Hashimoto’s Autoimmune Hypothyroid - The Perfect Storm

12 March 2019

Thyroid hormone is vitally important: every cell in the body - be that a gut cell, brain cell, immune cell or muscle cell - has receptors for it, and thus it quite literally instructs each of those cells to do what they are designed to do and drives the speed at which all of these cells work. This is known as our metabolic rate. Like an accelerator pedal, turn it up and your metabolism will speed up; slow it down and you will also start to slow down - manifesting as fatigue, drying skin, slower bowel movements, constant infections, poor immunity, thinning hair and impaired digestion.

How does your thyroid work


/hypothalamus secretes TRH, Pituitary secretes TSH, Thyroid secretes T3 and T4.Under the control of a clever feedback loop, the thyroid axis begins within the hypothalamus. This is a portion of the brain that contains a number of small nuclei called the paraventricular nucleus (PNV), which regulate hormone output. Once the PNV has been stimulated by neurotransmitters (predominantly serotonin and dopamine), the hypothalamus releases Thyroid Releasing Hormone (TRH).  

This affects a second gland, the pituitary, causing it to release Thyroid Stimulating Hormone (TSH), which in turn triggers the thyroid gland to produce thyroxine (T4) 94% and triiodothyronine (T3) 7%. The T4 is inactive at this time, and the hormones produced by the thyroid are bound (to another protein: thyroid binding globulin) so it is not until they reach the peripheral tissues (such as the liver and gastrointestinal tract) where they become both unbound and converted to the active form of T3. This is when the thyroid hormone can finally do its job: bind to a receptor site of a cell and activate a response.

Hypothyroidism, by its very definition, is a condition where the body has inadequate levels of thyroid hormone. Hyperthyroidism is a less common condition that exists when excess thyroid hormones are present. As every cell of the body is affected by thyroid hormones, symptoms of imbalances are often varied and can affect multiple body systems.

Symptoms of low thyroid function

Symptoms of high thyroid function

  • Brittle hair and nails

  • Cold temperature intolerance

  • Cold hands and feet

  • Constipation

  • Decreased sweating

  • Depression

  • Dry skin

  • Fatigue

  • Inability to lose weight

  • Low libido

  • Menstrual irregularities

  • Shortness of breath

  • Sluggishness

  • Weight gain

  • Anxiety

  • Diarrhoea

  • Eye/vision changes

  • Fatigue

  • Hair loss

  • Insomnia

  • Palpitations

  • Rapid heart beat

  • Sweating

  • Weakness

  • Weight loss

Estimates show that a massive 95% of those that are hypothyroid actually have Hashimoto's Autoimmune Hypothyroidism, but, if antibodies are not run on a blood test, patients are sent away with a ‘clean bill of health’, being assured that there is nothing wrong with their thyroid at all. In fact, a TSH can remain ‘normal’ for years while the autoimmune attack is insidiously at play.

Testing for thyroid function

Laboratory tests are available to check thyroid function and autoimmune thyroid markers. Often people with thyroid symptoms will ask their doctors to be tested, but will be told that their thyroid function is normal. Unfortunately, this is because GP’s typically only run TSH and T4 - not a broader panel (as shown below). However, TSH does not become permanently elevated until Hashimoto’s is advanced. Therefore it is not uncommon for people to have many unpleasant thyroid symptoms (such as brain fog, weight gain, bloating, sluggish bowel movements and fatigue) then to be tested for thyroid function by only a TSH measurement, and to be told they are ‘fine’ and that their thyroid is completely ‘normal’.

Furthermore, under certain conditions, the conversion of T4 to T3 - the most active thyroid hormone - can be impaired, resulting in high levels of a hormone called reverse T3 (rT3). Although chemically similar to T3, reverse T3 is completely inactive and lowers the amount of active T3 available to the cells. The way I describe it to clients is as though you are driving a car with the handbrake on. This can all occur in the face of ‘normal’ TSH FT4 and FT3 readings.

Here is a comprehensive list of the top 6 thyroid tests I run (often in conjunction with a comprehensive metabolic blood panel) before an initial consultation:

  1. TSH (Thyroid Stimulating Hormone)
  2. Thyroid peroxidase antibodies (TPO Antibodies)
  3. Thyroglobulin Antibodies (TG Antibodies)
  4. Total T3
  5. Total t4
  6. Free T4 and Free T3

These tests measure the levels of active thyroid hormone circulating in the body, but contrary to what many practitioners say, they don’t impact on the TSH feedback loop.

Hashimoto’s Autoimmune Hypothyroidism causes

A general outline of how Hashimoto’s Autoimmune Hypothyroidism (HAH) develops is best explained by an analogy that has been adopted in functional medicine as the ‘The three-legged stool of autoimmune disease’.

Dr. Alessio Fasano, a world-renowned gastroenterologist and expert in autoimmune disease and coeliac disease, coined this term, meaning that three essential components must be present in order for someone to develop an autoimmune disease:

  1. Genetic predisposition: certain genes make individuals more likely to develop certain diseases.

  2. A trigger: specific antigen, or protein, that the immune system recognises as a threat (real or not), that sets off the cascade of over-activation.

  3. Intestinal permeability (also referred to as ‘leaky gut’): this increased permeability means that the normally tightly-knit cells of the intestines are weakened and ‘leaky’. This allows large compounds, such as proteins from food or bacteria, entry into our bloodstream. The immune system is highly dependent on the health of the intestines.

If all of these three components line up, then the scene is set for a perfect storm of an autoimmune fire. A feed-forward cycle of a chronic state of intestinal permeability and therefore immune system overload starts: you become vulnerable to more infections which depletes immunity further, intestinal permeability worsens and nutrient depletions occur, together with poor digestion, increased inflammation and demands upon the endocrine system. Overall hormone anarchy is the result.

My approach to Hypothyroidism and Hashimoto’s Thyroiditis

Most people with hypothyroidism and Hashimoto’s Thyroiditis need to take thyroid hormone medication, as having low or depressed thyroid hormone levels can lead to moderate to severe symptoms. However, we must also get to work on addressing the root causes.

Triggers and roots causes

I group triggers or root causes into six areas. Triggers can both cause and/or contribute to the development of symptoms:

  1. Food intolerances or sensitivities - e.g. gluten, casein, lactose, histamine or oxalates

  2. An impaired ability to handle “stress”

  3. Gut Permeability

  4. Assessing for nutrient depletions - vitamin D, iron/ferritin, zinc, essential fatty acids, magnesium, B1, B12, B9, and selenium being the most common

  5. Environmental toxins - such as mercury, pollen, dental work

  6. Infections:

    1. Viral, such as Epstein-Barr (EBV)

    2. Bacterial - Yersinia has associated with autoimmune thyroid conditions,

    3. Stealth (e.g. Lyme)

    4. Gut ‘infections’: Dysbiosis or SIBO

It is still not known how exactly EBV and other infections can trigger autoimmune disease. It seems that there are multiple factors involved. There are three leading theories that explain the connection:

  • Molecular mimicry: This happens when your immune system attacks the infection or creates antibodies to the peptide(protein, i.e gliadin), but also accidentally attacks your tissues as well because it mistakes it for the structurally similar infection. (1)

  • Bystander activation: In this instance, the virus or pathogen invades your organ. As a response, your immune system sends immune cells to “kill” and “destroy”. There is collateral damage to the surrounding tissues which creates inflammation( as damage results in inflammation) that leads to the cycle of a further immune response. (2)

  • The Hijack theory: The infection essentially hijacks your cells’ DNA to hide from your immune system. Though your immune system can still identify the virus, it ends up attacking your cells along with the virus.(3)

  • Thyroid-triggered autoimmune reaction proposes that any kind of damage to the thyroid results in the gland secreting danger-associated molecular patterns or damage-associated molecular patterns (DAMPs) that recruit inflammatory cells into the thyroid and further damage the thyroid gland. Like whiplash, following a car accident.

My upcoming Functional Day Retreat - Taming Inflammation, Inflamm-ageing & Autoimmunity is an entire day dedicated to this topic. You’ll will learn how to lessen autoimmune symptoms, dampen inflammation, which tests might be appropriate for you to run to uncover triggers and balance your immune system through a functional medicine approach.

I hope you have found this helpful in your own health journey.

In health, Tanya x


  1. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3266166/

  2. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1360274/

  3. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2192044/