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🌿 Understanding Autoimmune Disease from a Functional Medicine Perspective

And How Red/Infrared Laser Can Help

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​Autoimmune diseases are complex, personal, and often misunderstood. At Regenerative Immunology, we take a different approach — looking beyond symptoms to uncover and treat the root causes of immune dysfunction.
 
We also offer red and near-infrared laser therapy (PBM) to reduce inflammation and support natural healing.

🔬 How Functional Medicine Approaches Autoimmunity

 

At Regenerative Immunology, we assess for:
  • Leaky gut and gut-brain axis dysfunction (gut microbiome, functional testing)
  • Chronic infections (viral, mold, Lyme, EBV)
  • Nutrient deficiencies (B12, D, magnesium, omega-3s)
  • Toxic burden (heavy metals, glyphosate, chemical sensitivity)
  • Immune markers and neural-specific antibodies
  • Neuroinflammation via lab tests and symptom analysis
  • Kinesiology - muscle testing
  • Electromagnetic and high frequency testing

 

Treatment combines:

  • Anti-inflammatory nutrition
  • Mitochondrial support (CoQ10, NAD, herbal combinations, Chaga mushroom)
  • Immune modulation with red/infrared/NIR laser
  • Gut and BBB repair protocols, binders
  • Photobiomodulation (PBM) therapy to calm microglial activation, improve circulation, and stimulate neuroregeneration
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telemedicine for people with decreased mobility

Why We Offer Telemedicine for Autoimmune Patients

While I truly believe that best diagnosis and treatment can be done through the personal communication, we offer on-line consultations for:

1. Out-of-State Patients

2. For those living far from our office (more than 1 hour drive)

3. Patients with mobility problems

4. Patients in the hospital or medical facilities

5. Immunocompromised patients with significant risk of infections

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At Regenerative Immunology, we understand that autoimmune disease is not just a diagnosis — it’s a journey. Many of our patients deal with fatigue, brain fog, flares, pain, or environmental sensitivities that make it hard to travel to in-person appointments.

🧠 Autoimmune Care Requires Time, Listening & Strategy

​Unlike conventional 10-minute visits, our telemedicine sessions are designed to:

 

  • Understand your full medical history and triggers

  • Review labs and imaging in detail

  • Personalize your nutrition, supplement, and treatment plan

  • Support you in real-time as your condition evolves

 

Autoimmunity is not a “one-pill” problem — it requires a whole-person approach. And that can be done powerfully, effectively, and respectfully through telehealth.

Many of our autoimmune patients say that telemedicine allows them to stay more consistent, connected, and in control of their care.

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gut problems

🧬 What Is Autoimmune Disease?

Autoimmune disease happens when the immune system — your body’s defense system — starts attacking its own cells and tissues. This can cause pain, fatigue, and damage to organs or systems over time.

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Common autoimmune conditions include:

  • Rheumatoid arthritis (RA)

  • Hashimoto’s thyroiditis

  • Lupus (SLE)

  • Psoriasis

  • Multiple sclerosis (MS)

  • Inflammatory bowel disease (IBD)

  • Sjögren's syndrome

  • Celiac disease

  • Chronic Lyme

  • Chronic fatigue

  • Long COVID

Why is the Body Attacking Itself?

From a functional medicine perspective, autoimmunity is not random — it’s a response to deeper imbalances and environmental stressors.

Common triggers include:

  • Chronic infections (e.g., Epstein-Barr virus, Lyme, herpesviruses)

  • Leaky gut (intestinal permeability) – allows foreign antigens into the bloodstream

  • Toxic exposures (mold, pesticides, heavy metals)

  • Vaccinations or drugs (in rare cases, molecular mimicry may be involved)

  • Nutrient deficiencies (e.g., Vitamin D, selenium, omega-3s)

  • Hormonal shifts (e.g., postpartum, menopause)

  • Chronic stress – which alters immune regulation

🛡️ The Immune System's Job: Distinguish “Self” from “Non-Self”

The immune system is designed to detect and eliminate:

  • Pathogens (bacteria, viruses, fungi, parasites)

  • Damaged or infected cells

  • Environmental toxins

To do this, immune cells constantly survey the body, using receptors and antigen-presenting cells to recognize threats.

In a healthy person, tolerance mechanisms prevent the immune system from reacting to your own tissues (self-tolerance). These mechanisms are controlled by T regulatory cells, immune checkpoints, and antigen screening in the thymus and bone marrow.

❌ Autoimmunity Begins When Tolerance Fails

​Autoimmunity arises when the immune system:

  1. Mistakes normal tissue as a threat

  2. Cannot repair program of identifying self and non-self fails (as in Celiac)

  3. Produces autoantibodies or autoreactive T cells

  4. Begins a chronic inflammatory attack on that tissue

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neuroimmune diseases

🧠 Neurodegeneration and Autoimmunity

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Neurodegenerative diseases — such as multiple sclerosis (MS), Parkinson’s disease (PD), Alzheimer’s disease (AD), and ALS — are often viewed as diseases of aging or genetic fate. But growing evidence suggests that many of these conditions are deeply connected to immune dysfunction, chronic inflammation, and even autoimmunity.
In other words, the immune system — the body’s natural defense — may actually play a role in attacking and damaging its own nervous system.

The Hidden Link Between Brain Decline and Immune Dysregulation

🔁 The Brain and Immune System Are Connected

The central nervous system (CNS) was once thought to be immune “privileged,” meaning the immune system didn’t interact with it. We now know that’s not true.

The brain and immune system communicate constantly through:

  • The glymphatic system (the brain’s waste-clearing system)

  • The blood-brain barrier (BBB)

  • Microglia, the brain’s resident immune cells

  • Cytokines, chemical messengers that signal inflammation

When this delicate balance is disrupted — by infection, trauma, toxin exposure, or gut inflammation — the immune system can become overactive, leading to damage inside the brain.

 

⚠️ When the Immune System Turns on the Brain

In autoimmune neurodegeneration, the immune system:

  1. Mistakes brain proteins for threats (molecular mimicry)

  2. Crosses the blood-brain barrier when it becomes “leaky”

  3. Activates microglia, which release inflammatory cytokines

  4. Destroys neurons and myelin sheaths, accelerating degeneration

 

This process contributes to:

  • Multiple sclerosis (MS) – autoimmune demyelination of CNS

  • Alzheimer’s disease (AD) – chronic microglial activation, possibly driven by infections or amyloid-immune responses

  • Parkinson’s disease (PD) – autoimmune attack on dopamine-producing neurons

  • Autism spectrum disorders (ASD) – in some cases, maternal or early-life immune dysregulation and brain inflammation

📖 Citation: Schwartz, M. & Baruch, K. (2014). The resolution of neuroinflammation in neurodegeneration: leukocyte recruitment via the choroid plexus. EMBO Journal, 33(1), 7–22.

 
🧬 The Role of Molecular Mimicry

Autoimmunity often begins when the immune system encounters a virus, bacteria, or toxin that contains proteins similar to the body’s own tissues. This can lead to:

  • Cross-reactivity with brain or nerve proteins

  • Generation of autoantibodies that target neurons, myelin, or synaptic receptors

 

This mechanism has been proposed in:

  • MS following Epstein-Barr virus (EBV) infection

  • Parkinson’s linked to gut pathogens and alpha-synuclein autoimmunity

  • AD linked to herpesvirus reactivation and chronic immune activation

📖 Citation: Woulfe, J. M. (2007). Molecular mimicry and Parkinson’s disease: does alpha-synuclein have a role? NeuroReport, 18(10), 959–961.

 
🧠 Blood-Brain Barrier Breakdown

In both autoimmunity and chronic inflammation, the blood-brain barrier (BBB) can become “leaky,” allowing immune cells, antibodies, and inflammatory molecules to enter the brain.

 

Factors that compromise the BBB include:

  • Chronic stress

  • Infections (viral or bacterial)

  • Environmental toxins (mold, metals)

  • Poor gut health (leaky gut often parallels leaky brain)

Once breached, the BBB allows autoimmune attack to target brain tissue — worsening neurodegeneration and making recovery more difficult.

📖 Citation: Varatharaj, A., & Galea, I. (2017). The blood-brain barrier in systemic inflammation. Brain, Behavior, and Immunity, 60, 1–12.

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🔴 Laser Therapy for Brain & Autoimmune Support

Photobiomodulation (PBM), also called transcranial red/NIR laser therapy, delivers healing light to the brain. It helps:

  • Reduce neuroinflammation

  • Support mitochondrial energy (ATP) in neurons

  • Improve blood-brain barrier integrity

  • Promote neural regeneration and connectivity

  • Modulate microglial overactivation

This therapy is being studied for MS, Parkinson’s, TBI, brain fog, and long COVID.

📖 Citation: Salehpour, F. et al. (2022). Photobiomodulation therapy for neuroinflammation and neurodegenerative diseases: a review. Brain Sciences, 12(5), 619. DOI:10.3390/brainsci12050619

 

🧠 Summary

Autoimmunity and neurodegeneration are deeply connected through immune dysfunction, gut-brain axis disruption, and barrier breakdown. By restoring balance — especially in the gut, brain, and immune system — we can support the body’s ability to protect and repair itself.

At Regenerative Immunology, we combine science, diagnostics, and therapies like PBM, detox support, and functional medicine to target the root causes of both immune and neurological decline.

leaky gut

🧬 The Gut - Autoimmune Connection

How Healing the Gut Can Calm Autoimmune Disease​​

Autoimmune conditions affect millions of people — yet their true root causes are often overlooked. While conventional treatments focus on suppressing the immune system, functional medicine aims to understand what’s driving the immune imbalance.

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One of the most important and well-studied triggers of autoimmunity is gut health. The connection between the gut, the immune system, and inflammation is at the core of healing autoimmune diseases — and often the key to long-term recovery.

Role of the Gut in Autoimmunity

🌱 Why the Gut Matters

Nearly 70–80% of the immune system resides in the gut. The intestinal lining is designed to act as a selective barrier — allowing nutrients to pass into the bloodstream while keeping toxins, pathogens, and undigested food particles out.

When this barrier becomes damaged or porous — a condition known as increased intestinal permeability or “leaky gut” — it can trigger an immune response. Over time, this can lead to chronic inflammation and autoimmunity.

📖 Citation: Fasano, A. (2012). Leaky gut and autoimmune diseases. Clinical Reviews in Allergy & Immunology, 42(1), 71–78. DOI:10.1007/s12016-011-8291-x

 
🔁 The Gut–Immune Feedback Loop

Once the gut barrier is compromised, substances that don’t belong in the bloodstream — like bacterial toxins (LPS), gluten fragments, or food proteins — can escape and activate the immune system. This can lead to:

  • Chronic inflammation

  • Activation of T cells and autoantibodies

  • Cross-reactivity with the body’s own tissues

  • Chronic fatigue

  • Chronic pain

 

Over time, this contributes to or worsens conditions like:

  • Hashimoto’s thyroiditis
  • Rheumatoid arthritis
  • Celiac disease
  • Lupus
  • Multiple sclerosis
  • Psoriasis
  • Type 1 diabetes

📖 Citation: Vojdani, A., & Lambert, J. (2011). The role of intestinal permeability in autoimmune diseases. Alternative Therapies in Health and Medicine, 17(4), 14–22.

 

🔬 What Causes Leaky Gut?

Several common factors contribute to intestinal permeability:

  • Dysbiosis (imbalanced gut bacteria)

  • Processed foods, gluten, refined sugar

  • Chronic stress

  • Environmental toxins (pesticides, mold, metals)

  • Food additives with abrasive and toxic properties

  • Infections (viruses, bacteria, candida, parasites)

  • Medications (NSAIDs, antibiotics, PPIs)

📖 Citation: de Punder, K., & Pruimboom, L. (2015). Stress induces leaky gut. Frontiers in Immunology, 6, 223. DOI:10.3389/fimmu.2015.00223

 

🌿 Functional Medicine Approach

At Regenerative Immunology, we address the root of gut-autoimmune issues using the 5R Framework:

  1. Remove triggers (inflammatory foods, toxins, infections) and remove toxins from the gut (with milk thistle and binders)

  2. Reboot the immunity with our proprietary regimen

  3. Replace digestive support (enzymes, acids)

  4. Reinoculate beneficial gut flora (probiotics, prebiotics)

  5. Repair the gut lining (with nutrients like fish oil, psyllium husk, fennel, collagen)

  6. Rebalance the nervous system (electromagnetic balancing, red laser, acupoint treatment, stress reduction, lifestyle)

 

We also use advanced testing for gut health, immune markers, and food sensitivities to create personalized plans.
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🔴 Where Does PBM (Laser Therapy) Fit In?

Photobiomodulation therapy (PBM) supports gut healing by:

  • Reducing intestinal inflammation

  • Enhancing microcirculation in the gut wall

  • Promoting mucosal repair and lymphatic drainage

  • Modulating the gut-immune axis

Studies show PBM improves gut permeability and immune regulation when applied transabdominally or systemically.

📖 Citation: Hamblin, M. R. (2017). Mechanisms and applications of the anti-inflammatory effects of photobiomodulation. APL Photonics, 2(4), 041101. DOI:10.1063/1.4973901

 
💡 Final Thoughts

If you’re living with an autoimmune disease, don’t overlook your gut. Healing the gut lining and balancing the microbiome can calm immune overactivity, reduce flares, and restore your health from the inside out.

Pairing this with targeted laser therapy offers a powerful way to accelerate healing — naturally, safely, and effective!

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Red/Infrared/NIR laser is a powerful treatment for autoimmune chronic conditions

PBM uses therapeutic light wavelengths to stimulate healing at the cellular level. It is painless, non-invasive, and safe for regular use.

​Emerging research suggests that photobiomodulation therapy (PBM), commonly known as low-level laser therapy (LLLT), may offer benefits for individuals experiencing any type of chronic autoimmune diseases. Recently we started using laser for long COVID symptoms, which we believe has a huge autoimmune component just like Chronic Lyme disease.​

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Evidence-Based Support for Brain Fog, Fatigue, Pain, and Inflammation

Long COVID — also known as Post-Acute Sequelae of SARS-CoV-2 (PASC) — can cause persistent symptoms long after the infection resolves. Common complaints include brain fog, fatigue, chronic inflammation, loss of taste or smell, and chronic pain. Many patients struggle to find relief in conventional medicine alone.

Photobiomodulation therapy (PBM), also known as low-level laser therapy (LLLT), is emerging as a safe, non-invasive option to help restore balance and support healing in Long COVID patients.

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🧠 Cognitive Function (Brain Fog) Improvement

A 2023 pilot study examined the use of transcranial PBM (tPBM) and whole-body PBM in patients with Long COVID experiencing brain fog and cognitive impairments. Over 12 treatments across four weeks, patients showed significant improvement in memory, attention, and executive function as measured by neuropsychological testing.

📖 Citation: Fernandes, F. M. S. et al. (2023). Photobiomodulation therapy improves cognitive performance in patients with long COVID: A pilot study. Journal of Neurology Research. PubMed PMID: 37018063

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🔥 Anti-Inflammatory & Immune-Modulating Effects

Long COVID is linked to chronic immune activation and residual inflammation. PBM is well-documented for its anti-inflammatory effects, including modulation of cytokine activity. A review of PBM during the acute COVID-19 phase also suggested its ability to reduce cytokine storm intensity, improve lung function, and promote tissue regeneration — effects likely relevant to Long COVID as well.

📖 Citation: de Freitas, L. F., & Hamblin, M. R. (2020). Proposed mechanisms of photobiomodulation therapy for COVID-19 and respiratory disease. Photobiomodulation, Photomedicine, and Laser Surgery. PMC7428000

 
👅 Restoration of Taste (Dysgeusia)

Loss or alteration of taste (dysgeusia) is a common lingering symptom. A 2024 clinical study found that both local and systemic PBM over 8 weeks significantly improved taste function in Long COVID patients compared to controls. PBM is believed to support nerve repair and local circulation, promoting faster sensory recovery.

📖 Citation: de Carvalho, R. R. et al. (2024). Efficacy of photobiomodulation in the treatment of dysgeusia in long COVID: A randomized clinical trial. Lasers in Medical Science. PubMed PMID: 38416635

 
💥 Pain and Headache Relief

Persistent headaches, orofacial pain, and musculoskeletal tension are frequently reported by post-COVID patients. A 2024 randomized clinical trial published in Scientific Reports demonstrated that vascular PBM significantly reduced pain intensity and improved function in Long COVID patients experiencing chronic pain syndromes.

📖 Citation: Martins, J. L. et al. (2024). Vascular photobiomodulation for pain management in post-COVID patients: A randomized trial. Scientific Reports, Nature Publishing. DOI:10.1038/s41598-024-82412-9

 
⚙️ How PBM Works in Long COVID

PBM uses low-level red and near-infrared light (630–1064 nm) to stimulate mitochondrial function, increase ATP production, and reduce oxidative stress. It helps:

  • Modulate immune responses

  • Improve microcirculation and tissue oxygenation

  • Support nerve and brain tissue regeneration

  • Alleviate pain, brain fog, and fatigue

PBM is non-invasive, relaxing, and typically performed 2–3 times per week over several weeks for best results.

 

💡 Final Thoughts

While research is still evolving, early evidence strongly supports PBM as a promising adjunctive therapy for Autoinflammation Long COVID symptoms. Its effects on the brain, immune system, and cellular energy metabolism make it a natural fit for supporting recovery in post-viral syndromes.

Patients seeking drug-free, restorative approaches may benefit from adding PBM to their care plan under supervision from trained integrative providers.

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References

  1. Fernandes, F. M. S., et al. (2023).
    Photobiomodulation therapy improves cognitive performance in patients with long COVID: A pilot study.
    PubMed PMID: 37018063

  2. de Freitas, L. F., & Hamblin, M. R. (2020).
    Proposed mechanisms of photobiomodulation therapy for COVID-19 and respiratory disease.
    Photobiomodulation, Photomedicine, and Laser Surgery.
    PMC ID: PMC7428000

  3. de Carvalho, R. R., et al. (2024).
    Efficacy of photobiomodulation in the treatment of dysgeusia in long COVID: A randomized clinical trial.
    Lasers in Medical Science.
    PubMed PMID: 38416635

  4. Martins, J. L., et al. (2024).
    Vascular photobiomodulation for pain management in post-COVID patients: A randomized trial.
    Scientific Reports (Nature).
    DOI: 10.1038/s41598-024-82412-9

  5. Fasano, A. (2012).
    Leaky gut and autoimmune diseases.
    Clinical Reviews in Allergy & Immunology, 42(1), 71–78.
    DOI: 10.1007/s12016-011-8291-x

  6. Vojdani, A., & Lambert, J. (2011).
    The role of intestinal permeability in autoimmune diseases.
    Alternative Therapies in Health and Medicine, 17(4), 14–22.

  7. de Punder, K., & Pruimboom, L. (2015).
    Stress induces leaky gut: mechanisms and clinical implications.
    Frontiers in Immunology, 6, 223.
    DOI: 10.3389/fimmu.2015.00223

  8. Schwartz, M., & Baruch, K. (2014).
    Resolution of neuroinflammation in neurodegeneration: Leukocyte recruitment via the choroid plexus.
    EMBO Journal, 33(1), 7–22.
    DOI: 10.1002/embj.201386609

  9. Woulfe, J. M. (2007).
    Molecular mimicry and Parkinson’s disease: Does alpha-synuclein have a role?
    NeuroReport, 18(10), 959–961.
    DOI: 10.1097/WNR.0b013e3281337d93

  10. Varatharaj, A., & Galea, I. (2017).
    The blood-brain barrier in systemic inflammation.
    Brain, Behavior, and Immunity, 60, 1–12.
    DOI: 10.1016/j.bbi.2016.03.010

  11. Hamblin, M. R. (2017).
    Mechanisms and applications of the anti-inflammatory effects of photobiomodulation.
    APL Photonics, 2(4), 041101.
    DOI: 10.1063/1.4973901

  12. Salehpour, F., et al. (2022).
    Photobiomodulation therapy for neuroinflammation and neurodegenerative diseases: A review.
    Brain Sciences, 12(5), 619.
    DOI: 10.3390/brainsci12050619

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