
Welcome to part III of The Thyroid: Beyond the Immune System! Last week’s post introduced the function and mechanism of TSH, T3 and T4, and the roles they play in thyroid health. This week’s post brings us into the heart of the series. The thyroid can affect and be affected by many different systems in the body, including the liver, the GI tract and hormonal functions.
Click Here to read part I.
Click Here to read part II.
Click Here to read part IV
What if the thyroid gland works fine, but the message is not being sent from the brain?
This can be called secondary hypothyroid as opposed to primary hypothyroid. Primary hypothyroid is when the brain and pituitary gland are sending the message, but the thyroid just can’t get the job done, so TSH goes up, and T4 remains low.
Secondary hypothyroid is when the pituitary gland does not send the message loud and clear that the body needs to make more thyroid hormone. This will result in low TSH, and thus, T4 remains low. This can be caused by disease of the pituitary, but it can also occur without disease. It is now known that excess cortisol, due to the body perceiving stress or danger for an extended period of time, can cause this problem. The cortisol will inhibit the signals from the hypothalamus to the pituitary and suppress TSH output.
These pathways can also be impacted by drugs that alter dopamine and serotonin levels. These include drugs that impact anxiety, depression, attention deficit, hyperactivity, etc. Millions of people are taking these medications daily.
Inflammation and immune functions can alter thyroid hormone function.
Sometimes the body treats immune reactions as if they are chronic infections, such as food sensitivities. Autoimmune diseases have increased, in many cases, over 400 percent in just two or three decades.
“Immune disorders have great potential to disrupt thyroid physiology and promote concomitant dysfunction in cellular metabolism.”
“Thyroid hormones are classified as immune system modulators, and thyroid function and metabolism should be considered in cases of immune challenges.”
–Dr. Datis Kharrazian, Mastering the Thyroid course manual, page 25
Chronic illness related to any autoimmune disease, chronic bacterial, viral, or microbial infections can include:
- Epstein barr virus
- Cytomegalovirus
- Herpes simplex virus
- Lyme disease
- Hepatitis, yeast and parasitic infections
- Failed root canals
- Gum disease
The immune system, like the nervous system, has an advanced communication system using chemicals called cytokines. These cytokines have the ability to shut down certain bodily processes, such as thyroid hormone physiology. In the short term during a crisis like the flu, this can be a wise and healthy response. However, immune responses that are chronic result in long-term suppression of important hormones like thyroid hormone and cause chronic inflammation.
The immune system can act at many different points of the thyroid hormone story – the receptors, the enzymes, the conversion, etc.
What else can go wrong?
Liver:
Liver health and/or function can be compromised. The enzymes that are responsible for the conversion of T4 to T3 are located in the liver.
Think of the liver as a bridge going from the inside of your body to the outside. The cars on that bridge are toxins and byproducts of our own normal metabolism that need to be removed from the body. The bridge has six lanes of detoxification for the cars to travel on. Each lane has a name: glutathione conjugation, methylation, acetylation, glucuronidation, sulfation, and amino acid conjugation. If one or more of those lanes are shut down for any reason, traffic will build up, and toxicity will increase inside the liver and the body. Sometimes, there are just excessive toxins, and even though all lanes are working, traffic can still build up. If liver function is compromised, it will interfere with the conversion of T4 to T3.
Liver detoxification pathways can be compromised due to impairment of the pathways by enzyme deficiencies as we see with common genetic disorders of methylation (for more information on MTHFR defects, read my blog post on this topic). Methylation is one of the major pathways of detoxification that occur in the liver. If there is a defect in that pathway, it’s like one of the major lanes on the bridge shutting down, resulting in a bottle neck and more traffic and toxins building up in the body.
Liver function can be taxed by medications, drugs such as alcohol (beer belly is actually called ascites, a condition where backed up liver function is actually visible), blood sugar dysregulation, systemic inflammation, and hormone imbalances, among other causes.
Digestion:
Conversion from T4 to T3 in the digestive system requires a healthy environment and requires the presence of healthy bacteria. The importance of healthy bacteria cannot be over-emphasized, and the role bacteria play in thyroid health is just one of their many functions. Merely taking a supplement of probiotics, although a very good idea in many cases, cannot be the only consideration. If abnormal bacteria populations are present, we call this dysbiosis. We have to ask why and not just address the symptom by providing more healthy bacteria through eating yogurt or taking probiotics.
The GI tract can be a central source of conversion problems and at the same time be responsible for taxing the liver due to excessive inflammation caused by an unhealthy GI environment. (Please see the posts on GI function on this site for more GI-specific information.) The digestive system has enzyme activity that is directly responsible for thyroid hormone conversion processes.
Bacteria in the small intestines, where they don’t belong, can release a toxin called lipopolysaccharide that can cause a cascade of immune events that alter thyroid hormone function as described above.
Signs and symptoms of GI dysfunction and inflammation that would contribute to poor thyroid hormone conversion and general thyroid hormone physiology include:
- Acid reflux
- Gas and bloating
- Constipation
- Alternating constipation and diarrhea
- Excessively loose stool
- History of inflammatory bowel disease
- Irritable bowel syndrome
- Gallbladder removal or disease
Hormone Health:
A basic principle in physiology and in my practice is the fact that all hormones affect all hormones. We have hormones for stress that can be released when we sense physical or emotional danger, and stress hormones can be released when we have excessive inflammation due to an infection, allergy, or food sensitivity. We have hormones that regulate our blood sugar and appetite and hormones that are related to our sexual health, such as testosterone, progesterone, and estrogen. Vitamin D is technically a hormone and not a vitamin. Melatonin is a hormone produced in our brain that regulates circadian rhythm cycles.
If all hormones affect all hormones, then all of those mentioned above can impact thyroid hormone function. Books could be written on this subject, so I am going to scratch the surface with some common causes of how hormones can directly impact thyroid hormone health.
The use of birth control pills or any form of contraception that influences sex hormones, such as progesterone and estrogen, can cause the excessive production of the protein that transports the T3 (and T4, for that matter) hormone to where it needs to go. This usually results in the inability of the T3 hormone to get out of the cab, as we discussed above. The decreased ability to get off the transport protein will result in a normal total T3 (protein-bound) count and an abnormally low free T3 number, resulting in not enough active hormone entering the cells.
Next week will summarize potential problem areas for the thyroid and guide you through taking charge of your own thyroid health. Stay tuned!
Thanks for reading!
Have you or a loved one ever experienced any of these thyroid complications? Please share your stories and thoughts below!


Thank you for this. I feel that past use of medication (though several years ago) has affected my thyroid and hormones. What is your suggested path for healing with this reason being the culprit? Thank you
Medication use can definitely alter how thyroid hormones travel and go through the chain of events that leads to healthy cell function. Medications can also impact the cofactors for normal thyroid hormone physiology. Getting off of medications if possible is the 1st step to normalizing function, and identifying what part of the process has been impacted is the next step. Then supporting that process is the next step after that. Sorry to be so general, but without more information its difficult to advise.
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