) have been used to describe a debilitating multisystemic condition characterized by chronic, disabling fatigue and various other symptoms. The term CFS was introduced in the 1980s after research failed to identify a clear viral association with what was previously labeled chronic Epstein–Barr virus syndrome (1–4).

Other terms, such as postviral fatigue syndrome and chronic fatigue immune dysfunction syndrome, were also used in attempts to associate the syndrome with possible underlying causes (1–2, 5–6). Although the most recent international consensus report advocates moving away from the term CFS in favor of the term ME to better reflect an underlying disease process involving widespread inflammation and neuropathology (7–8), experts do not agree about these mechanisms and the cause of CFS remains unclear.

A recent Institute of Medicine (IOM) report proposes a name, systemic exertion intolerance disease (SEID), that describes the central elements of the disease. The report focuses on the adverse effect that physical, cognitive, or emotional exertion can have on patients with this condition and acknowledges that this is a complex and severe disorder for which specific causes are not yet proven (9).

The diagnosis of ME/CFS is based on clinical criteria that attempt to distinguish it from other conditions that also present with fatigue. Eight published case definitions have been used since the first one established by the Centers for Disease Control and Prevention (CDC) in 1988 (2), and the IOM proposed a ninth in February 2015 (9). All include persistent fatigue not attributable to a known underlying medical condition, as well as additional clinical signs and symptoms that do not all need to be present to establish the diagnosis (10). However, there has been no consensus about which, if any, of these clinical criteria should be considered the reference standard.

The variations in case definitions imply that they may describe different conditions and lead to different diagnoses, complicating ME/CFS research and clinical care. For example, depending on the case definition, prevalence rates of ME/CFS in the United States range from 0.3% to 2.5% (1, 11–12).

This systematic review is part of a larger report to inform a research agenda for the National Institutes of Health (NIH) 2014 Pathways to Prevention Workshop, an evidence-based methodology workshop (13). The purpose of this systematic review was to evaluate and compare studies of methods to diagnose ME/CFS, identify limitations of current studies, and determine needs for future research.

Diagnostic Methods for Myalgic Encephalomyelitis/Chronic Fatigue Syndrome: A Systematic Review for a National Institutes of Health Pathways to Prevention Workshop, by Elizabeth Haney, MD; M.E. Beth Smith, DO; Marian McDonagh, PharmD; Miranda Pappas, MA; Monica Daeges, BA; Ngoc Wasson, MPH; and Heidi D. Nelson, MD, MPH  in Ann Intern Med. 2015;162(12):834-840

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Gene expression can differentiate CFS, FM and depression

Research abstract:

OBJECTIVE

To determine if independent candidate genes can be grouped into meaningful biological factors and if these factors are associated with the diagnosis of chronic fatigue syndrome (CFS) and fibromyalgia (FMS) while controlling for co-morbid depression, sex, and age.

METHODS

We included leukocyte mRNA gene expression from a total of 261 individuals including healthy controls (n=61), patients with FMS only (n=15), CFS only (n=33), co-morbid CFS and FMS (n=79), and medication-resistant (n=42) or medication-responsive (n=31) depression. We used Exploratory Factor Analysis (EFA) on 34 candidate genes to determine factor scores and regression analysis to examine if these factors were associated with specific diagnoses.

RESULTS

EFA resulted in four independent factors with minimal overlap of genes between factors explaining 51% of the variance. We labeled these factors by function as: 1) Purinergic and cellular modulators; 2) Neuronal growth and immune function; 3) Nociception and stress mediators; 4) Energy and mitochondrial function.

Regression analysis predicting these biological factors using FMS, CFS, depression severity, age, and sex revealed that greater expression in Factors 1 and 3 was positively associated with CFS and negatively associated with depression severity (QIDS score), but not associated with FMS.

CONCLUSION

Expression of candidate genes can be grouped into meaningful clusters, and CFS and depression are associated with the same 2 clusters but in opposite directions when controlling for co-morbid FMS. Given high co-morbid disease and interrelationships between biomarkers, EFA may help determine patient subgroups in this population based on gene expression.

Gene expression factor analysis to differentiate pathways linked to fibromyalgia, chronic fatigue syndrome, and depression in a diverse patient sample, by E Iacob, AR Light, GW Donaldson, A Okifuji, RW Hughen, AT White, KC Light in Arthritis Care Res (Hoboken). 2015 Jun 19 [Epub ahead of print]

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The role of infections & moulds in chronic fatigue

Abstract

Patients who present with severe intractable apparently idiopathic fatigue accompanied by profound physical and or cognitive disability present a significant therapeutic challenge.

The effect of psychological counseling is limited, with significant but very slight improvements in psychometric measures of fatigue and disability but no improvement on scientific measures of physical impairment compared to controls.

Similarly, exercise regimes either produce significant, but practically unimportant, benefit or provoke symptom exacerbation. Many such patients are afforded the exclusionary, non-specific diagnosis of chronic fatigue syndrome if rudimentary testing fails to discover the cause of their symptoms.

More sophisticated investigations often reveal the presence of a range of pathogens capable of establishing life-long infections with sophisticated immune evasion strategies, including Parvoviruses, HHV6, variants of Epstein-Barr, Cytomegalovirus, Mycoplasma, and Borrelia burgdorferi.

Other patients have a history of chronic fungal or other biotoxin exposure. Herein, we explain the epigenetic factors that may render such individuals susceptible to the chronic pathology induced by such agents, how such agents induce pathology, and, indeed, how such pathology can persist and even amplify even when infections have cleared or when biotoxin exposure has ceased.

The presence of active, reactivated, or even latent Herpes virus could be a potential source of intractable fatigue accompanied by profound physical and or cognitive disability in some patients, and the same may be true of persistent Parvovirus B12 and mycoplasma infection.

A history of chronic mold exposure is a feasible explanation for such symptoms, as is the presence of B. burgdorferi. The complex tropism, life cycles, genetic variability, and low titer of many of these pathogens makes their detection in blood a challenge. Examination of lymphoid tissue or CSF in such circumstances may be warranted.

The putative role of viruses, bacteria, and chronic fungal biotoxin exposure in the genesis of intractable fatigue accompanied by cognitive and physical disability by G Morris, M Berk, K Walder, M Maes in Mol Neurobiol, 2015 Jun 17.

 

 

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Fecal microbiota transplantation – a treatment in CFS?

Research abstract:

Intestinal dysbiosis is now known to be a complication in a myriad of diseases. Fecal microbiota transplantation (FMT), as a microbiota-target therapy, is arguably very effective for curing Clostridium difficile infection and has good outcomes in other intestinal diseases.

New insights have raised an interest in FMT for the management of extra-intestinal disorders associated with gut microbiota. This review shows that it is an exciting time in the burgeoning science of FMT application in previously unexpected areas, including metabolic diseases, neuropsychiatric disorders, autoimmune diseases, allergic disorders, and tumors.

A randomized controlled trial was conducted on FMT in metabolic syndrome by infusing microbiota from lean donors or from self-collected feces, with the resultant findings showing that the lean donor feces group displayed increased insulin sensitivity, along with increased levels of butyrate-producing intestinal microbiota.

Case reports of FMT have also shown favorable outcomes in Parkinson’s disease, multiple sclerosis, myoclonus dystonia, chronic fatigue syndrome, and idiopathic thrombocytopenic purpura. FMT is a promising approach in the manipulation of the intestinal microbiota and has potential applications in a variety of extra-intestinal conditions associated with intestinal dysbiosis.

Fecal microbiota transplantation broadening its application beyond intestinal disorders, by Meng-Que Xu et al in World J Gastroenterol. 2015 Jan 7; 21(1): 102–111.

 

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CFS v SEID as diagnostic criteria

Research abstract:

Background:

The Institute of Medicine has recommended a change in the name and criteria for chronic fatigue syndrome (CFS), renaming the illness systemic exertion intolerance disease (SEID). The new SEID case definition requires substantial reductions or impairments in the ability to engage in pre-illness activities, unrefreshing sleep, post-exertional malaise, and either cognitive impairment or orthostatic intolerance.

Purpose:

In the current study, samples were generated through several different methods and were used to compare this new case definition to previous case definitions for CFS, the International Consensus Criteria for myalgic encephalomyelitis (ME-ICC), the Canadian myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) definition, as well as a case definition developed through empirical methods.

Methods:

We used a cross-sectional design with samples from tertiary care settings, a BioBank sample, and other forums. Seven hundred and ninety-six patients from the USA, Great Britain, and Norway completed the DePaul Symptom Questionnaire.

Results:

Findings indicated that the SEID criteria identified 88% of participants in the samples analyzed, which is comparable to the 92% that met the Fukuda criteria. The SEID case definition was compared to a four-item empiric criteria, and findings indicated that the four-item empiric criteria identified a smaller, more functionally limited and symptomatic group of patients.

Conclusion:

The recently developed SEID criteria appears to identify a group comparable in size to the Fukuda et al. criteria, but a larger group of patients than the Canadian ME/CFS and ME criteria, and selects more patients who have less impairment and fewer symptoms than a four-item empiric criteria.

Chronic fatigue syndrome versus systemic exertion intolerance disease, by Leonard A. Jason, Madison Sunnquist, Abigail Brown, Julia L. Newton, Elin Bolle Strand & Suzanne D. Vernon in Fatigue: Biomedicine, Health & Behavior [Published online: 15 Jun 2015]

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Autophagy in bacterial infections

Research abstract:

Autophagy is a highly conserved catabolic process for the degradation of cytosolic components including damaged organelles, protein aggregates, and intracellular bacteria through a lysosome-dependent pathway. Autophagy can be induced in response to stress conditions.

Furthermore, autophagy has been described as involved in both innate and adaptive immune responses, and several studies have shown that certain microorganisms can be eliminated by the autophagic route in a process known as xenophagy. However, several pathogens have developed different strategies to evade or exploit autophagy to ensure their survival. Here, we review the role of autophagy in response to bacterial pathogens.

The role of autophagy in bacterial infections, by Castrejón-Jiménez NS, Leyva-Paredes K, Hernández-González JC, Luna-Herrera J, García-Pérez BE in Biosci Trends. 2015 Jun;9(3):149-59.

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ME/CFS: ethical and unethical uses of NLP

In this article by Nancy Blake, she argues that it is unethical and harmful to use Neuro Linguistic Programming (NLP) to persuade a person with ME to deny the biomedical realities of ME/CFS, to tell them that all will be well if they just deny their illness, give up the habits of rest and energy conservation they have learned to use, and any aids they may also rely on.

Instead she believes that NLP can be used to encourage a patient to change the way they think about exercise, how to fight the illness and how to rest, in order to promote better health.

ME/CFS: Ethical and Unethical Uses of NLP, by Nancy Blake on Positive Health online

[Image: Nancy Blake]

 

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Time loaded standing in women with CFS

Research abstract

Patients with chronic fatigue syndrome (CFS), like patients with osteoporosis, have similar difficulties in standing and sitting.

The aim of the study was to compare combined trunk and arm endurance among women with CFS (n=72), women with osteoporosis (n=30), nondisabled women (n=55), and women from non-industrialized countries (n=58) using the timed loaded standing (TLS) test.

TLS measures how long a person can hold a 1 kg dumbbell in each hand in front of him or her with straight arms. TLS was higher in the industrialized nondisabled population than in the non-industrialized study population (p<0.001) and in patients with osteoporosis (p=0.002).

TLS was lower in patients with CFS than in nondisabled controls (p<0.001). After adjusting for age, body height, and weight, combined trunk and arm endurance was even lower in CFS than in osteoporotic patients more than 25 yr old (p<0.001). In CFS, TLS was lower than in the non-industrialized group (p=0.02).

Since only women were studied, external validity of the results is limited to adult female patients with CFS. TLS revealed a specific biomechanical weakness in CFS patients that can be taken into account from the onset of a rehabilitation program. We propose that influencing the quality, rather than the quantity, of movement could be used in the rehabilitation.

Timed loaded standing in female chronic fatigue syndrome compared with other populations by Jan B Eyskens, Jo Nijs, Kristiaan D’Aout, Alain Sand, Kristien Wouters, Greta Moorkens in Journal of Rehabilitation Research & Development Vol 52, no.1, pp 21-30, June 2015

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