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Hypothyroidism–Part Two: How to Diagnose Hypothyroid-Autoimmune Syndrome

Hypothyroidism is just the smoke we see, rising above the smoldering fire of inflammation, autoimmunity, and unmet nutritional needs. It’s a symptom of the hypothyroid-autoimmune syndrome that is the root cause of hypothyroidism in the vast majority of Americans.

In part one of this series (Hypothyroidism–Part One: Just the Smoke) we explored this relationship, introducing the concept that hypothyroidism is just a symptom of a larger and more damaging disease process–not a disease itself. We addressed how treating the low thyroid function alone, while important, does not tackle the larger problem. Treating hypothyroidism with thyroid hormone alone, fails to address its inflammatory-autoimmune and nutritional underpinnings, putting you at risk for bigger problems.

Unresolved, now and down the road, the inflammatory-autoimmune process and unmet nutritional needs lead to further symptoms–think unresolved fatigue, joint pain, muscle aches, and fuzzy brain, and disease–heart disease, dementia, and cancer–to name just a few.

In this article–part two of my series on hypothyroidism as part of a hypothyroid-autoimmune syndrome–we explore the comprehensive diagnostic process that leads to deeper understanding of the root causes that exist for you. And, ultimately, the solutions you seek.

How to Diagnose Hypothyroidism: Hypothyroid-Autoimmune Syndrome

Part One: Assess Thyroid Function

Let’s find out if low thyroid function is playing a role in your symptoms. The most common symptoms of hypothyroidism are: fatigue, sluggishness, brain fog, depression, lack of motivation, constipation, skin and hair changes.

You’ll need a panel of tests to thoroughly understand thyroid function. This should include:

  • Thyroid stimulating hormone (TSH)
  • Free T4
  • Free T3
  • Reverse T3
  • Antibodies to Thyroglobulin and Thyroperoxidase enzyme

TSH is made by the pituitary gland and controls thyroid synthesis of thyroid hormone (T4 primarily, and T3) in response to the brain’s perception of need. Conventional lab reference ranges are typically from 0.2 to 4.5–with some variation from lab to lab. In Functional Medicine, we consider the ideal TSH range to be between 1 and 2, using this as our goal for thyroid hormone replacement.

Free T4 levels represent how well the thyroid gland is keeping up with thyroid hormone synthesis. Free T3 levels show us the robustness of T4-to-T3 conversion that takes place within the body cells (T3 is the more biologically active thyroid hormone in terms of driving metabolism, or work of the cells).

I often order a reverse T3, which represents an alternate pathway for thyroid hormone synthesis. Reverse T3 does not have appreciable metabolic activity. We see elevations of it when people are severely ill or stressed. Elevated reverse T3 represents an adaptation by the body to the potential crisis of low energy reserve or resilience. It shifts us to a reduction in metabolic activity that stops us in our tracks, to preserve what reserve we have for survival. Reverse T3 is an excellent indicator of having much bigger underlying problems to address.

I also order thyroid antibodies as part of my initial assessment of thyroid function. They are not indicators of function, per se, but provide us with evidence of the inflammatory-autoimmune process underlying the changes in thyroid function.

Part Two: Assess Function of the Brain-Thyroid-Adrenal-Mitochondrial (BTAM) Axis Nodes

When someone presents to me suffering from persistent fatigue and other symptoms of energy deficit, I will evaluate the other aspects of the body energy system–the BTAM axis discussed in part one of this series.

This can be done quite easily as part of the initial consultation and lab evaluation:

  • Morning cortisol level (between 7-8 am): this is a fast way to screen for adrenal cortisol production problems. For a deeper look at this system I also like to look at saliva cortisol levels at four times during my client’s waking day. This way I can assess the circadian rhythm of cortisol secretion–an excellent indicator of adrenal resilience. I may also choose to order an ACTH-Stimulation test if I suspect more profound loss of adrenal function. This is essentially an adrenal stress test–it measures cortisol levels before and after provocation with an injection of the hormone, ACTH.
  • Sex hormone levels: estradiol, total and free testosterone–these are good indicators of pituitary-hypothalamic (brain energy node) function.
  • Organic acid testing (OAT): this is functional testing from urine that allows us to see blocks in the metabolic pathways of energy production. We can learn about global mitochondrial function (energy production within the mitochondria of the cells) and adequacy of nutrients involved in energy production. This can be obtained as part of a more comprehensive nutrition-energy-toxicity test panel called NutrEval, from Genova Diagnostics Lab.
  • A thorough review of symptoms and physical exam: this will help us reveal problems with energy production within the BTAM axis, evidence of underlying inflammation, and unmet nutritional needs.

Part Three: Assess Inflammatory-Autoimmune Status

This is how we look for evidence of an inflammatory-autoimmune process that likely accompanies the low thyroid function. Some of this assessment will be based on symptoms. We can also capture clues from our lab evaluation. This investigation looks for direct evidence of  inflammation and autoimmunity, as well as potential causes or risk factors that make inflammation and autoimmunity more likely.

  • Thyroid antibodies as mentioned above with the assessment of thyroid function.
  • Inflammation-autoimmunity markers: sensitive C-reactive protein (hCRP), erythrocyte sedimentation rate (ESR), anti-nuclear antibody (ANA). These are all blood tests that can be ordered from conventional labs.
  • Toxicity markers:
    • GGT (liver enzyme sensitive to toxicity levels)–simple blood test from conventional lab.
    • RBC heavy metal levels (gives us a three month exposure assessment to inflammation-provoking and energy-damaging heavy metals like mercury and lead)–part of NutrEval from Genova Diagnostics lab.
    • Glutathione levels (the most important anti-oxidant/detoxicant in the human body)–also part of NutrEval.
    • Urine lipid peroxides (evidence of damaged fats from oxidative stress–fallout from inflammation)–NutrEval.
    • Urine 8-OHdG (evidence of damaged DNA)–NutrEval.
    • Urine heavy metal levels after a “provocation.” By using a chelating agent, such as DMSA, we can measure the amount of heavy metals drawn from tissues that are otherwise hard to test. These may indicate an increased body burden of metals that contribute to inflammation, autoimmunity, energy deficit, and thyroid dysfunction.
  • Blood sugar and insulin resistance markers: these are common, profound drivers of inflammation and autoimmunity.
    • Fasting blood sugar
    • Fasting insulin
    • Hemoglobin A1C: provides assessment of three-month average glucose levels.
    • Post-prandial glucose and insulin (a glucose-insulin challenge test done 1-2 hours after a meal.
    • 3-4 hour glucose-insulin tolerance test: more standardized than post-meal challenge, but I find the latter is perfectly accurate and less logistically challenging for my clients.
  • Stool evaluation for inflammation and the make-up of the microbiome. I usually order this test based on symptoms, but will often order if someone has a compelling need to have this data–if they’ve been sick a long time, highly dysfunctional, preponderance of gut-related symptoms, clear gut-related inflammation (inflammatory bowel disease, for instance), client needs data to motivate behavior change. My work with clients always includes gut and microbiome optimization–if testing doesn’t change what we do or how we do it, we save the expense for something else.

Part Four: Assess Nutritional Status

This part of the assessment starts with a thorough history and physical exam that can provide clues to nutritional needs. I also find comprehensive nutrition lab testing to be very helpful.

  • NutrEval from Genova Diagnostics lab:
    • Organic acid testing for energy pathway assessment, micronutrient (essential vitamins and minerals) function, toxicity markers, gut microbiome markers.
    • Amino acids
    • Fatty acid levels
    • Oxidative/inflammatory stress markers: glutathione, lipid peroxides, 8-OHdG
    • RBC heavy metal screen
  • Homocysteine level: good marker for adequate levels of folate, vitamin B12, vitamin B6, B-vitamins involved in methylation–a critical physiological process that helps manage inflammation and toxicity. This can be obtained from conventional lab and great marker for following over time as corrections are made.
  • Methylmalonic acid level: used in addition to homocysteine level to assess vitamin B12 adequacy.
  • Fasting glucose, insulin and hemoglobin A1C are excellent markers for glucose-insulin resistance status. This provides clues to the make up of a client’s diet (carbohydrates, essential fats, and micronutrients), guiding advise for food plan changes.

Part Five: Assess Lifestyle and Stress

My assessment of new clients with fatigue always includes an extensive evaluation of lifestyle, stress levels, how they manage stress, and history of trauma (which can drive persistent levels of stress in the body). Excesses of stress, negative stress mindset, and myriad lifestyle attributes can be potent drivers of inflammation and autoimmunity.

  • History of severe emotional or physical trauma.
  • Overwhelming stress, anxiety, depression.
  • Suboptimal stress coping skills.
  • Tendency to think of stress as bad (this is a stress mindset that puts people at risk for increased inflammation).
  • Inadequate sleep (both duration and quality).
  • Lack of movement, poor posture, excesses of sitting.
  • Poor diet–the Standard American Diet (SAD).
  • Lack of love and social support (increased risk of inflammatory diseases).
  • Resistance to change–makes the behavior changes needed to improve health difficult.

Part Six: Hypothyroidism and the Emotions

Now, this I have no scientific proof to support, but I want to throw it out there for your consideration. The thyroid gland sits right at the base of the neck, between the chest and head, just below the Adam’s apple. The neck is considered to be the emotional center of the body most associated with our voices and ability to speak our truths.

In the Vedic Chakra system, it is said to be the energetic location of both hearing and speaking the truth. This represents the art of communication and using our voices to most make known who we are and what we believe–an incredible challenge for most of us.

While I can’t prove this, I find it interesting that so many of my clients with hypothyroidism are introverts, shy, and have difficulty standing up for themselves by using their voices. Why are the vast majority of people diagnosed with hypothyroidism women? Who are more likely to be culturally inhibited to using their full voices? Who tend to suck it up, make due, please, and make nice?

Whether you buy the thyroid-voice connection or not, there is ample scientific evidence associating repressed emotions with higher inflammation markers, increased activation of the stress system (which includes the BTAM energy system), and a host of negative chronic disease outcomes. These relationships make this topic well worth pursuing.

How to Treat Hypothyroid-Autoimmune Syndrome

Stay tuned for next week’s article: Hypothyroidism–Part Three: How to Treat Hypothyroid-Autoimmune Syndrome.


Karyn Shanks, MD. Hypothyroidism–Part One: Just the Smoke. 2017.

Genova Diagnostics Lab: www Can order functional testing from them through your physician: NutrEval, Urine Provoked Heavy Metal testing, Adrenal Stress Profile (saliva cortisol and DHEA).

Karyn Shanks MD


Karyn Shanks, MD, is a physician who lives and practices in Iowa City. Her work is inspired by the revolutionary science of Functional Medicine, body-mind wisdom, and the transformational journeys of thousands of clients over her twenty-eight year career. She believes that the bones of healing are in what we do for ourselves.

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