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The Massachusetts ME/CFS & FM Association, a 501(c)3 founded in 1985, exists to meet the needs of patients with ME (Myalgic Encephalomyelitis), CFS (Chronic Fatigue Syndrome) or FM (Fibromyalgia), their families and loved ones. The Massachusetts ME/CFS & FM Association works to educate health-care providers and the general public regarding these severely-disabling physical illnesses. We also support patients and their families and advocate for more effective treatment and research.

Research articles

Kerr’s Team in London Finds Significant Differences in Gene Expression Between CFS Patients and Healthy Controls

Summary of journal article, Kaushik, N.; Kerr, J.R., et al.,“Gene Expression in peripheral blood mononuclear cells from patients with chronic fatigue syndrome,”  Journal of Clinical Pathology Aug 58(8) (2005): 826-32.

The aim of the research was “to test the hypothesis that there are reproducible abnormalities of gene expression in patients with CFS compared to normal healthy persons.”

Gene expression in peripheral blood mononuclear cells was compared between a group of 25 CFS patients and a group of 25 healthy controls. The groups were matched for age, sex, and geographical location. Patients in the CFS group were selected according to the 1994 CDC diagnostic criteria. However, the reliability of the data was (in our view) enhanced by the fact that the most of the CFS subjects were severely ill and required bed rest for much of the day.

Analysis of the cells for both groups was conducted using a single color microarray representing 9522 genes. Average difference values for each gene were compared between the two groups. For a gene to qualify as differentially expressed between the two groups, a standard of p value of 0.001 was used. (This means that a difference in expression according to chance would occur only once in a thousand times. So a high standard of reliability was used.) When a gene showed differential expression, a second test with greater specificity was used—the Taqman real-time polymerase chain reaction (PCR).


35 genes were differentiated between the groups by the microarray analysis.

The PCR further limited the differential to 16 genes—“15 of which were upregulated… and one of which was downregulated…”

“This profile suggests T-cell activation and perturbation of neuronal and mitochondrial function.”


“The expression of the 16 genes was significantly different…” between the patient and control groups. Most of the remaining portion of the article catalogs the potential effects of the upregulation and downregulation of the particular genes in the pathophysiology of ME/CFS, according to the following system and metabolic process dysfunctions:

Immune response:

T-cell activation hypothesized by the upregulation of one gene and the down regulation of a second.

Neuronal component:

Six genes may be implicated in neuronal and other disturbances in ME/CFS patients. One of these genes is involved in the mitochondrial process and “mutations have been shown to be associated with central nervous system hypomyelination [breakdown of nerve sheathing] and encephalopathy [brain pathology].”

The article speculates this could account for the findings of changes in the brain’s white matter in ME/CFS as well as the cognitive dysfunctions.

Other mitochondrial involvement may be caused by the upregulation of 3 other genes.

The cell cycle in ME/CFS patients may be disrupted by the upregulation of two genes, which assist in controlling cell division.

“The upregulation of [gene] EIF4G1 identified in our present study may represent a common host response to persistent infection with several viruses.”

Upregulation of two genes may be involved in transcriptional perturbation. Two other upregulated genes may be responsible for an increased defense to oxidative stress seen in CFS.

An important aspect of this article is the citing of similar research findings by gene, either for CFS or other illnesses of possible similar origins or pathophysiology. The recent gene expression research by the CDC (Whistler et al.) is cited: “…which is interesting in light of our finding of upregulation of EIF4G1 transcript 5…Whistler and his colleagues have also reported this finding in patients with CFS who have rapid onset ('triggered' by virus infection) as compared with insidious onset…Various viruses have developed strategies to divert EIF4G1 from utilization by the cellular machinery…The best characterized example is that of poliovirus…” as well as a number of other viruses.

Further Update as of Sept. 2005:

Attention US-based CFS patients

Dr. Derek Enlander, of NYC, is collaborating in the research led by Dr. Jonathan Kerr, St George's Hospital, London on an exciting RNA genetic study of CFS. Dr. Kerr's team believes that it has discovered biological markers for CFS. They have found differences in gene expression in white blood cells, which could explain how viruses trigger ME/CFS. There is a genetic abnormality in the protein production in the mitochondria.

So far the work has been carried out on 25 patients and 25 healthy controls, and the results will be published in the Journal of Clinical Pathology.

Now Dr. Kerr 's team is going to be testing 1000 patients. Not only do they hope to find this a diagnostic marker for ME/CFS but also they believe that this will lead to a treatment.

Dr. Enlander will be taking samples from ME/CFS patients who can get to NYC. The samples will then be sent to Dr. Kerr.

Funding for the research is by the British CFS Research Foundation and a small grant from the National CFIDS Foundation.

U.S. Centers for Disease Control publishes pilot study on gentically-based metabolic differences on exercise challenge between CFIDS patients and controls.

The following excerpted article was published by researchers at the U.S. Centers for Disease Control & Prevention (CDC). We have, ourselves, italicized some of the more interesting findings. 

The findings contained in the article demonstrate distinct metabolic changes on exercise challenge as a result of altered gene expression in Chronic Fatigue Syndrome (CFS) patients versus healthy controls.

Please note: The pilot study report excerpted below is based on an extremely small sample: 5 women with CFS and 5 female healthy controls. Therefore, a new study with a larger sample-size would have to be done to confirm these findings.

Moreover, the CFS subjects were selected according to the 1994 CDC CFS case definition. As we know, this definition is a very broad one that can lead to a confounding of research findings due to inclusion of subjects who may not have ME/CFS.

We do, however, find the results interesting and hope they will be replicated in a larger study.

Toni Whistler, James F. Jones, Elizabeth R. Unger and Suzanne D. Vernon, "Exercise responsive genes measured in peripheral blood of women with Chronic Fatigue Syndrome and matched control subjects," BMC Physiology (2005) 5:5 doi:10.1186/1472-6793-5-5



Chronic fatigue syndrome (CFS) is defined by debilitating fatigue that is exacerbated by physical or mental exertion. To search for markers of CFS-associated post-exertional fatigue, we measured peripheral blood gene expression profiles of women with CFS and matched controls before and after exercise challenge.


Women with CFS and healthy, age-matched, sedentary controls were exercised on a stationary bicycle at 70% of their predicted maximum workload. Blood was obtained before and after the challenge, total RNA was extracted from mononuclear cells…We identified differences in gene expression among and between subject groups before and after exercise challenge and evaluated differences in terms of Gene Ontology categories.

Exercise-responsive genes differed between CFS patients and controls... Differences in ion transport and ion channel activity were evident at baseline and were exaggerated after exercise, as evidenced by greater numbers of differentially expressed genes in these molecular functions.


These results highlight the potential use of an exercise challenge combined with microarray gene expression analysis in identifying gene ontologies associated with CFS.


In a state of health, physical exercise has a quantifiable effect on neuroendocrine, autonomic, and immune systems influencing metabolic and immune responses. However, in the initial phase of acute illness, there is an avoidance of physical stressors so energy can be dedicated to healing and a return to homeostasis. While physiologic disturbance in acute illness is transient, chronic illnesses, such as chronic fatigue syndrome (CFS), have prolonged disturbances that have a debilitating effect both physiologically and psychologically. Consequently, activities that are physiologic stressors, such as physical exercise, exacerbate the symptoms that define CFS.

CFS is a complex, multifactorial illness whose etiology and pathophysiology remain unclear [1]. CFS is defined by a characteristic symptom complex in the absence of other medical or psychiatric conditions with similar clinical characteristics [2,3]. Subtle differences in hypothalamic-pituitary-adrenal axis function [4], immune system function [5], and psychological profiles [6] between CFS patients and controls have been reported; however, no consistent distinguishing difference or frank abnormality has been confirmed [7,8], and it remains unclear whether CFS represents a unique disease or a common illness response to a variety of insults.

Perhaps the greatest methodological problem with studying CFS is that many individuals identified in population studies have been sick for at least 5 years [9]. During this time, the illness waxes and wanes, making it difficult to identify biomarkers or define pathogenesis. Physical, mental, and emotional stress exacerbate CFS and result in case-defining post-exertional fatigue [2] with measurable physiologic differences [10]. Therefore, exercise challenge of people with CFS is an effective method for calibrating CFS subjects and thus increasing the likelihood of uniformly identifying biomarkers and/or physiologic abnormalities.

We used gene expression profiling of peripheral blood to evaluate differences between CFS subjects and sedentary healthy controls both before and following an exercise challenge. Overall, we found the gene expression profiles to be quite similar, and of importance, most differences were present prior to exercise challenge. These differences were in G protein-coupled receptor and ion transport and ion channel activity ontologies. The latter was exaggerated after exercise as evidenced by differential expression of a greater number of genes involved in these molecular functions. Differences were also evident in exercise response, including chromatin and nucleosome assembly, cytoplasmic vesicles, membrane transport and G-protein coupled receptor ontologies. These differences may help explain the symptoms of CFS.


Exercise response genes were evaluated using a random variance test in a paired, class comparison analysis of control subjects before and after exercise, and 21 genes were identified as being differentially expressed…

Since these 21 genes reflect a healthy subject's peripheral blood gene expression response to exercise challenge, we reasoned that the expression of these would be altered in CFS subjects… The response of 10 of the 21 genes was quite similar in terms of magnitude and direction for both CFS and control subjects… For the other 11 genes, the magnitude of the exercise change was considerably smaller in CFS subjects… than in control subjects… However, 5 genes classified in vesicle-mediated and protein-transport ontologies differed between CFS and control subjects…
…Exercise-related changes that were seen only in CFS subjects were related to G-protein-coupled receptor signaling (purple, Figure 2b).

Gene ontology comparison was also used to evaluate differences between control and CFS subjects before…and after…exercise. Baseline differences between CFS subjects and controls that continued after exercise involved GO terms relating to ion transport… After exercise, these differences appear to be amplified, as evidenced by increased numbers of genes present in these GO categories and also by inclusion of more GO terms pertaining to ATPase transmembrane movement of ions… G-protein-coupled receptor binding… part of the broad functional category of signal transduction, differed between CFS subjects and controls prior to exercise. This baseline difference between controls and CFS subjects was not significant after exercise. Interestingly, complement activation…was one of the exercise-induced differences between subjects and controls that was present only after challenge. Genes in most of the ontologies identified as different between CFS and control subjects had lower expression levels in CFS subjects.


Gene expression profiling affords a unique opportunity to characterize CFS at a systems biology level. Changes in gene expression underlie many biologic processes and may provide insight into disease-specific gene expression and the response of genes to environmental stimuli. In a proof-of-concept study, we found that CFS patients had different blood mononuclear cell gene expression patterns than non-fatigued controls… and that CFS is a heterogeneous illness as evidenced by different gene expression profiles for patients reporting gradual onset of their illness compared with those reporting sudden onset of illness… In addition, differential display polymerase chain reaction on a small number of CFS and control subjects identified candidate biomarkers in the peripheral blood…

CFS is defined by a post-exertional fatigue that does not subside 24 hours following physical stress. In contrast, exercise in healthy, untrained people induces changes in cellular homeostasis in 1 to 4 hours and a return to basal levels within 24 hours, as measured in muscle… In contrast, 11 of the genes were unchanged in CFS subjects before and after exercise; with 5 being classified in a transport-related ontology. Because this difference in gene expression is so dramatic, it implicates a fundamental perturbation in the biochemical activity of lymphocyte and monocyte peripheral blood fractions from CFS subjects compared with control subjects that does not affect classical immunologic markers (i.e, CD45) that have been shown to be unaffected in CFS patients… Rather, low expression of these genes may have subtle effects on immune function. Immune dysfunction has been inconsistently implicated in CFS pathogenesis…

Class comparison was used to identify these 21 differentially expressed genes, which indicated the possible disturbance of biologic pathways… To explore this possibility, we used the GO comparison that is based on the knowledge that gene expression levels are dependent variables in biological processes, cellular components, and molecular functions. In this way, multiple genes in the same category reinforce each other and enhance the power for identifying the significance of the category. The GO categories considered significantly different (p < 0.005) when comparing CFS subjects with controls after exercise challenge were those pertaining to ion transporter activity (a total of 87 genes applied to this category in the comparison of CFS and controls after exercise) and ATPase activity coupled to transmembrane movement (42 genes). When the CFS and control classes are compared prior to exercise, ion transport activity and voltage-gated, ion channel activity are identified (38 and 44 genes within the GO categories, respectively).

It is evident that ion transport and ion channel activity segregate cases from controls and that exercise seems to intensify these differences. Several other conditions have been reported in which fluctuating fatigue occurs that are known to be caused by abnormal ion channels. These conditions include genetically determined channelopathies and acquired conditions such as neuromyotonia, myasthenic syndromes, multiple sclerosis, and polyneuropathies… There are other transmembrane functions associated with differences between controls and CFS patients, including signal transducer activity through receptor binding/activity… Signal transduction of transmembrane receptors occurs by a number of mechanisms, including structural changes, ion channels, and changes of transmembrane potentials. The G-protein-coupled receptors play an important role in the membrane trafficking machinery… The most obvious exercise-induced changes in CFS cases pertain to gene regulation at the point of chromatin structure; whether these changes reflect the differences seen in the mRNA transcripts relating to membrane trafficking differences between cases and controls has not yet been determined. One interesting correlate of this study was the finding that the complement pathway showed significant differences between CFS and control subjects after exercise. This has been reported previously in the analysis of these same exercise challenge-derived specimens. Sorensen et al.… measured levels of complement split products in the sera of these subjects and found differences between CFS and control subjects in C4a after exercise challenge. Complement activation was identified as an ontology that was significantly different between CFS and control subjects after exercise. The correlates on the data are interesting as their study measured protein levels (i.e., gene product levels) and this study measured the transcript levels…

The lack of statistical significance in the 3 other class comparison analyses performed (CFS cases compared before and after exercise, comparison of cases to controls at baseline, and the comparison of cases to controls 24 hours after exercise) reflects low experimental sensitivity, most likely due to a small number of subjects, rather than an absence of biological effect…

The next line of research will detail larger numbers of subjects in the expression arrays. The emphasis in such studies will be on developing a gene expression-based multivariate function, or predictor, that accurately predicts the class membership of a new sample on the basis of the expression levels of key genes. Class discovery tools will also be applied to CFS subjects' expression profiles in an attempt to further describe discrete subsets of this disease on the basis of gene expression as we have done for gradual and sudden onset of illness… However, the methods used in this study will be applied to these data sets too, as these analytical tools will prove to be very helpful in defining the pathophysiology of CFS. It is hoped that this broader, more fully encompassing approach to CFS research will open many doors to the understanding of this syndrome and perhaps of fatigue and un-wellness in general.

Exciting and Hopeful News for ME/CFS Research and Treatment from Genetic Analysis

A research team from Glasgow University in Scotland announced in 2005 an altered pattern of gene activity in 50 patients with Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS). Dr. John Gow, the senior researcher, said, "We have identified genes which were up-regulated compared with genes in normal healthy individuals... This means the genes are switched on or off an at inappropriate time... It looks like the immune system is working overtime when it shouldn't be..."

Dr. Gow and his team mapped the entire genome of 33,000 genes in the ME/CFS sufferers and then compared them with the genes of healthy people. Despite the initial results, Dr. Gow stressed that more testing of ME/CFS patients is needed to make sure that the unusual gene activity is specific for Chronic Fatigue Syndrome. He thinks this further testing would take about a year.

Diagnostic Test and Treatments

The research team is hopeful that the potential "CFS gene signature" could lead to a specific diagnostic test, and has already patented the genes which would be involved in diagnostic testing. A prototype diagnostic testing kit has been developed which would give a yes or no answer as to whether CFS is present.

Even more exciting is the promise of medication to treat the abnormal gene/immune dysfunction. Dr. Gow stated, "Our work has given us clues as to which pathways are up- or down-regulated and we know which drugs activate different pathways, so we think we can find drug treatments that will be beneficial to patients."

These specific drugs are already on the market and therefore could be available to ME/CFS patients in the immediate future. Dr. Gow said, " ...it really needs to go through proper trials before these drugs become widely available."

This is important research since it includes a possible mechanism of action, a diagnostic test, and potential medication. Of course, we must wait and see.

Sources: BBC News, UK Edition, 28 May 2005; The Scotsman, 20 May 2005; Co-Cure; ME Association.

Updated Information on Dr. Gow's Research

Since this article was written, two groups in Britain: MERGE (ME Research Group for Education and Support) and the ME Association have provided substantial funding to enable Dr. Gow and his associates to begin the second phase of their research. MERGE has provided an interim award of 8,000 pounds and the ME Association has granted 28,675 pounds (in addition to the nearly 9,000 pounds that the MEA has already provided).

The following update on the research is taken with permission from a Co-Cure post dated June 27, 2005:

"So the second phase of the study should now be able to commence in August.

Why is this type of genetic research so important in ME/CFS?

In very simple terms, the Glasgow University research group will be using a technique called DNA chip microassay analysis to map out what is happening to a vast amount of individual genetic informationover 33,000 gene sequences in each individual. The scientists will be carrying out this genetic analysis on a large group of people with ME/CFS, another large group of healthy matched controls, and a further large group of people with a range of other illnessessuch a multiple sclerosis and depressionin which fatigue is a major clinical symptom. In particular, the scientists will be trying to identify whether there is a unique profile of genetic abnormalities in people with ME/CFS by looking for data which indicates that certain specific genes are either up-regulated or down-regulatedroughly meaning that they are being over-active, under-active or 'switched-off'.

The activity of these genesgene expression in medical jargoncan have very important consequences on the types of cellular activity, including crucial biochemical pathways, that they control in the nervous system, immune system, and all other parts of the body. So the ultimate aim of the study is to identify specific gene abnormalities which may then lead to new avenues of research and the presence of a diagnostic biomarker or diagnostic biomakers which is/are only present in ME/CFS.

Preliminary results from phase one of this study already indicate that significant abnormalities in gene expression are present in the ME/CFS group, but this data now needs to be confirmed in a much larger trial.

This type of information on gene expression will also be highly relevant to new forms of treatment which are worth assessing. And as the data becomes clearer, a further phase of the research will hopefully then involve a clinical trial of drug treatment aimed at the underlying cause of ME/CFS."


Notice about names

The Massachusetts ME/CFS & FM Association would like to clarify the use of the various acronyms for Chronic Fatigue Syndrome (CFS), Chronic Fatigue & Immune Dysfunction Syndrome (CFIDS) and  Myalgic Encephalomyelitis (ME) on this site. When we generate our own articles on the illness, we will refer to it as ME/CFS, the term now generally used in the United States. When we are reporting on someone else’s report, we will use the term they use. The National Institutes of Health (NIH) and other federal agencies, including the CDC, are currently using ME/CFS. 

Massachusetts ME/CFS & FM Association changed its name in July, 2018, to reflect this consensus.