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Saturday, November 11, 2023

Chronic fatigue syndrome

From Wikipedia, the free encyclopedia
https://en.wikipedia.org/wiki/Chronic_fatigue_syndrome
 
Chronic fatigue syndrome
Other namesMyalgic encephalomyelitis/ chronic fatigue syndrome (ME/CFS), myalgic encephalomyelitis (ME), post-viral fatigue syndrome (PVFS), chronic fatigue immune dysfunction syndrome (CFIDS), systemic exertion intolerance disease (SEID), others

Chart of the symptoms of CFS according to various definitions

SpecialtyRheumatology, rehabilitation medicine, endocrinology, Infectious disease, neurology, immunology, internal medicine, paediatrics, other specialists in ME/CFS
SymptomsWorsening of symptoms with activity, long-term fatigue, others
Usual onset10 to 30 years old
DurationOften for years
CausesUnknown
Risk factorsFemale sex, virus and bacterial infections, blood relatives with the illness, major injury, bodily response to severe stress and others
Diagnostic methodBased on symptoms
TreatmentSymptomatic
PrevalenceAbout 0.68 to 1% globally

Chronic fatigue syndrome (CFS), also called myalgic encephalomyelitis (ME) or ME/CFS, is a complex, debilitating, long-term medical condition. Core symptoms are lengthy flare-ups of the illness following ordinary minor physical or mental activity, known as post-exertional malaise (PEM); greatly diminished capacity to do tasks that were routine before the illness; and sleep disturbances. The Center for Disease Control and Prevention's (CDC) diagnostic criteria also require at least one of the following: (1) orthostatic intolerance (difficulty sitting and standing upright) or (2) impaired memory or attention. Frequently and variably, other symptoms occur involving numerous body systems, and chronic pain is very common. The often incapacitating fatigue in ME/CFS is different from that caused by normal strenuous exertion, is not significantly relieved by rest, and is not due to a previous medical condition. Diagnosis is based on the person's symptoms because no confirmed diagnostic test is available.

The root cause(s) of the disease are unknown and the mechanisms are not fully understood. ME/CFS often starts after a flu-like infection, for instance after infectious mono. In some people, physical or mental stress may also act as a trigger. A genetic component is suspected, as ME/CFS can run in families. ME/CFS is associated with physical changes, including the nervous and immune system, and hormone production.

People with ME/CFS may recover or improve over time, but some will become severely affected and disabled for an extended period. No therapies or medications are approved to treat the cause of the illness; treatment is aimed at alleviation of symptoms. Pacing (personal activity management) can help to prevent flare-ups. Limited evidence suggests that counseling, personalized activity management, and the use of rintatolimod help improve some patients' functional abilities.

About 1% of primary-care patients have ME/CFS; estimates of incidence vary widely because various epidemiological studies have used different definitions. It has been estimated that 836,000 to 2.5 million Americans and 250,000 to 1,250,000 people in the United Kingdom have ME/CFS. ME/CFS occurs 1.5 to 2 times as often in women as in men. It most commonly affects adults between 40 and 60 years old, but can occur at other ages, including childhood. Other studies suggest that about 0.5% of children have ME/CFS, and that it is more common in adolescents than in younger children. Chronic fatigue syndrome is a major cause of school absence. ME/CFS significantly reduces health, happiness, productivity, and can also cause socio-emotional disruptions such as loneliness and alienation.

There is controversy over many aspects of the disorder. Various physicians, researchers, and patient advocates promote different names and diagnostic criteria. Results of studies of proposed causes and treatments are often poor or contradictory.

Signs and symptoms

The United States Centers for Disease Control and Prevention (CDC) recommends these criteria for diagnosis:

  1. Greatly lowered ability to do activities that were usual before the illness. This drop in activity level occurs along with fatigue and must last six months or longer.
  2. Worsening of symptoms after physical or mental activity that would not have caused a problem before the illness. The amount of activity that might aggravate the illness is difficult for a person to predict, and the decline often presents 12 to 48 hours after the activity. The 'relapse', or 'crash', may last days, weeks or longer. This is known as post-exertional malaise (PEM).
  3. Sleep problems; people may still feel weary after full nights of sleep, or may struggle to stay awake, fall asleep or stay asleep.

Additionally, one of the following symptoms must be present:

  • Problems with thinking and memory (cognitive dysfunction, sometimes described as "brain fog")
  • While standing or sitting upright; lightheadedness, dizziness, weakness, fainting or vision changes may occur (orthostatic intolerance)

Other common symptoms

Many, but not all people with ME/CFS report:

Increased sensitivity to sensory stimuli and pain have also been observed in CFS.

Onset

The onset of ME/CFS may be gradual or sudden. When it begins suddenly, it often follows an episode of infectious-like symptoms or a known infection, and between 25% and 80% of patients report an infectious-like onset. When gradual, the illness may begin over the course of months or years with no apparent trigger. It's also frequent for the onset of ME/CFS to involve multiple triggering events that begin with minor symptoms and culminate in a final trigger leading to a noticeable onset. Studies disagree as to which pattern is more common. ME/CFS may also occur after physical trauma such as a car accident or surgery.

Physical functioning

Results of a study on quality of life of people with CFS, showing it to be lower than in 20 other chronic conditions

CFS often causes significant disability, but the degree can vary greatly. Some people with mild CFS may lead relatively normal lives with vigilant energy management, while moderately affected patients may be unable to work or spend much time upright. People with severe CFS are generally housebound or bedbound, and may be unable to care for themselves.

The majority of people with CFS have significant difficulty engaging in work, school, and family activities for extended periods of time. An estimated 75% are unable to work because of their illness, and about 25% are housebound or bedridden for long periods, often decades. In one review on employment status, more than half of CFS patients were on disability benefits or temporary sick leave, and less than a fifth worked full-time. In children, CFS is a major cause of school absence. According to a 2009 study, patients exhibit a reduction in the complexity of their activities. Many people with CFS also experience strongly disabling chronic pain.

Symptoms can fluctuate over time, making the condition difficult to manage. Persons who feel better for a period may overextend their activities, triggering post-exertional malaise and a worsening of symptoms. Severity may also change over time, with periods of worsening, improvement or remission sometimes occurring.

People with CFS have decreased quality of life according to the SF-36 questionnaire, especially in the domains of vitality, physical functioning, general health, physical role, and social functioning. However, their scores in the "role emotional" and mental health domains were not substantially lower than healthy controls. A 2015 study found that people with CFS had lower health-related quality of life than 20 other chronic conditions, including multiple sclerosis, kidney failure, and lung cancer.

Cognitive functioning

Cognitive dysfunction is one of the most disabling aspects of CFS due to its negative impact on occupational and social functioning. 50–80% of people with CFS are estimated to have serious problems with cognition. Cognitive symptoms are mainly due to deficits in attention, memory, and reaction time. Measured cognitive abilities are found to be below projected normal values and likely to affect day-to-day activities, causing increases in common mistakes, forgetting scheduled tasks, or having difficulty responding when spoken to.

Simple and complex information-processing speed and functions entailing working memory over long time periods are moderately to extensively impaired. These deficits are generally consistent with the patient's perceptions. Perceptual abilities, motor speed, language, reasoning, and intelligence do not appear to be significantly altered. Patients who report poorer health status tend to also report more severe cognitive trouble, and better physical functioning is associated with less visuoperceptual difficulty and fewer language-processing complaints.

Inconsistencies of subjective and observed values of cognitive dysfunction reported across multiple studies are likely caused by a number of factors. Differences of research participants' cognitive abilities pre- and post-illness onset are naturally variable and are difficult to measure because of a lack of specialized analytical tools that can consistently quantify the specific cognitive difficulties in CFS.

Cause

The cause of ME/CFS is unknown. Both genetic and environmental factors are believed to contribute, but the genetic component is unlikely to be a single gene. Problems with the nervous and immune systems, and energy metabolism, may be factors. ME/CFS is a biological disease, not a psychiatric or psychological condition, and is not caused by deconditioning. However, the biological abnormalities found in research are not sensitive or specific enough for diagnosis.

Because the illness often follows a known or apparent viral illness, various infectious agents have been proposed, but a single cause has not been found. For instance, ME/CFS may start after mononucleosis, a H1N1 influenza infection, a varicella zoster virus infection (the virus that causes chickenpox), or SARS-CoV-1.

Risk factors

All ages, ethnic groups, and income levels are susceptible to the illness. The CDC states that while Caucasians may be diagnosed more frequently than other races in America, the illness is at least as prevalent among African Americans and Hispanics. A 2009 meta-analysis found that Asian Americans have a lower risk of CFS than White Americans, while Native Americans have a higher (probably a much higher) risk and African Americans probably have a higher risk. The review acknowledged that studies and data were limited.

More women than men get ME/CFS. A large 2020 meta-analysis estimated that between 1.5 and 2.0 times more cases are women. The review noted that different case definitions and diagnostic methods within datasets yielded a wide range of prevalence rates. The CDC estimates ME/CFS occurs up to four times more often in women than in men. The illness can occur at any age, but has the highest prevalence in people aged 40 to 60. ME/CFS is less prevalent among children and adolescents than among adults.

People with affected relatives appear to be more likely to get ME/CFS, implying the existence of genetic risk factors. People with a family history of neurological or autoimmune diseases are also at increased risk. Results of genetic studies have been largely contradictory or unreplicated. One study found an association with mildly deleterious mitochondrial DNA variants, and another found an association with certan variants of human leukocyte antigen genes.

Viral and other infections

Post-viral fatigue syndrome (PVFS) or post-viral syndrome describes a type of chronic fatigue syndrome that occurs following a viral infection. Viral infection is a significant risk factor for ME/CFS. Different types of viral infection can lead to ME/CFS, including airway infections, bronchitis, gastroenteritis, or an acute "flu-like illness". One review found higher Epstein–Barr virus (EBV) antibody activity in patients with ME/CFS, and that a subset were likely to have increased EBV activity compared to controls. Of people infected with EBV, around 8% to 15% develop ME/CFS, depending on criteria. Between 15% to 50% of people with long COVID also meet the diagnostic criteria for ME/CFS.

A systematic review found that fatigue severity was the main predictor of prognosis in CFS, and did not identify psychological factors linked to prognosis. Another review found that risk factors for developing post-viral fatigue or CFS after mononucleosis, dengue fever, or Q-fever included longer bed-rest during the illness, poorer pre-illness physical fitness, attributing symptoms to physical illness, belief that a long recovery time is needed, as well as pre-infection distress and fatigue. The same review found biological factors such as CD4 and CD8 activation and liver inflammation are predictors of sub-acute fatigue but not CFS.

A study analyzing the relationship between diagnostic labels and prognosis found that patients diagnosed with ME had the worst prognosis, and that patients with PVFS had the best. According to a review, it is unclear whether this was because people labeled with ME had a more severe or persistent illness, or because being labelled with ME adversely affects prognosis. The National Academy of Medicine report says it is a misconception that diagnosing ME/CFS worsens prognosis, and that accurate diagnosis is key to appropriate management.

Pathophysiology

ME/CFS is associated with changes in several areas, including the nervous, immune, and endocrine systems. Reported neurological differences include altered brain structure and metabolism, and autonomic nervous system dysfunction. Observed immunological changes include decreased natural killer cell activity, increased cytokines, and slightly increased levels of certain antibodies. Endocrine differences, such as modestly low cortisol and HPA axis dysregulation, have been noted as well. Impaired energy production and the possibility of autoimmunity are other areas of interest.

Neurological

Brain imaging, comparing adolescents with CFS and healthy controls showing abnormal network activity in regions of the brain.
Brain imaging, comparing adolescents with CFS and healthy controls showing abnormal network activity in regions of the brain

A range of neurological structural and functional abnormalities is found in people with CFS, including lowered metabolism at the brain stem and reduced blood flow to cortical areas of the brain; these differences are consistent with neurological illness, but not depression or psychological illness. The World Health Organization classes chronic fatigue syndrome as a central nervous system disease.

Some neuroimaging studies have observed prefrontal and brainstem hypometabolism; however, sample size was limited. Neuroimaging studies in persons with CFS have identified changes in brain structure and correlations with various symptoms. Results were not consistent across the neuroimaging brain structure studies, and more research is needed to resolve the discrepancies found between the disparate studies.

Tentative evidence suggests a relationship between autonomic nervous system dysfunction and diseases such as CFS, fibromyalgia, irritable bowel syndrome, and interstitial cystitis. However, it is unknown if this relationship is causative. Reviews of CFS literature have found autonomic abnormalities such as decreased sleep efficiency, increased sleep latency, decreased slow wave sleep, and abnormal heart rate response to tilt table tests, suggesting a role of the autonomic nervous system in CFS. However, these results were limited by inconsistency.

Central sensitization, or increased sensitivity to sensory stimuli such as pain have been observed in CFS. Sensitivity to pain increases after exertion, which is opposite to the normal pattern.

Immunological

Immunological abnormalities are frequently observed in those with CFS. Decreased NK cell activity is found more often in people with CFS and this correlates with severity of symptoms. People with CFS have an abnormal response to exercise, including increased production of complement products, increased oxidative stress combined with decreased antioxidant response, and increased Interleukin 10, and TLR4, some of which correlates with symptom severity. Increased levels of cytokines have been proposed to account for the decreased ATP production and increased lactate during exercise;however, the elevations of cytokine levels are inconsistent in specific cytokine, albeit frequently found. Similarities have been drawn between cancer and CFS with regard to abnormal intracellular immunological signaling. Abnormalities observed include hyperactivity of ribonuclease L, a protein activated by IFN, and hyperactivity of NF-κB.

Endocrine

Evidence points to abnormalities in the hypothalamic-pituitary-adrenal axis (HPA axis) in some people with ME/CFS, which may include lower cortisol levels, a decrease in the variation of cortisol levels throughout the day and decreased responsiveness of the HPA axis. This can be considered to be a "HPA axis phenotype" that is also present in some other conditions, including post-traumatic stress disorder and some autoimmune conditions. It is unclear whether or not decreased cortisol levels of the HPA axis plays a primary role as a cause of CFS, or has a secondary role in the continuation or worsening of symptoms later in the illness. In most healthy adults, the cortisol awakening response shows an increase in cortisol levels averaging 50% in the first half-hour after waking. In people with CFS, this increase apparently is significantly less, but methods of measuring cortisol levels vary, so this is not certain.

Autoimmunity

Autoimmunity has been proposed to be a factor in ME/CFS, but there are only a few relevant findings so far. There is a subset of patients with increased B cell activity and autoantibodies, possibly as a result of decreased NK cell regulation or viral mimicry. In 2015, a large German study found 29% of ME/CFS patients had elevated autoantibodies to M3 and M4 muscarinic acetylcholine receptors as well as to ß2 adrenergic receptors. Problems with these receptors can lead to impaired blood flow.

Energy metabolism

Objective signs of PEM have been found with the 2-day CPET, a test that involves taking VO2max tests on successive days. People with ME/CFS have lower performance and heart rate compared to healthy controls on the first test. On the second test, healthy people's scores stay the same or increase slightly, while people with ME/CFS have a decrease in anaerobic threshold, peak power output, and VO2max. Potential causes include impaired oxygen transport, impaired aerobic metabolism, and mitochondrial dysfunction.

Studies have observed mitochondrial abnormalities in cellular energy production, but recent focus has concentrated on secondary effects that may result in aberrant mitochondrial function because inherent problems with the mitochondria structure or genetics have not been replicated.

Diagnosis

Could You Have ME/CFS? from US Centers for Disease Control

No characteristic laboratory abnormalities are approved to diagnose ME/CFS; while physical abnormalities can be found, no single finding is considered sufficient for diagnosis. Blood, urine, and other tests are used to rule out other conditions that could be responsible for the symptoms. The CDC states that a medical history should be taken and a mental and physical examination should be done to aid diagnosis.

Diagnostic tools

The CDC recommends considering the questionnaires and tools described in the 2015 Institute of Medicine report, which include:

  • The Chalder Fatigue Scale
  • Multidimensional Fatigue Inventory
  • Fisk Fatigue Impact Scale
  • The Krupp Fatigue Severity Scale
  • DePaul Symptom Questionnaire
  • CDC Symptom Inventory for CFS
  • Work and Social Adjustment Scale (WSAS)
  • SF-36 / RAND-36

A two-day cardiopulmonary exercise test (CPET) is not necessary for diagnosis, although lower readings on the second day may be helpful in supporting a claim for Social Security disability. A two-day CPET cannot be used to rule out chronic fatigue syndrome.

Definitions

Many sets of diagnostic criteria for ME/CFS have been proposed. Required symptoms vary. The four most commly cited are post-exertional malaise, fatigue, cognitive impairment, and sleep disruption. Notable definitions include:

  • Centers for Disease Control and Prevention (CDC) definition (1994), is also called the Fukuda definition and is a revision of the Holmes or CDC 1988 scoring system. The 1994 criteria require the presence of four or more symptoms beyond fatigue, while the 1988 criteria require six to eight.
  • The 2003 Canadian consensus criteria state: "A patient with ME/CFS will meet the criteria for fatigue, post-exertional malaise and/or fatigue, sleep dysfunction, and pain; have two or more neurological/cognitive manifestations and one or more symptoms from two of the categories of autonomic, neuroendocrine, and immune manifestations; and the illness persists for at least 6 months".
  • The Myalgic Encephalomyelitis International Consensus Criteria (ICC) published in 2011 is based on the Canadian working definition and has an accompanying primer for clinicians. The ICC does not have a six months waiting time for diagnosis. The ICC requires post-exertional neuroimmune exhaustion (PENE) which has similarities with post-exertional malaise, plus at least three neurological symptoms, at least one immune or gastrointestinal or genitourinary symptom, and at least one energy metabolism or ion transportation symptom. Unrefreshing sleep or sleep dysfunction, headaches or other pain, and problems with thinking or memory, and sensory or movement symptoms are all required under the neurological symptoms criterion. According to the ICC, patients with post-exertional neuroimmune exhaustion but only partially meeting the criteria should be given the diagnosis of atypical myalgic encephalomyelitis.
  • The 2015 definition by the National Academy of Medicine (then referred to as the "Institute of Medicine") is not a definition of exclusion (differential diagnosis is still required). "Diagnosis requires that the patient have the following three symptoms: 1) A substantial reduction or impairment in the ability to engage in pre-illness levels of occupational, educational, social, or personal activities, that persists for more than 6 months and is accompanied by fatigue, which is often profound, is of new or definite onset (not lifelong), is not the result of ongoing excessive exertion, and is not substantially alleviated by rest, and 2) post-exertional malaise* 3) Unrefreshing sleep*; At least one of the two following manifestations is also required: 1) Cognitive impairment* 2) Orthostatic intolerance" and notes that "*Frequency and severity of symptoms should be assessed. The diagnosis of ME/CFS should be questioned if patients do not have these symptoms at least half the time with moderate, substantial, or severe intensity."

The 2021 UK NICE guidelines employ a definition of ME/CFS that requires severe fatigue, post-exertional malaise, unrefreshing sleep or sleep disturbance, and cognitive difficulties.

Differential diagnosis

Certain medical conditions have similar symptoms as ME/CFS and should be evaluated before a diagnosis of ME/CFS can be confirmed. While alternative diagnoses are explored, advice can be given on symptom management, to avoid delays in care. Post-exertional malaise often acts as a distinguishing feature of ME/CFS. A diagnosis of ME/CFS is only confirmed after 6 months of symptoms, to exclude acute medical conditions or problems related to lifestyle, which may resolve within that time frame.

Examples of possible differential diagnoses span a large set of specialties, and depend on patient history. Examples are infectious diseases (such as Epstein–Barr virus, HIV infection, tuberculosis, Lyme disease), neuroendocrine disorder (such as diabetes, hypothyroidism, Addison's disease, adrenal insufficiency), blood disorders (such as anemia) and some cancers. Various rheumatological and auto-immune diseases may also have overlapping symptoms with ME/CFS, such as Sjögren's syndrome, lupus and arthritis. Furthermore, evaluation of psychiatric diseases (such as depression, substance use disorder and anorexia nervosa) and neurological disorders (such as obstructive sleep apnea, narcolepsy, Parkinson's, multiple sclerosis, craniocervical instability) may be warranted. Finally, sleep disorders, coeliac disease, connective tissue disorders and side effects of medications may also explain symptoms.

Joint and muscle pain without swelling or inflammation is a feature of ME/CFS, but is more associated with fibromyalgia. Modern definitions of fibromyalgia not only include widespread pain, but also fatigue, sleep disturbances and cognitive issues, making the two syndromes difficult to distinguish. The two are often co-diagnosed. Ehlers–Danlos syndromes (EDS) may also have similar symptoms.

Like with other chronic illnesses, depression and anxiety co-occur frequently with ME/CFS. Depression may be differentially diagnosed from ME/CFS by feelings of worthlessness, the inability to feel pleasure, loss of interest and/or guilt; and the absence of bodily symptoms such autonomic dysfunction, pain, migraines or post-exertional malaise.

Symptom Management

There is no approved drug treatment, therapy or cure for ME/CFS, although some symptoms can be treated or managed. Pacing, or managing one's activities to stay within their energy limits, can reduce episodes of post-exertional malaise. Addressing sleep problems with good sleep hygiene, or medication if required, may be beneficial. Chronic pain is common in ME/CFS, and the CDC recommends consulting with a pain management specialist if over-the-counter painkillers are insufficient. The debilitating nature of ME/CFS can cause depression or other psychological problems, which should be treated accordingly. For cognitive impairment, adaptations like organizers and calendars may be helpful. Comorbid conditions are common and should be treated if present.

The CDC recommends a strategy treating the most disabling symptom first, and the NICE guideline specifies the need for shared decision-making between patients and medical teams. NICE recognized that symptoms of severe ME/CFS may be misunderstood as neglect or abuse and recommends assessment for safeguarding of persons suspected of having ME/CFS be evaluated by professionals with experience and understanding of the illness. Clinical management varies widely, with many patients receiving combinations of therapies.

Comorbid conditions that may interact with and worsen ME/CFS symptoms care are common, and treating these may be beneficial. The most commonly diagnosed include fibromyalgia, irritable bowel syndrome, depression, anxiety, allergies, and chemical sensitivities.

Pacing

Pacing, or activity management, is an illness management strategy based on the observation that symptoms tend to increase following mental or physical exertion. It was developed for ME/CFS in the 1980s, and is now commonly used as a management strategy in chronic illnesses and in chronic pain.

Its two forms are symptom-contingent pacing, in which the decision to stop (and rest or change an activity) is determined by self-awareness of an exacerbation of symptoms, and time-contingent pacing, which is determined by a set schedule of activities that a patient estimates he or she is able to complete without triggering post-exertional malaise (PEM). Thus, the principle behind pacing for CFS is to avoid overexertion and an exacerbation of symptoms. It is not aimed at treating the illness as a whole. Those whose illness appears stable may gradually increase activity and exercise levels, but according to the principle of pacing, must rest or reduce their activity levels if it becomes clear that they have exceeded their limits. Use of a heart-rate monitor with pacing to monitor and manage activity levels is recommended by a number of patient groups, and the CDC considers it useful for some individuals to help avoid post-exertional malaise.

Energy envelope theory

Energy envelope theory, considered to be consistent with pacing, is a management strategy suggested in the 2011 international consensus criteria for ME, which refers to using an "energy bank budget". Energy envelope theory was devised by psychologist Leonard Jason, who previously had CFS. Energy envelope theory states that patients should stay within, and avoid pushing through, the envelope of energy available to them, so as to reduce the post-exertional malaise "payback" caused by overexertion. This may help them make "modest gains" in physical functioning. Several studies have found energy envelope theory to be a helpful management strategy, noting that it reduces symptoms and may increase the level of functioning in CFS. Energy envelope theory does not recommend unilaterally increasing or decreasing activity and is not intended as a therapy or cure for CFS. It has been promoted by various patient groups. Some patient groups recommend using a heart rate monitor to increase awareness of exertion and enable patients to stay within their aerobic threshold envelope.

Exercise

Stretching, movement therapies, and toning exercises are recommended for pain in patients with ME/CFS. In many chronic illnesses, aerobic exercise is beneficial, but in chronic fatigue syndrome, the CDC does not recommend it. The CDC states:

Any activity or exercise plan for people with ME/CFS needs to be carefully designed with input from each patient. While vigorous aerobic exercise can be beneficial for many chronic illnesses, patients with ME/CFS do not tolerate such exercise routines. Standard exercise recommendations for healthy people can be harmful for patients with ME/CFS. However, it is important that patients with ME/CFS undertake activities that they can tolerate...

Short periods of low-intensity exercise to improve stamina may be possible in a subset of people with ME/CFS. Exercise should only be attempted after pacing has been implemented effectively. The amount of exercise should be varied based on the symptom severity of each day, to avoid PEM.

Graded exercise therapy (GET) involving fixed increments in exercise over time, is not recommended for people with ME/CFS. Newer reviews of GET dispute it's effectiveness and safety. Few clinical trials contained enough detail about adverse effects.

Counseling

Chronic illness often impacts mental health. Psychotherapy may help patients manage the stress of being ill, apply self-management strategies for their symptoms, and cope with physical pain. Cognitive behavioral therapy (CBT) may be offered to people with a new ME/CFS diagnosis to give them tools to cope with the disease and help with rehabilitation. Family sessions may be useful to teach about the severe disability from ME/CFS. Depression or anxiety resulting from ME/CFS is common, and CBT may be a useful treatment.

Diet and nutrition

A proper diet is a significant contributor to the health of any individual. Medical consultation about diet and supplements is recommended for persons with ME/CFS. Persons with ME/CFS may also benefit from nutritional support if deficiencies are detected by medical testing. However, nutritional supplements may interact with prescribed medication.

Bowel issues are a common symptom of ME/CFS. For some, eliminating certain food groups, such as caffeine, alcohol or dairy, can alleviate symptoms. People with severe ME/CFS may have significant trouble getting nutrition. Intravenous feeding (via blood) or tube feeding may be necessary to address this, or to address electrolyte imbalances.

Proposed treatments for curative intent

There are no approved treatments for ME/CFS. Cognitive behavior therapy (CBT) and graded exercise therapy (GET) have been proposed, but their safety and efficacy are disputed. The drug rintatolimod has been trialed and has been approved in Argentina.

Graded exercise therapy

Graded exercise therapy (GET) is a programme of physical therapy that starts at a patient's baseline and gradually increases over time. Like CBT, it assumes that patients' fears of activity and deconditioning play a significant role, and its safety and efficacy are debated.

The 2021 NICE guidelines removed GET as a recommended treatment due to low quality evidence regarding benefit, with the guidelines now telling clinicians not to prescribe "any programme that ... uses fixed incremental increases in physical activity or exercise, for example, graded exercise therapy." The CDC withdrew their recommendation for GET in 2017.

Cognitive behavioral therapy

Cognitive behavioral therapy for ME/CFS is a variant of CBT that assumes a cognitive-behavioral model of ME/CFS. In this model, people with ME/CFS mistakenly attribute their illness solely to physical causes, and their condition is perpetuated by a fear of triggering symptoms, which leads to a vicious cycle of deconditioning and avoidance of activity. CBT aims to help patients view unhelpful thoughts and behaviors as factors in their illness. This model has been criticized as lacking evidence and being at odds with the biological changes associated with ME/CFS, and the use of this type of CBT has been the subject of much controversy.

NICE removed their recommendation for this form of CBT in 2021, replacing it with a recommendation to offer patient CBT for help coping with distress that illness causes. The guidelines emphasize that CBT for people with ME/CFS should not assume that unhelpful beliefs cause their illness, and should not be portrayed as curative. Similarly, the CDC stopped recommending CBT as a treatment in 2017, recommending counseling as a coping method instead.

Rintatolimod

Rintatolimod is a double-stranded RNA drug developed to modulate an antiviral immune reaction through activation of toll-like receptor 3. In several clinical trials of CFS, the treatment has shown a reduction in symptoms, but improvements were not sustained after discontinuation. Evidence supporting the use of rintatolimod is deemed low to moderate. The US FDA has denied commercial approval, called a new drug application, citing several deficiencies and gaps in safety data in the trials, and concluded that the available evidence is insufficient to demonstrate its safety or efficacy in CFS. Rintatolimod has been approved for marketing and treatment for persons with ME/CFS in Argentina, and in 2019, FDA regulatory requirements were met for exportation of rintatolimod to the country.

Prognosis

Information on the prognosis of ME/CFS is limited, and the course of the illness is variable. According to the NICE guideline, ME/CFS "varies in long-term outlook from person to person." Complete recovery, partial improvement, and worsening are all possible. Symptoms generally fluctuate over days, weeks, or longer periods, and some people may experience periods of remission. Overall, "many will need to adapt to living with ME/CFS." Some people who improve need to manage their activities in order to prevent relapse. Children and teenagers are more likely to recover or improve than adults.

A 2005 systematic review found that for untreated CFS, "the median full recovery rate was 5% (range 0–31%) and the median proportion of patients who improved during follow-up was 39.5% (range 8–63%)," and that 8 to 30% of patients were able to return to work. Age at onset, a longer duration of follow-up, less fatigue severity at baseline, and other factors were occasionally, but non consistently, related to outcome. Another review found that children have a better prognosis than adults, with 54–94% having recovered by follow-up, compared to less than 10% of adults returning to pre-illness levels of functioning.

Epidemiology

Graph showing that people most frequently get CFS between the ages of 10 and 39, and that it is about 3 times as common in females
Incidence rates by age and sex, from a 2014 study in Norway

Reported prevalence rates vary widely depending on how CFS/ME is defined and diagnosed. Based on the 1994 CDC diagnostic criteria, the global prevalence rate for CFS is 0.89%. In comparison, estimates using the 1988 CDC "Holmes" criteria and 2003 Canadian criteria for ME produced an incidence rate of only 0.17%. Between 836,000 and 2.5 million Americans have ME/CFS, but 84–91% of these are undiagnosed, and over 250,000 people in England and Wales are estimated to be affected. The worldwide prevalence is 17 and 24 million.

Females are diagnosed about 1.5 to 2.0 times more often with CFS/ME than males. An estimated 0.5% of children have ME/CFS, and more adolescents are affected with the illness than younger children.

The incidence rate according to age has two peaks, one at 10–19 and another at 30–39 years, and the rate of prevalence is highest between ages 40 and 60.

History

Myalgic encephalomyelitis

  • From 1934 onwards, outbreaks of a previously unknown illness began to be recorded by doctors. Initially considered to be occurrences of poliomyelitis, the illness was subsequently referred to as "epidemic neuromyasthenia".
  • In the 1950s, the term "benign myalgic encephalomyelitis" was used in relation to a comparable outbreak at the Royal Free Hospital in London. The descriptions of each outbreak were varied, but included symptoms of malaise, tender lymph nodes, sore throat, pain, and signs of encephalomyelitis. The cause of the condition was not identified, although it appeared to be infectious, and the term "benign myalgic encephalomyelitis" was chosen to reflect the lack of mortality, the severe muscular pains, symptoms suggesting damage to the nervous system, and to the presumed inflammatory nature of the disorder. Björn Sigurðsson disapproved of the name, stating that the illness is rarely benign, does not always cause muscle pain, and is possibly never encephalomyelitic. The syndrome appeared in sporadic as well as epidemic cases.
  • In 1969, benign myalgic encephalomyelitis appeared as an entry to the International Classification of Diseases under Diseases of the nervous system.
  • In 1986, Ramsay published the first diagnostic criteria for ME, in which the condition was characterized by: 1) muscle fatiguability in which, even after minimal physical effort, three or more days elapse before full muscle power is restored; 2) extraordinary variability or fluctuation of symptoms, even in the course of one day; and 3) chronicity.
  • By 1988, the continued work of Ramsay had demonstrated that, although the disease rarely resulted in mortality, it was often severely disabling. Because of this, Ramsay proposed that the prefix "benign" be dropped.

Chronic fatigue syndrome

  • In the mid-1980s, two large outbreaks of an illness that resembled mononucleosis drew national attention in the United States. Located in Nevada and New York, the outbreaks involved an illness characterized by "chronic or recurrent debilitating fatigue, and various combinations of other symptoms, including a sore throat, lymph node pain and tenderness, headache, myalgia, and arthralgias". An initial link to the Epstein–Barr virus had the illness acquire the name "chronic Epstein–Barr virus syndrome".
  • In 1987, the CDC convened a working group to reach a consensus on the clinical features of the illness. The working group concluded that CFS was not new, and that the many different names given to it previously reflected widely differing concepts of the illness's cause and epidemiology. The CDC working group chose "chronic fatigue syndrome" as a more neutral and inclusive name for the illness, but noted that "myalgic encephalomyelitis" was widely accepted in other parts of the world.
  • In 1988, the first definition of CFS was published. Although the cause of the illness remained unknown, several attempts were made to update this definition, most notably in 1994.
  • The most widely referenced diagnostic criteria and definition of CFS for research and clinical purposes were published in 1994 by the CDC.
  • In 2006, the CDC commenced a national program to educate the American public and health-care professionals about CFS.

Other medical terms

A range of both theorised and confirmed medical entities and naming conventions have appeared historically in the medical literature dealing with ME and CFS. These include:

  • Epidemic neuromyasthenia was a term used for outbreaks with symptoms resembling poliomyelitis.
  • Iceland disease and Akureyri disease were synonymous terms used for an outbreak of fatigue symptoms in Iceland.
  • Low natural killer syndrome, a term used mainly in Japan, reflected research showing diminished in vitro activity of natural killer cells isolated from patients.
  • Neurasthenia had been proposed as a historical diagnosis that occupied a similar medical and cultural space to CFS.
  • Royal Free disease was named after the historically significant outbreak in 1955 at the Royal Free Hospital used as an informal synonym for "benign myalgic encephalomyelitis".
  • Tapanui flu was a term commonly used in New Zealand, deriving from the name of a town, Tapanui, where numerous people had the syndrome.

Society and culture

Presentation of a petition to the National Assembly for Wales relating to ME support in South East Wales

Naming

Many names have been proposed for the illness. Currently, the most commonly used are "chronic fatigue syndrome", "myalgic encephalomyelitis", and the umbrella term "myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS)". Reaching consensus on a name is challenging because the cause and pathology remain unknown.

Many patients object to the term "chronic fatigue syndrome". They consider the term too simplistic and trivialising, which in turn prevents the illness from being taken seriously. At the same time, there are also issues with the use of "myalgic encephalomyelitis, as there is only limited evidence of brain inflammation implied by the name. The umbrella term ME/CFS would retain the better-known phrase CFS without trivialising the disease, but some people object to this name too as they see CFS and ME as distinct illnesses.

A 2015 report from the Institute of Medicine recommended the illness be renamed "systemic exertion intolerance disease", (SEID), and suggested new diagnostic criteria, proposing post-exertional malaise (PEM), impaired function, and sleep problems are core symptoms of ME/CFS. While the new name was not widely adopted, the diagnostic criteria were taken over by the CDC. Like CFS, SEID only focuses on a single symptom and patient opinions have generally been negative.

Economic impact

Economic costs due to CFS are "significant". A 2021 paper by Leonard Jason and Arthur Mirin estimated the impact in the US to be $36-51 billion per year, or $31,592 to $41,630 per person, considering both lost wages and healthcare costs. The CDC estimated direct healthcare costs alone at $9–14 billion annually. A 2017 estimate for the annual economic burden in the United Kingdom was £3.3 billion.

Awareness day

12 May is designated as ME/CFS International Awareness Day. The day is observed so that stakeholders have an occasion to improve the knowledge of "the public, policymakers, and health-care professionals about the symptoms, diagnosis, and treatment of ME/CFS, as well as the need for a better understanding of this complex illness." It was chosen because it is the birthday of Florence Nightingale, who had an illness appearing similar to ME/CFS or fibromyalgia.

Doctor–patient relations

People with CFS face stigma in healthcare settings, and doctors may have trouble managing an illness that lacks a clear cause or treatment. There has been much disagreement over proposed causes, diagnosis, and treatment of the illness. Some doctors believe it is psychological. Most patients are convinced their illness is physical instead, straining doctor-patient relationships. Clinicians may be unfamiliar with CFS, as it is often not covered in medical school. Due to this unfamiliarity, patients may go undiagnosed for years, or be misdiagnosed with mental conditions. A substantial portion of doctors are uncertain about how to diagnose or manage CFS. In a 2006 survey of GPs in southwest England, 75% accepted it as a "recognisable clinical entity", but 48% did not feel confident in diagnosing it, and 41% in managing it.

The NAM report refers to CFS as "stigmatized", and the majority of patients report negative healthcare experiences. These patients may feel that their doctor inappropriately calls their illness psychological or doubts the severity of their symptoms. They may also feel forced to prove that they are legitimately ill. Some may be given outdated treatments that provoke symptoms or assume their illness is due to unhelpful thoughts and deconditioning. In a 2009 survey, only 35% of patients considered their physicians experienced with CFS and only 23% thought their doctors knew enough to treat it.

Blood donation

In 2010, several national blood banks adopted measures to discourage or prohibit individuals diagnosed with CFS from donating blood, based on concern following the 2009 claim of a link between CFS and a retrovirus which was subsequently shown to be unfounded. Organizations adopting these or similar measures included the Canadian Blood Services, the New Zealand Blood Service, the Australian Red Cross Blood Service and the American Association of Blood Banks. In November 2010, the UK National Blood Service permanently deferred ME/CFS patients from donating blood to prevent potential harm to the donor. Donation policy in the UK now states, "The condition is relapsing by nature and donation may make symptoms worse, or provoke a relapse in an affected individual."

Controversy

Much contention has arisen over the cause, pathophysiology, nomenclature, and diagnostic criteria of CFS. Historically, many professionals within the medical community were unfamiliar with CFS, or did not recognize it as a real condition; nor did agreement exist on its prevalence or seriousness. Some people with CFS reject any psychological component.

In 1970, two British psychiatrists, McEvedy and Beard, reviewed the case notes of 15 outbreaks of benign myalgic encephalomyelitis and concluded that it was caused by mass hysteria on the part of patients, or altered medical perception of the attending physicians. Their conclusions were based on previous studies that found many normal physical test results, a lack of a discernible cause, and a higher prevalence of the illness in females. Consequently, the authors recommended that the disease should be renamed "myalgia nervosa". This perspective was rejected in a series of case studies by Melvin Ramsay and other staff of the Royal Free Hospital, the center of a significant outbreak. The psychological hypothesis posed by McEvedy and Beard created great controversy, and convinced a generation of health professionals in the UK that this could be a plausible explanation for the condition, resulting in neglect by many medical specialties. The specialty that did take a major interest in the illness was psychiatry.

Because of the controversy, sociologists hypothesized that stresses of modern living might be a cause of the illness, while some in the media used the term "Yuppie flu" and called it a disease of the middle class. People with disabilities from CFS were often not believed and were accused of being malingerers. The November 1990 issue of Newsweek ran a cover story on CFS, which although supportive of an organic cause of the illness, also featured the term 'yuppie flu', reflecting the stereotype that CFS mainly affected yuppies. The implication was that CFS is a form of burnout. The term 'yuppie flu' is considered offensive by both patients and clinicians.

In 2009, the journal Science published a study that identified the XMRV retrovirus in a population of people with CFS. Other studies failed to reproduce this finding, and in 2011, the editor of Science formally retracted its XMRV paper while the Proceedings of the National Academy of Sciences similarly retracted a 2010 paper which had appeared to support the finding of a connection between XMRV and CFS.

Research funding

United Kingdom

The lack of research funding and the funding bias towards biopsychosocial studies and against biomedical studies has been highlighted a number of times by patient groups and a number of UK politicians. A parliamentary inquiry by an ad hoc group of parliamentarians in the United Kingdom, set up and chaired by former MP, Dr Ian Gibson, called the Group on Scientific Research into CFS/ME, was addressed by a government minister claiming that few good biomedical research proposals have been submitted to the Medical Research Council (MRC) in contrast to those for psychosocial research. They were also told by other scientists of proposals that have been rejected, with claims of bias against biomedical research. The MRC confirmed to the group that from April 2003 to November 2006, it has turned down 10 biomedical applications relating to CFS/ME and funded five applications relating to CFS/ME, mostly in the psychiatric/psychosocial domain.

In 2008, the MRC set up an expert group to consider how the MRC might encourage new high-quality research into CFS/ME and partnerships between researchers already working on CFS/ME and those in associated areas. It currently lists CFS/ME with a highlight notice, inviting researchers to develop high-quality research proposals for funding. In February 2010, the All-Party Parliamentary Group on ME (APPG on ME) produced a legacy paper, which welcomed the recent MRC initiative, but felt that far too much emphasis in the past had been on psychological research, with insufficient attention to biomedical research, and that further biomedical research must be undertaken to help discover a cause and more effective forms of management for this disease.

A 2016 report by ME Research looking at UK funding for ME/CFS between January 2006 and December 2015 found that 99 grants had been funded, totalling £49 million, with the largest number of studies being related to "Biological and endogenous factors".

Controversy surrounds psychologically oriented models of the disease and behavioral treatments conducted in the UK.

United States

In 1998, $13 million for CFS research was found to have been redirected or improperly accounted for by the United States CDC, and officials at the agency misled Congress about the irregularities. The agency stated that they needed the funds to respond to other public-health emergencies. The director of a US national patient advocacy group charged the CDC had a bias against studying the disease. The CDC pledged to improve their practices and to restore the $13 million to CFS research over three years.

On 29 October 2015, the National Institutes of Health declared its intent to increase research on ME/CFS. The NIH Clinical Center was to study individuals with ME/CFS, and the National Institute of Neurological Disorders and Stroke would lead the Trans-NIH ME/CFS Research Working Group as part of a multi-institute research effort.

Notable cases

In 1989, The Golden Girls (1985–1992) featured chronic fatigue syndrome in a two-episode arc, "Sick and Tired: Part 1" and "Part 2", in which protagonist Dorothy Zbornak, portrayed by Bea Arthur, after a lengthy battle with her doctors in an effort to find a diagnosis for her symptoms, is finally diagnosed with CFS. American author Ann Bannon had CFS. Laura Hillenbrand, author of the popular book Seabiscuit, has struggled with CFS since age 19.

Research

Graph of ME/CFS papers published by year, showing an increasing trend since about 1985
Graph of CFS papers published by year:
  Papers mentioning ME or CFS
  Papers whose title mentions ME/CFS

Current research into ME/CFS may lead to a better understanding of the disease's causes, biomarkers to aid in diagnosis, and treatments to relieve symptoms. The emergence of long COVID has sparked increased interest in ME/CFS, as the two conditions may share pathology, and a treatment for one may treat the other.

Causes

Recent research suggests dysfunction in many biological processes. These changes may share a common cause, but the true relationship between them is currently unknown. Metabolic areas of interest include disruptions in amino acid metabolism, the TCA cycle, ATP synthesis, and potentially increased lipid metabolism. Other research has investigated immune dysregulation and its potential connections to mitochondrial dysfunction. Autoimmunity has been proposed as a cause, but evidence is scant. People with ME/CFS may have abnormal gut microbiota, which has been proposed to affect mitochondria or nervous system function.

Several small studies have investigated the genetics of ME/CFS, but none of their findings have been replicated. A larger study, DecodeME, is currently underway in the United Kingdom.

Treatments

Various drug treatments for ME/CFS are being explored. The types of drugs under investigation often target the nervous system, the immune system or autoimmunity, or pain directly. More recently, there has been a growing interest in drugs targeting energy metabolism.

Drugs targetting the immune system include rintatolimod. Low-dose naltrexone, which works against neuro-inflammation, is being studied as of 2023. Rituximab, a drug that depletes B cells, was studied and found to be ineffective. Other options targetting auto-immunity are immune absorption, whereby a large set of (auto)antibodies is removed from the blood.

Biomarkers

Many biomarkers for ME/CFS have been proposed based on research findings. But due to the use of a number of case definitions in research, some of which are non-specific such as the Sharpe ("Oxford") and Fukuda ("old CDC") definitions, no biomarkers have been widely validated or broadly clinically implemented. Proposed markers include electrical measurements of blood cells and a combination of immune cell death rate and function.

Challenges

ME/CFS affects multiple bodily systems, varies widely in severity, and fluctuates over time, creating heterogeneity within patient groups and making it very difficult to identify a singular cause. This variation may also cause treatments that are effective for some patients to have no effect or a negative effect in others. Dividing patients into subtypes may help manage this heterogeneity.

The existence of multiple diagnostic criteria, and variations in how scientists apply them, complicate comparisons between studies. Some definitions, like the Oxford and Fukuda criteria, may fail to distinguish between chronic fatigue in general and ME/CFS, which requires PEM in modern definitions. Definitions also vary in which co-occurring conditions preclude a diagnosis of ME/CFS.

Hysteria

From Wikipedia, the free encyclopedia
refer to caption
An 1893 depiction of a woman with hysteria

Hysteria is a term used colloquially to mean ungovernable emotional excess and can refer to a temporary state of mind or emotion. In the nineteenth century, female hysteria was considered a diagnosable physical illness in women. It is assumed that the basis for diagnosis operated under the belief that women are predisposed to mental and behavioral conditions; an interpretation of sex-related differences in stress responses. In the twentieth century, it shifted to being considered a mental illness. Many influential people such as Sigmund Freud and Jean-Martin Charcot dedicated research to hysteria patients.

Currently, most doctors practicing medicine do not accept hysteria as a medical diagnosis. The blanket diagnosis of hysteria has been fragmented into myriad medical categories such as epilepsy, histrionic personality disorder, conversion disorders, dissociative disorders, or other medical conditions. Furthermore, lifestyle choices, such as choosing not to wed, are no longer considered symptoms of psychological disorders such as hysteria.

History

The word hysteria originates from the Greek word for uterus, hystera. The oldest record of hysteria dates back to 1900 BCE when Egyptians recorded behavioral abnormalities in adult women on the Kahun Papyrus. The Egyptians attributed the behavioral disturbances to a wandering uterus – thus the condition later being dubbed hysteria. To treat hysteria Egyptian doctors prescribed various medications. For example, doctors put strong smelling substances on the patients' vulvas to encourage the uterus to return to its proper position. Another tactic was to smell or swallow unsavory herbs to encourage the uterus to flee back to the lower part of the female's abdomen.

The ancient Greeks accepted the ancient Egyptians' explanation for hysteria; however, they included in their definition of hysteria the inability to bear children or the unwillingness to marry. Plato and Aristotle believed that hysteria, which Plato also called female madness, was directly related to these women’s lack of sexual activity and described the uterus as those who suffered from it as having a sad, bad, or melancholic uterus. In the 5th century BCE Hippocrates first used the term hysteria. Ancient Romans also attributed hysteria to an abnormality in the womb; however, discarded the traditional explanation of a wandering uterus. Instead, the ancient Romans credited hysteria to a disease of the womb or a disruption in reproduction (i.e., a miscarriage, menopause, etc.). Hysteria theories from the ancient Egyptians, ancient Greeks, and ancient Romans were the basis of the Western understanding of hysteria.

Between the fifth and thirteenth centuries, however, the increasing influence of Christianity in the Latin West altered medical and public understanding of hysteria. St. Augustine's writings suggested that human suffering resulted from sin, thus hysteria became perceived as satanic possession. With the shift in perception of hysteria came a shift in treatment options. Instead of admitting patients to a hospital, the church began treating patients through prayers, amulets, and exorcisms. At this time, writings such as Constantine the African’s Viaticum and Pantegni, described women with hysteria as the cause of amor heroycus, a form of sexual desire so strong that it caused madness, rather than someone with a problem who should be cured.

Trota de Ruggiero is considered the first female doctor in Christian Europe as well as the first gynecologist, though she could not become a magister. She recognized that women were often ashamed to go to a doctor with gynecological issues, and studied women’s diseases and attempted to avoid common misconceptions and prejudice of the era. She prescribed remedies such as mint for women suffering from hysteria. Hildegard of Bingen was another female doctor, whose work was part of an attempt to combine science and faith. She agreed with the theories of Hippocrates and suggested hysteria may be connected to the idea of original sin; She believed that men and women were both responsible for original sin, and could both suffer from hysteria. Furthermore, during the Renaissance period many patients of hysteria were prosecuted as witches and underwent interrogations, torture, exorcisms, and execution. During this time the common point of view was that women were inferior beings, connected to Aristotle’s ideas of male superiority. Saint Thomas Aquinas supported this idea and in his writing, Summa Theologica stated “'some old women' are evil-minded; they gaze on children in a poisonous and evil way, and demons, with whom the witches enter into agreements, interacting through their eyes”. This type of fear of witches and sorcery is part of the rules of celibacy and chastity imposed on the clergy. Philippe Pinel believed that there was little difference between madness and healthy people, and believed that people should be treated if they were unwell. He considered hysteria a female disorder.

However, during the sixteenth and seventeenth centuries activists and scholars worked to change the perception of hysteria back to a medical condition. Particularly, French physician Charles Le Pois insisted that hysteria was a malady of the brain. In addition, in 1697, English physician Thomas Sydenham theorized that hysteria was an emotional condition, instead of a physical condition. Many physicians followed Lepois and Sydenham's lead and hysteria became disassociated with the soul and the womb. During this time period, science started to focalize hysteria in the central nervous system. As doctors developed a greater understanding of the human nervous system, the neurological model of hysteria was created, which further propelled the conception of hysteria as a mental disorder. Joseph Raulin published a work in 1748, associating hysteria with the air quality in cities, he suggested that men and women could both have hysteria, women would be more likely to have it due to laziness.

In 1859 Paul Briquet defined hysteria as a chronic syndrome manifesting in many unexplained symptoms throughout the body's organ systems. What Briquet described became known as Briquet's syndrome, or Somatization disorders, in 1971. Over a ten-year period, Briquet conducted 430 case studies of patients with hysteria. Following Briquet, Jean-Martin Charcot studied women in an asylum in France and used hypnosis as treatment. Charcot detailed the intricacies of hysteria, understanding it as being caused by patriarchy. He also mentored Pierre Janet, another French psychologist, who studied five of hysteria's symptoms (anesthesia, amnesia, abulia, motor control diseases, and character change) in depth and proposed that hysteria symptoms occurred due to a lapse in consciousness. Both Charcot and Janet inspired Freud's work. Freud theorized hysteria stemmed from childhood sexual abuse or repression. Briquet, Freud and Charcot noted male hysteria; both genders could exhibit the syndrome. Hysterics may be able to manipulate their caretakers thus complicating treatment.

During the twentieth century, as psychiatry advanced in the West, anxiety and depression diagnoses began to replace hysteria diagnoses in Western countries. For example, from 1949 to 1978, annual admissions of hysteria patients in England and Wales decreased by roughly two-thirds. With the decrease of hysteria patients in Western cultures came an increase in anxiety and depression patients. Theories for why hysteria diagnoses began to decline vary, but many historians infer that World War II, along with the use of the diagnosis of shell-shock, westernization, and migration shifted Western mental health expectations. Twentieth-century western societies expected depression and anxiety manifest itself more in post World War II generations and displaced individuals; and thus, individuals reported or were diagnosed accordingly. In addition, medical advancements explained ailments that were previously attributed to hysteria such as epilepsy or infertility. World Wars caused military doctors to become focused on hysteria as during this time there seemed to be a rise in cases, especially under instances of high stress, in 1919 Arthur Frederick Hurst wrote that “many cases of gross hysterical symptoms occurred in soldiers who had no family or personal history of neuroses, and who were perfectly fit”. In 1970 Colin P. McEvedy and Alanson W. Beard suggested that Royal Free Disease (Royal Free Hospital outbreak, now also known as myalgic encephalomyelitis/chronic fatigue syndrome), which mainly affected young women, was an epidemic of hysteria. They also said that hysteria had a historically negative connotation, however that should not prevent doctors from assessing symptoms of the patient. In 1980, after a gradual decline in diagnoses and reports, hysteria was removed from the American Psychiatric Association's Diagnostic and Statistical Manual of Mental Disorders (DSM), which had included hysteria as a mental disorder from its second publication in 1968.

The term is still used in the twenty-first century, though not as a diagnosis. When used, it is often a general term for any dramatic displays of outrage or emotion.

André Brouillet: A Clinical Lesson at the Salpêtrière

Historical symptoms

Historically, the symptoms of hysteria have a large range.

  • Shortness of breath
  • Anxiety
  • Insomnia
  • Fainting
  • Amnesia
  • Paralysis
  • Pain
  • Spasms
  • Convulsive fits
  • Vomiting
  • Deafness
  • Bizarre movements
  • Seizures
  • Hallucinations
  • Inability to speak
  • Infertility

Historical treatment

  • Regular marital sex
  • Pregnancy
  • Childbirth
  • "Paroxysmal convulsions" (orgasms)
  • Rest cure

Notable theorists

Charcot

In the late nineteenth century, French neurologist Jean-Martin Charcot tackled what he referred to as "the great neurosis" or hysteria. Charcot theorized that hysteria was a hereditary, physiological disorder. He believed hysteria impaired areas of the brain which provoked the physical symptoms displayed in each patient. While Charcot believed hysteria was hereditary, he also thought that environmental factors such as stress could trigger hysteria in an individual.

Charcot published more than 120 case studies of patients who he diagnosed with hysteria, including Marie "Blanche" Whittman. Whittman was referred to as the "Queen of Hysterics," and remains the most famous patient of hysteria. To treat his patients, Charcot used hypnosis, which he determined was successful only when used on hysterics. Using patients as props, Charcot executed dramatic public demonstrations of hysterical patients and his cures for hysteria, which many suggest produced the hysterical phenomenon. Furthermore, Charcot noted similarities between demon possession and hysteria, and thus, he concluded "demonomania" was a form of hysteria.

Freud

In 1896 Sigmund Freud, an Austrian neurologist, published "The Aetiology of Hysteria". The paper explains how Freud believes his female patients' neurosis, which he labels hysteria, resulted from sexual abuse as children. Freud named the concept of physical symptoms resulting from childhood trauma: hysterical conversion. Freud hypothesized that in order to cure hysteria the patient must relive the experiences through imagination in the most vivid form while under light hypnosis. However, Freud later changed his theory. His new theory claimed that his patients imagined the instances of sexual abuse, which were instead repressed childhood fantasies. By 1905, Freud retracted the theory of hysteria resulting from repressed childhood fantasies. Freud was also one of the first noted psychiatrists to attribute hysteria to men. He diagnosed himself with hysteria, writing that he feared his work had exacerbated his condition.

Modern perceptions

For the most part, hysteria does not exist as a medical diagnosis in Western culture and has been replaced by other diagnoses such as conversion or functional disorders. The effects of hysteria as a diagnosable illness in the eighteenth and nineteenth centuries has had a lasting effect on the medical treatment of women's health. The term hysterical, applied to an individual, can mean that they are emotional, irrationally upset, or frenzied. When applied to a situation not involving panic, hysteria means that that situation is uncontrollably amusing – the connotation being that it invokes hysterical laughter.

Race in hysteria

According to Laura Briggs’s The Race of Hysteria: “Overcivilization” and the “Savage” Woman in Late Nineteenth-Century Obstetrics and Gynecology, women could be categorized into three steps of civilization: the savage, the civilized, and the overcivilized. Referencing Edward Tylor’s conception that humans evolve through three stages: savage, barbarian, and civilized. Briggs believes that Hysteria was thought to be caused by overcivilization. Terms such as “savage” were reserved for people in extreme poverty or of minority descent (Africans, Asians, Indigenous, Jewish, etc). Because of this distinction between the civilized and the savage during the 19th Century, Hysteria was diagnosed as a disease among mostly middle and upper-class white women.

Many middle and upper-class white men, identified middle and upper-class white women as endangering the race with their low fertility, while non-white women, immigrants, and poor people had many children. During the 19th Century, white women were categorized as “weak, frail and nervous” which reflected the diagnosed symptoms for hysteria such as nervousness, fainting, and ill reproductive bodies. On the contrary, minority, and impoverished women were seen as “strong, hardy, and prolifically fertile.” This caused worry among white men who feared that middle and upper-class white women were causing the depopulation of their race. This growing conception would later be coined, “race suicide” by Edward A. Ross.

As race suicide became a more recognizable fear in Europe and the U.S., many people attempted to solve it by targeting white women's nutrition, overeducation, sexual limbo, and physical health. Additionally, press and Nativist parties ushered a national concern by connecting the reproduction of white women to the reproduction of first and second-generation immigrant women.  “[Race suicide] pitted white women against the more-fecund women of supposedly ‘‘inferior’’ races supports interpretations of race suicide in terms of anti-immigrant sentiment.” As the white public became more unsettled by increased immigration and the declining birthrates of white children, white women were blamed if they lacked the “American ideal” of 4-6 children. Additionally, Immigrants from all minorities were the target of xenophobic remarks and eventually forced sterilization in the U.S. due to eugenics legislation.

Transposable element

From Wikipedia, the free encyclopedia

A bacterial DNA transposon

A transposable element (TE, transposon, or jumping gene) is a nucleic acid sequence in DNA that can change its position within a genome, sometimes creating or reversing mutations and altering the cell's genetic identity and genome size. Transposition often results in duplication of the same genetic material. In the human genome, L1 and Alu elements are two examples. Barbara McClintock's discovery of them earned her a Nobel Prize in 1983. Its importance in personalized medicine is becoming increasingly relevant, as well as gaining more attention in data analytics given the difficulty of analysis in very high dimensional spaces.

Transposable elements make up a large fraction of the genome and are responsible for much of the mass of DNA in a eukaryotic cell. Although TEs are selfish genetic elements, many are important in genome function and evolution. Transposons are also very useful to researchers as a means to alter DNA inside a living organism.

There are at least two classes of TEs: Class I TEs or retrotransposons generally function via reverse transcription, while Class II TEs or DNA transposons encode the protein transposase, which they require for insertion and excision, and some of these TEs also encode other proteins.

Discovery by Barbara McClintock

Barbara McClintock discovered the first TEs in maize (Zea mays) at the Cold Spring Harbor Laboratory in New York. McClintock was experimenting with maize plants that had broken chromosomes.

In the winter of 1944–1945, McClintock planted corn kernels that were self-pollinated, meaning that the silk (style) of the flower received pollen from its own anther. These kernels came from a long line of plants that had been self-pollinated, causing broken arms on the end of their ninth chromosomes. As the maize plants began to grow, McClintock noted unusual color patterns on the leaves. For example, one leaf had two albino patches of almost identical size, located side by side on the leaf. McClintock hypothesized that during cell division certain cells lost genetic material, while others gained what they had lost. However, when comparing the chromosomes of the current generation of plants with the parent generation, she found certain parts of the chromosome had switched position. This refuted the popular genetic theory of the time that genes were fixed in their position on a chromosome. McClintock found that genes could not only move but they could also be turned on or off due to certain environmental conditions or during different stages of cell development.

McClintock also showed that gene mutations could be reversed. She presented her report on her findings in 1951, and published an article on her discoveries in Genetics in November 1953 entitled "Induction of Instability at Selected Loci in Maize".

At the 1951 Cold Spring Harbor Symposium where she first publicized her findings, her talk was met with dead silence. Her work was largely dismissed and ignored until the late 1960s–1970s when, after TEs were found in bacteria, it was rediscovered. She was awarded a Nobel Prize in Physiology or Medicine in 1983 for her discovery of TEs, more than thirty years after her initial research.

Classification

Transposable elements represent one of several types of mobile genetic elements. TEs are assigned to one of two classes according to their mechanism of transposition, which can be described as either copy and paste (Class I TEs) or cut and paste (Class II TEs).

Retrotransposon

Class I TEs are copied in two stages: first, they are transcribed from DNA to RNA, and the RNA produced is then reverse transcribed to DNA. This copied DNA is then inserted back into the genome at a new position. The reverse transcription step is catalyzed by a reverse transcriptase, which is often encoded by the TE itself. The characteristics of retrotransposons are similar to retroviruses, such as HIV.

Retrotransposons are commonly grouped into three main orders:

Retroviruses can also be considered TEs. For example, after the conversion of retroviral RNA into DNA inside a host cell, the newly produced retroviral DNA is integrated into the genome of the host cell. These integrated DNAs are termed proviruses. The provirus is a specialized form of eukaryotic retrotransposon, which can produce RNA intermediates that may leave the host cell and infect other cells. The transposition cycle of retroviruses has similarities to that of prokaryotic TEs, suggesting a distant relationship between the two.

DNA transposons

A. Structure of DNA transposons (Mariner type). Two inverted tandem repeats (TIR) flank the transposase gene. Two short tandem site duplications (TSD) are present on both sides of the insert.
B. Mechanism of transposition: Two transposases recognize and bind to TIR sequences, join and promote DNA double-strand cleavage. The DNA-transposase complex then inserts its DNA cargo at specific DNA motifs elsewhere in the genome, creating short TSDs upon integration.

The cut-and-paste transposition mechanism of class II TEs does not involve an RNA intermediate. The transpositions are catalyzed by several transposase enzymes. Some transposases non-specifically bind to any target site in DNA, whereas others bind to specific target sequences. The transposase makes a staggered cut at the target site producing sticky ends, cuts out the DNA transposon and ligates it into the target site. A DNA polymerase fills in the resulting gaps from the sticky ends and DNA ligase closes the sugar-phosphate backbone. This results in target site duplication and the insertion sites of DNA transposons may be identified by short direct repeats (a staggered cut in the target DNA filled by DNA polymerase) followed by inverted repeats (which are important for the TE excision by transposase).

Cut-and-paste TEs may be duplicated if their transposition takes place during S phase of the cell cycle, when a donor site has already been replicated but a target site has not yet been replicated. Such duplications at the target site can result in gene duplication, which plays an important role in genomic evolution.

Not all DNA transposons transpose through the cut-and-paste mechanism. In some cases, a replicative transposition is observed in which a transposon replicates itself to a new target site (e.g. helitron).

Class II TEs comprise less than 2% of the human genome, making the rest Class I.

Autonomous and non-autonomous

Transposition can be classified as either "autonomous" or "non-autonomous" in both Class I and Class II TEs. Autonomous TEs can move by themselves, whereas non-autonomous TEs require the presence of another TE to move. This is often because dependent TEs lack transposase (for Class II) or reverse transcriptase (for Class I).

Activator element (Ac) is an example of an autonomous TE, and dissociation elements (Ds) is an example of a non-autonomous TE. Without Ac, Ds is not able to transpose.

Class III

Some researchers also identify a third class of transposable elements, which has been described as "a grab-bag consisting of transposons that don't clearly fit into the other two categories". Examples of such TEs are the Foldback (FB) elements of Drosophila melanogaster, the TU elements of Strongylocentrotus purpuratus, and Miniature Inverted-repeat Transposable Elements.

Distribution

Approximately 64% of the maize genome is made up of TEs, as is 44% of the human genome, and almost half of murine genomes.

New discoveries of transposable elements have shown the exact distribution of TEs with respect to their transcription start sites (TSSs) and enhancers. A recent study found that a promoter contains 25% of regions that harbor TEs. It is known that older TEs are not found in TSS locations because TEs frequency starts as a function once there is a distance from the TSS. A possible theory for this is that TEs might interfere with the transcription pausing or the first-intro splicing. Also as mentioned before, the presence of TEs closed by the TSS locations is correlated to their evolutionary age (number of different mutations that TEs can develop during the time).

Examples

  • The first TEs were discovered in maize (Zea mays) by Barbara McClintock in 1948, for which she was later awarded a Nobel Prize. She noticed chromosomal insertions, deletions, and translocations caused by these elements. These changes in the genome could, for example, lead to a change in the color of corn kernels. About 64% of the maize genome consists of TEs. The Ac/Ds system described by McClintock are Class II TEs. Transposition of Ac in tobacco has been demonstrated by B. Baker.
  • In the pond microorganism, Oxytricha, TEs play such a critical role that when removed, the organism fails to develop.
  • One family of TEs in the fruit fly Drosophila melanogaster are called P elements. They seem to have first appeared in the species only in the middle of the twentieth century; within the last 50 years, they spread through every population of the species. Gerald M. Rubin and Allan C. Spradling pioneered technology to use artificial P elements to insert genes into Drosophila by injecting the embryo.
  • In bacteria, TEs usually carry an additional gene for functions other than transposition, often for antibiotic resistance. In bacteria, transposons can jump from chromosomal DNA to plasmid DNA and back, allowing for the transfer and permanent addition of genes such as those encoding antibiotic resistance (multi-antibiotic resistant bacterial strains can be generated in this way). Bacterial transposons of this type belong to the Tn family. When the transposable elements lack additional genes, they are known as insertion sequences.
  • In humans, the most common TE is the Alu sequence. It is approximately 300 bases long and can be found between 300,000 and one million times in the human genome. Alu alone is estimated to make up 15–17% of the human genome.
  • Mariner-like elements are another prominent class of transposons found in multiple species, including humans. The Mariner transposon was first discovered by Jacobson and Hartl in Drosophila. This Class II transposable element is known for its uncanny ability to be transmitted horizontally in many species. There are an estimated 14,000 copies of Mariner in the human genome comprising 2.6 million base pairs. The first mariner-element transposons outside of animals were found in Trichomonas vaginalis.
  • Mu phage transposition is the best-known example of replicative transposition.
  • In Yeast genomes (Saccharomyces cerevisiae) there are five distinct retrotransposon families: Ty1, Ty2, Ty3, Ty4 and Ty5.
  • A helitron is a TE found in eukaryotes that is thought to replicate by a rolling-circle mechanism.
  • In human embryos, two types of transposons combined to form noncoding RNA that catalyzes the development of stem cells. During the early stages of a fetus's growth, the embryo's inner cell mass expands as these stem cells enumerate. The increase of this type of cells is crucial, since stem cells later change form and give rise to all the cells in the body.
  • In peppered moths, a transposon in a gene called cortex caused the moths' wings to turn completely black. This change in coloration helped moths to blend in with ash and soot-covered areas during the Industrial Revolution.
  • Aedes aegypti carries a large and diverse number of TEs. This analysis by Matthews et al. 2018 also suggests this is common to all mosquitoes.

Negative effects

Transposons have coexisted with eukaryotes for thousands of years and through their coexistence have become integrated in many organisms' genomes. Colloquially known as 'jumping genes', transposons can move within and between genomes allowing for this integration.

While there are many positive effects of transposons in their host eukaryotic genomes, there are some instances of mutagenic effects that TEs have on genomes leading to disease and malignant genetic alterations.

Mechanisms of mutagenesis

TEs are mutagens and due to the contribution to the formation of new cis-regulatory DNA elements that are connected to many transcription factors that are found in living cells; TEs can undergo many evolutionary mutations and alterations. These are often the causes of genetic disease, and gives the potential lethal effects of ectopic expression.

TEs can damage the genome of their host cell in different ways:

  • A transposon or a retrotransposon that inserts itself into a functional gene can disable that gene.
  • After a DNA transposon leaves a gene, the resulting gap may not be repaired correctly.
  • Multiple copies of the same sequence, such as Alu sequences, can hinder precise chromosomal pairing during mitosis and meiosis, resulting in unequal crossovers, one of the main reasons for chromosome duplication.

TEs use a number of different mechanisms to cause genetic instability and disease in their host genomes.

  • Expression of disease-causing, damaging proteins that inhibit normal cellular function.

Diseases

Diseases often caused by TEs include

  • Hemophilia A and B
    • LINE1 (L1) TEs that land on the human Factor VIII have been shown to cause haemophilia
  • Severe combined immunodeficiency
    • Insertion of L1 into the APC gene causes colon cancer, confirming that TEs play an important role in disease development.
  • Porphyria
    • Insertion of Alu element into the PBGD gene leads to interference with the coding region and leads to acute intermittent porphyria (AIP).
  • Predisposition to cancer
    • LINE1(L1) TE's and other retrotransposons have been linked to cancer because they cause genomic instability.
  • Duchenne muscular dystrophy.
    • Caused by SVA transposable element insertion in the fukutin (FKTN) gene which renders the gene inactive.
  • Alzheimer's Disease and other Tauopathies
    • Transposable element dysregulation can cause neuronal death, leading to neurodegenerative disorders

Rate of transposition, induction and defense

One study estimated the rate of transposition of a particular retrotransposon, the Ty1 element in Saccharomyces cerevisiae. Using several assumptions, the rate of successful transposition event per single Ty1 element came out to be about once every few months to once every few years. Some TEs contain heat-shock like promoters and their rate of transposition increases if the cell is subjected to stress, thus increasing the mutation rate under these conditions, which might be beneficial to the cell.

Cells defend against the proliferation of TEs in a number of ways. These include piRNAs and siRNAs, which silence TEs after they have been transcribed.

If organisms are mostly composed of TEs, one might assume that disease caused by misplaced TEs is very common, but in most cases TEs are silenced through epigenetic mechanisms like DNA methylation, chromatin remodeling and piRNA, such that little to no phenotypic effects nor movements of TEs occur as in some wild-type plant TEs. Certain mutated plants have been found to have defects in methylation-related enzymes (methyl transferase) which cause the transcription of TEs, thus affecting the phenotype.

One hypothesis suggests that only approximately 100 LINE1 related sequences are active, despite their sequences making up 17% of the human genome. In human cells, silencing of LINE1 sequences is triggered by an RNA interference (RNAi) mechanism. Surprisingly, the RNAi sequences are derived from the 5′ untranslated region (UTR) of the LINE1, a long terminal which repeats itself. Supposedly, the 5′ LINE1 UTR that codes for the sense promoter for LINE1 transcription also encodes the antisense promoter for the miRNA that becomes the substrate for siRNA production. Inhibition of the RNAi silencing mechanism in this region showed an increase in LINE1 transcription.

Evolution

TEs are found in almost all life forms, and the scientific community is still exploring their evolution and their effect on genome evolution. It is unclear whether TEs originated in the last universal common ancestor, arose independently multiple times, or arose once and then spread to other kingdoms by horizontal gene transfer. While some TEs confer benefits on their hosts, most are regarded as selfish DNA parasites. In this way, they are similar to viruses. Various viruses and TEs also share features in their genome structures and biochemical abilities, leading to speculation that they share a common ancestor.

Because excessive TE activity can damage exons, many organisms have acquired mechanisms to inhibit their activity. Bacteria may undergo high rates of gene deletion as part of a mechanism to remove TEs and viruses from their genomes, while eukaryotic organisms typically use RNA interference to inhibit TE activity. Nevertheless, some TEs generate large families often associated with speciation events. Evolution often deactivates DNA transposons, leaving them as introns (inactive gene sequences). In vertebrate animal cells, nearly all 100,000+ DNA transposons per genome have genes that encode inactive transposase polypeptides. The first synthetic transposon designed for use in vertebrate (including human) cells, the Sleeping Beauty transposon system, is a Tc1/mariner-like transposon. Its dead ("fossil") versions are spread widely in the salmonid genome and a functional version was engineered by comparing those versions. Human Tc1-like transposons are divided into Hsmar1 and Hsmar2 subfamilies. Although both types are inactive, one copy of Hsmar1 found in the SETMAR gene is under selection as it provides DNA-binding for the histone-modifying protein. Many other human genes are similarly derived from transposons. Hsmar2 has been reconstructed multiple times from the fossil sequences.

The frequency and location of TE integrations influence genomic structure and evolution and affect gene and protein regulatory networks during development and in differentiated cell types. Large quantities of TEs within genomes may still present evolutionary advantages, however. Interspersed repeats within genomes are created by transposition events accumulating over evolutionary time. Because interspersed repeats block gene conversion, they protect novel gene sequences from being overwritten by similar gene sequences and thereby facilitate the development of new genes. TEs may also have been co-opted by the vertebrate immune system as a means of producing antibody diversity. The V(D)J recombination system operates by a mechanism similar to that of some TEs. TEs also serve to generate repeating sequences that can form dsRNA to act as a substrate for the action of ADAR in RNA editing.

TEs can contain many types of genes, including those conferring antibiotic resistance and the ability to transpose to conjugative plasmids. Some TEs also contain integrons, genetic elements that can capture and express genes from other sources. These contain integrase, which can integrate gene cassettes. There are over 40 antibiotic resistance genes identified on cassettes, as well as virulence genes.

Transposons do not always excise their elements precisely, sometimes removing the adjacent base pairs; this phenomenon is called exon shuffling. Shuffling two unrelated exons can create a novel gene product or, more likely, an intron.

Some non-autonomous DNA TEs found in plants can capture coding DNA from genes and shuffle them across the genome. This process can duplicate genes in the genome (a phenomenon called transduplication), and can contribute to generate novel genes by exon shuffling.

Evolutionary drive for TEs on the genomic context

There is a hypothesis that states that TEs might provide a ready source of DNA that could be co-opted by the cell to help regulate gene expression. Research showed that many diverse modes of TEs co-evolution along with some transcription factors targeting TE-associated genomic elements and chromatin are evolving from TE sequences. Most of the time, these particular modes do not follow the simple model of TEs and regulating host gene expression.

Applications

Transposable elements can be harnessed in laboratory and research settings to study genomes of organisms and even engineer genetic sequences. The use of transposable elements can be split into two categories: for genetic engineering and as a genetic tool.

Genetic engineering

  • Insertional mutagenesis uses the features of a TE to insert a sequence. In most cases, this is used to remove a DNA sequence or cause a frameshift mutation.
    • In some cases the insertion of a TE into a gene can disrupt that gene's function in a reversible manner where transposase-mediated excision of the DNA transposon restores gene function.
    • This produces plants in which neighboring cells have different genotypes.
    • This feature allows researchers to distinguish between genes that must be present inside of a cell in order to function (cell-autonomous) and genes that produce observable effects in cells other than those where the gene is expressed.

Genetic tool

In addition to the qualities mentioned for Genetic engineering, a Genetic tool also:-

  • Used for analysis of gene expression and protein functioning in signature-tagging mutagenesis.
    • This analytical tool allows researchers the ability to determine phenotypic expression of gene sequences. Also, this analytic technique mutates the desired locus of interest so that the phenotypes of the original and the mutated gene can be compared.

Specific applications

  • TEs are also a widely used tool for mutagenesis of most experimentally tractable organisms. The Sleeping Beauty transposon system has been used extensively as an insertional tag for identifying cancer genes.
  • The Tc1/mariner-class of TEs Sleeping Beauty transposon system, awarded Molecule of the Year in 2009, is active in mammalian cells and is being investigated for use in human gene therapy.
  • TEs are used for the reconstruction of phylogenies by the means of presence/absence analyses. Transposons can act as biological mutagen in bacteria.
  • Common organisms which the use of Transposons has been well developed are:

De novo repeat identification

De novo repeat identification is an initial scan of sequence data that seeks to find the repetitive regions of the genome, and to classify these repeats. Many computer programs exist to perform de novo repeat identification, all operating under the same general principles. As short tandem repeats are generally 1–6 base pairs in length and are often consecutive, their identification is relatively simple. Dispersed repetitive elements, on the other hand, are more challenging to identify, due to the fact that they are longer and have often acquired mutations. However, it is important to identify these repeats as they are often found to be transposable elements (TEs).

De novo identification of transposons involves three steps: 1) find all repeats within the genome, 2) build a consensus of each family of sequences, and 3) classify these repeats. There are three groups of algorithms for the first step. One group is referred to as the k-mer approach, where a k-mer is a sequence of length k. In this approach, the genome is scanned for overrepresented k-mers; that is, k-mers that occur more often than is likely based on probability alone. The length k is determined by the type of transposon being searched for. The k-mer approach also allows mismatches, the number of which is determined by the analyst. Some k-mer approach programs use the k-mer as a base, and extend both ends of each repeated k-mer until there is no more similarity between them, indicating the ends of the repeats. Another group of algorithms employs a method called sequence self-comparison. Sequence self-comparison programs use databases such as AB-BLAST to conduct an initial sequence alignment. As these programs find groups of elements that partially overlap, they are useful for finding highly diverged transposons, or transposons with only a small region copied into other parts of the genome. Another group of algorithms follows the periodicity approach. These algorithms perform a Fourier transformation on the sequence data, identifying periodicities, regions that are repeated periodically, and are able to use peaks in the resultant spectrum to find candidate repetitive elements. This method works best for tandem repeats, but can be used for dispersed repeats as well. However, it is a slow process, making it an unlikely choice for genome-scale analysis.

The second step of de novo repeat identification involves building a consensus of each family of sequences. A consensus sequence is a sequence that is created based on the repeats that comprise a TE family. A base pair in a consensus is the one that occurred most often in the sequences being compared to make the consensus. For example, in a family of 50 repeats where 42 have a T base pair in the same position, the consensus sequence would have a T at this position as well, as the base pair is representative of the family as a whole at that particular position, and is most likely the base pair found in the family's ancestor at that position. Once a consensus sequence has been made for each family, it is then possible to move on to further analysis, such as TE classification and genome masking in order to quantify the overall TE content of the genome.

Adaptive TEs

Transposable elements have been recognized as good candidates for stimulating gene adaptation, through their ability to regulate the expression levels of nearby genes. Combined with their "mobility", transposable elements can be relocated adjacent to their targeted genes, and control the expression levels of the gene, dependent upon the circumstances.

The study conducted in 2008, "High Rate of Recent Transposable Element–Induced Adaptation in Drosophila melanogaster", used D. melanogaster that had recently migrated from Africa to other parts of the world, as a basis for studying adaptations caused by transposable elements. Although most of the TEs were located on introns, the experiment showed a significant difference in gene expressions between the population in Africa and other parts of the world. The four TEs that caused the selective sweep were more prevalent in D. melanogaster from temperate climates, leading the researchers to conclude that the selective pressures of the climate prompted genetic adaptation. From this experiment, it has been confirmed that adaptive TEs are prevalent in nature, by enabling organisms to adapt gene expression as a result of new selective pressures.

However, not all effects of adaptive TEs are beneficial to the population. In the research conducted in 2009, "A Recent Adaptive Transposable Element Insertion Near Highly Conserved Developmental Loci in Drosophila melanogaster", a TE, inserted between Jheh 2 and Jheh 3, revealed a downgrade in the expression level of both of the genes. Downregulation of such genes has caused Drosophila to exhibit extended developmental time and reduced egg to adult viability. Although this adaptation was observed in high frequency in all non-African populations, it was not fixed in any of them. This is not hard to believe, since it is logical for a population to favor higher egg to adult viability, therefore trying to purge the trait caused by this specific TE adaptation.

At the same time, there have been several reports showing the advantageous adaptation caused by TEs. In the research done with silkworms, "An Adaptive Transposable Element insertion in the Regulatory Region of the EO Gene in the Domesticated Silkworm", a TE insertion was observed in the cis-regulatory region of the EO gene, which regulates molting hormone 20E, and enhanced expression was recorded. While populations without the TE insert are often unable to effectively regulate hormone 20E under starvation conditions, those with the insert had a more stable development, which resulted in higher developmental uniformity.

These three experiments all demonstrated different ways in which TE insertions can be advantageous or disadvantageous, through means of regulating the expression level of adjacent genes. The field of adaptive TE research is still under development and more findings can be expected in the future.

TEs participates in gene control networks

Recent studies have confirmed that TEs can contribute to the generation of transcription factors. However, how this process of contribution can have an impact on the participation of genome control networks. TEs are more common in many regions of the DNA and it makes up 45% of total human DNA. Also, TEs contributed to 16% of transcription factor binding sites. A larger number of motifs are also found in non-TE-derived DNA, and the number is larger than TE-derived DNA. All these factors correlate to the direct participation of TEs in many ways of gene control networks.

Retrotransposon

 

From Wikipedia, the free encyclopedia

Simplified representation of the life cycle of a retrotransposon

Retrotransposons (also called Class I transposable elements or transposons via RNA intermediates) are a type of genetic component that copy and paste themselves into different genomic locations (transposon) by converting RNA back into DNA through the reverse transcription process using an RNA transposition intermediate.

Through reverse transcription, retrotransposons amplify themselves quickly to become abundant in eukaryotic genomes such as maize (49–78%) and humans (42%). They are only present in eukaryotes but share features with retroviruses such as HIV, for example, discontinuous reverse transcriptase-mediated extrachromosomal recombination.

These retrotransposons are regulated by a family of short non-coding RNAs termed as PIWI [P-element induced wimpy testis]-interacting RNAs (piRNAs). piRNA is a recently discovered class of ncRNAs, which are in the length range of ~24-32 nucleotides. Initially, piRNAs were described as repeat-associated siRNAs (rasiRNAs) because of their origin from the repetitive elements such as transposable sequences of the genome. However, later it was identified that they acted via PIWI-protein. In addition to having a role in the suppression of genomic transposons, various roles of piRNAs have been recently reported like regulation of 3’ UTR of protein-coding genes via RNAi, transgenerational epigenetic inheritance to convey a memory of past transposon activity, and RNA-induced epigenetic silencing.

There are two main types of retrotransposons, long terminal repeats (LTRs) and non-long terminal repeats (non-LTRs). Retrotransposons are classified based on sequence and method of transposition. Most retrotransposons in the maize genome are LTR, whereas in humans they are mostly non-LTR. Retrotransposons (mostly of the LTR type) can be passed onto the next generation of a host species through the germline.

The other type of transposon is the DNA transposon. DNA transposons encode a transposase which, when translated, catalyses the excision of the transposase gene and its flanking region and its insertion into a different genomic location: a 'jumping' DNA element. Hence retrotransposons can be thought of as replicative, whereas DNA transposons are non-replicative. Due to their replicative nature, retrotransposons can increase eukaryotic genome size quickly and survive in eukaryotic genomes permanently. It is thought that staying in eukaryotic genomes for such long periods gave rise to special insertion methods that do not affect eukaryotic gene function drastically.

LTR retrotransposons

Long strands of repetitive DNA can be found at each end of a LTR retrotransposon. These are termed long terminal repeats (LTRs) that are each a few hundred base pairs long, hence retrotransposons with LTRs have the name long terminal repeat (LTR) retrotransposon. LTR retrotransposons are over 5 kilobases long. Between the long terminal repeats there are genes that can be transcribed equivalent to retrovirus genes gag and pol. These genes overlap so they encode a protease that processes the resulting transcript into functional gene products. Gag gene products associate with other retrotransposon transcripts to form virus-like particles. Pol gene products include enzymes reverse transcriptase, integrase and ribonuclease H domains. Reverse transcriptase carries out reverse transcription of retrotransposon DNA. Integrase 'integrates' retrotransposon DNA into eukaryotic genome DNA. Ribonuclease cleaves phosphodiester bonds between RNA nucleotides.

LTR retrotransposons encode transcripts with tRNA binding sites so that they can undergo reverse transcription. The tRNA-bound RNA transcript binds to a genomic RNA sequence. Template strand of retrotransposon DNA can hence be synthesised. Ribonuclease H domains degrade eukaryotic genomic RNA to give adenine- and guanine-rich DNA sequences that flag where the complementary noncoding strand has to be synthesised. Integrase then 'integrates' the retrotransposon into eukaryotic DNA using the hydroxyl group at the start of retrotransposon DNA. This results in a retrotransposon flagged by long terminal repeats at its ends. Because the retrotransposon contains eukaryotic genome information it can insert copies of itself into other genomic locations within a eukaryotic cell.

Endogenous retrovirus

An endogenous retrovirus is a retrovirus without virus pathogenic effects that has been integrated into the host genome by inserting their inheritable genetic information into cells that can be passed onto the next generation like a retrotransposon. Because of this, they share features with retroviruses and retrotransposons. When the retroviral DNA is integrated into the host genome they evolve into endogenous retroviruses that influence eukaryotic genomes. So many endogenous retroviruses have inserted themselves into eukaryotic genomes that they allow insight into biology between viral-host interactions and the role of retrotransposons in evolution and disease. Many retrotransposons share features with endogenous retroviruses, the property of recognising and fusing with the host genome. However, there is a key difference between retroviruses and retrotransposons, which is indicated by the env gene. Although similar to the gene carrying out the same function in retroviruses, the env gene is used to determine whether the gene is retroviral or retrotransposon. If the gene is retroviral it can evolve from a retrotransposon into a retrovirus. They differ by the order of sequences in pol genes. Env genes are found in LTR retrotransposon types Ty1-copia (Pseudoviridae), Ty3-gypsy (Metaviridae) and BEL/Pao. They encode glycoproteins on the retrovirus envelope needed for entry into the host cell. Retroviruses can move between cells whereas LTR retrotransposons can only move themselves into the genome of the same cell. Many vertebrate genes were formed from retroviruses and LTR retrotransposons. One endogenous retrovirus or LTR retrotransposon has the same function and genomic locations in different species, suggesting their role in evolution.

Non-LTR retrotransposons

Like LTR retrotransposons, non-LTR retrotransposons contain genes for reverse transcriptase, RNA-binding protein, nuclease, and sometimes ribonuclease H domain but they lack the long terminal repeats. RNA-binding proteins bind the RNA-transposition intermediate and nucleases are enzymes that break phosphodiester bonds between nucleotides in nucleic acids. Instead of LTRs, non-LTR retrotransposons have short repeats that can have an inverted order of bases next to each other aside from direct repeats found in LTR retrotransposons that is just one sequence of bases repeating itself.

Although they are retrotransposons, they cannot carry out reverse transcription using an RNA transposition intermediate in the same way as LTR retrotransposons. Those two key components of the retrotransposon are still necessary but the way they are incorporated into the chemical reactions is different. This is because unlike LTR retrotransposons, non-LTR retrotransposons do not contain sequences that bind tRNA.

They mostly fall into two types – LINEs (Long interspersed nuclear elements) and SINEs (Short interspersed nuclear elements). SVA elements are the exception between the two as they share similarities with both LINEs and SINEs, containing Alu elements and different numbers of the same repeat. SVAs are shorter than LINEs but longer than SINEs.

While historically viewed as "junk DNA", research suggests in some cases, both LINEs and SINEs were incorporated into novel genes to form new functions.

LINEs

When a LINE is transcribed, the transcript contains an RNA polymerase II promoter that ensures LINEs can be copied into whichever location it inserts itself into. RNA polymerase II is the enzyme that transcribes genes into mRNA transcripts. The ends of LINE transcripts are rich in multiple adenines, the bases that are added at the end of transcription so that LINE transcripts would not be degraded. This transcript is the RNA transposition intermediate.

The RNA transposition intermediate moves from the nucleus into the cytoplasm for translation. This gives the two coding regions of a LINE that in turn binds back to the RNA it is transcribed from. The LINE RNA then moves back into the nucleus to insert into the eukaryotic genome.

LINEs insert themselves into regions of the eukaryotic genome that are rich in bases AT. At AT regions LINE uses its nuclease to cut one strand of the eukaryotic double-stranded DNA. The adenine-rich sequence in LINE transcript base pairs with the cut strand to flag where the LINE will be inserted with hydroxyl groups. Reverse transcriptase recognises these hydroxyl groups to synthesise LINE retrotransposon where the DNA is cut. Like with LTR retrotransposons, this new inserted LINE contains eukaryotic genome information so it can be copied and pasted into other genomic regions easily. The information sequences are longer and more variable than those in LTR retrotransposons.

Most LINE copies have variable length at the start because reverse transcription usually stops before DNA synthesis is complete. In some cases this causes RNA polymerase II promoter to be lost so LINEs cannot transpose further.

Genetic structure of murine LINE1 and SINEs. Bottom: proposed structure of L1 RNA-protein (RNP) complexes. ORF1 proteins form trimers, exhibiting RNA binding and nucleic acid chaperone activity.

Human L1

LINE-1 (L1) retrotransposons make up a significant portion of the human genome, with an estimated 500,000 copies per genome. Genes encoding for human LINE1 usually have their transcription inhibited by methyl groups binding to its DNA carried out by PIWI proteins and enzymes DNA methyltransferases. L1 retrotransposition can disrupt the nature of genes transcribed by pasting themselves inside or near genes which could in turn lead to human disease. LINE1s can only retrotranspose in some cases to form different chromosome structures contributing to differences in genetics between individuals. There is an estimate of 80–100 active L1s in the reference genome of the Human Genome Project, and an even smaller number of L1s within those active L1s retrotranspose often. L1 insertions have been associated with tumorigenesis by activating cancer-related genes oncogenes and diminishing tumor suppressor genes.

Each human LINE1 contains two regions from which gene products can be encoded. The first coding region contains a leucine zipper protein involved in protein-protein interactions and a protein that binds to the terminus of nucleic acids. The second coding region has a purine/pyrimidine nuclease, reverse transcriptase and protein rich in amino acids cysteines and histidines. The end of the human LINE1, as with other retrotransposons is adenine-rich.

Human L1 actively retrotransposes in the human genome. A recent study identified 1,708 somatic L1 retrotransposition events, especially in colorectal epithelial cells. These events occur from early embryogenesis and retrotransposition rate is substantially increased during colorectal tumourigenesis.

SINEs

SINEs are much shorter (300bp) than LINEs. They share similarity with genes transcribed by RNA polymerase II, the enzyme that transcribes genes into mRNA transcripts, and the initiation sequence of RNA polymerase III, the enzyme that transcribes genes into ribosomal RNA, tRNA and other small RNA molecules. SINEs such as mammalian MIR elements have tRNA gene at the start and adenine-rich at the end like in LINEs.

SINEs do not encode a functional reverse transcriptase protein and rely on other mobile transposons, especially LINEs. SINEs exploit LINE transposition components despite LINE-binding proteins prefer binding to LINE RNA. SINEs cannot transpose by themselves because they cannot encode SINE transcripts. They usually consist of parts derived from tRNA and LINEs. The tRNA portion contains an RNA polymerase III promoter which the same kind of enzyme as RNA polymerase II. This makes sure the LINE copies would be transcribed into RNA for further transposition. The LINE component remains so LINE-binding proteins can recognise the LINE part of the SINE.

Alu elements

Alus are the most common SINE in primates. They are approximately 350 base pairs long, do not encode proteins and can be recognized by the restriction enzyme AluI (hence the name). Their distribution may be important in some genetic diseases and cancers. Copy and pasting Alu RNA requires the Alu's adenine-rich end and the rest of the sequence bound to a signal. The signal-bound Alu can then associate with ribosomes. LINE RNA associates on the same ribosomes as the Alu. Binding to the same ribosome allows Alus of SINEs to interact with LINE. This simultaneous translation of Alu element and LINE allows SINE copy and pasting.

SVA elements

SVA elements are present at lower levels than SINES and LINEs in humans. The starts of SVA and Alu elements are similar, followed by repeats and an end similar to endogenous retrovirus. LINEs bind to sites flanking SVA elements to transpose them. SVA are one of the youngest transposons in great apes genome and among the most active and polymorphic in the human population.

Role in human disease

Retrotransposons ensure they are not lost by chance by occurring only in cell genetics that can be passed on from one generation to the next from parent gametes. However, LINEs can transpose into the human embryo cells that eventually develop into the nervous system, raising the question whether this LINE retrotransposition affects brain function. LINE retrotransposition is also a feature of several cancers, but it is unclear whether retrotransposition itself causes cancer instead of just a symptom. Uncontrolled retrotransposition is bad for both the host organism and retrotransposons themselves so they have to be regulated. Retrotransposons are regulated by RNA interference. RNA interference is carried out by a bunch of short non-coding RNAs. The short non-coding RNA interacts with protein Argonaute to degrade retrotransposon transcripts and change their DNA histone structure to reduce their transcription.

Role in evolution

LTR retrotransposons came about later than non-LTR retrotransposons, possibly from an ancestral non-LTR retrotransposon acquiring an integrase from a DNA transposon. Retroviruses gained additional properties to their virus envelopes by taking the relevant genes from other viruses using the power of LTR retrotransposon.

Due to their retrotransposition mechanism, retrotransposons amplify in number quickly, composing 40% of the human genome. The insertion rates for LINE1, Alu and SVA elements are 1/200 – 1/20, 1/20 and 1/900 respectively. The LINE1 insertion rates have varied a lot over the past 35 million years, so they indicate points in genome evolution.

Notably a large number of 100 kilobases in the maize genome show variety due to the presence or absence of retrotransposons. However since maize is unusual genetically as compared to other plants it cannot be used to predict retrotransposition in other plants.

Mutations caused by retrotransposons include:

  • Gene inactivation
  • Changing gene regulation
  • Changing gene products
  • Acting as DNA repair sites

Equality (mathematics)

From Wikipedia, the free encyclopedia https://en.wikipedia.org/wiki/Equality_...