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Case Studies · Autoimmune · Thyroid & Autoimmune · Gut & SIBO
Autoimmune Alopecia Areata Gut & SIBO Hormones Anxiety & Burnout

Off Work. Hair Falling Out. Immune System in Overdrive.
Back to Full-Time Life.

A woman in her late twenties went from long-term sick leave — losing her hair, skin inflamed, system in collapse — to returning to full-time work six months later. This is what finding the root cause looks like.

Sick leave
Where she started
Full-time
Returned to work
55 → 30
MSQ symptom score
6 months
Duration of programme
This Was Her Reality
She couldn't work. She was losing her hair.
Her body was failing her — visibly, all at once.
"I've been working with Paul for around six months following an autoimmune diagnosis. He's gone above and beyond to understand root causes rather than just managing symptoms. My energy is soooo much better than it has been when I started. My autoimmune symptoms are also finally in a place where I can return to work."
— Female client · Autoimmune · Alopecia · Gut
She was functioning.
Just not living.

When you're in your twenties and you stand in front of a mirror and see a strip of scalp — defined, deliberate-looking, following the hairline from ear to ear — it triggers something beyond concern. It's panic. It's grief. It's the kind of thing you sit with until 2am reading about, already knowing what it is before you find the name, and discovering that knowing the name doesn't make it easier to look at.

She was already off work by then. Long-term sick leave — not a vague burnout, but a body that had genuinely stopped cooperating. The eyes had gone first: burning, chronically dry, corneal erosions bad enough to keep her from screens. She'd noticed they improved when she was off work. That detail mattered, though she wasn't sure how yet. Then the rosacea deepened. Then the hair. Her GP had run bloods. Everything came back within range. She wasn't reassured. She was right not to be.

She'd had blepharitis since childhood. Digestive sensitivity since her teens. A gut that bloated, that reacted, that had always required managing. She'd been on the pill for six years. None of it had seemed connected — until the summer of 2024, when a new high-responsibility role added a pressure that never fully switched off, and her system finally ran out of capacity to absorb it. The symptoms weren't new. They were familiar patterns, finally exceeding the threshold her body had quietly held for years.

She came in not looking for reassurance. She wanted to understand the mechanism — and she wanted her life back. She got both.

The Pattern
This wasn't a collection of bad luck. This was one cascade — gut, immune, hormonal, neurological — expressing itself across every surface at once. And it had a source.
This wasn't one problem.
It was one system failing in four places at once.
01
Gut–Immune Dysregulation & Intestinal Permeability
Clinical mechanism: Stool analysis revealed severely elevated gut inflammation (S100A12: 116, ref ≤50), depleted pancreatic enzyme output (Elastase: 124.7, ref ≥200), and a hyper-activated secretory IgA (1652, ref 426–1450). Inflammatory bacteria dominated — Porphyromonas gingivalis, Fusobacterium, Staphylococcus pasteuri. Protective Lactobacillus species were below threshold. Short-chain fatty acids — the gut's primary repair fuel — were critically low.

What this meant for her: Her immune system had lost the ability to distinguish friend from foe. Food antigens were crossing into circulation. The gut — not managing the autoimmune load, amplifying it.
02
HPA-Axis Dysregulation & Chronic Stress Physiology
Clinical mechanism: Hormone panel showed night cortisol significantly elevated (4.28, ref 0.5–1.1) with total daily cortisone output nearly three times the reference range (pooled: 288, ref 35–102). Corticosterone also elevated — a marker of immune-driven, sustained stress activation. The HPA axis had no functional off-switch.

What this meant for her: Her body had been running in emergency mode for so long, it no longer recognised calm. This was driving immune dysregulation, estrogen imbalance, and systemic inflammation simultaneously — three problems from one unresolved root.
03
Neuroimmune Activation & EBV Reactivation
Clinical mechanism: Neural Zoomer revealed a significant neuroautoimmune profile — anti-dopamine receptor antibodies (DR1: 17.1, DR2: 13.1), blood-brain barrier disruption markers, cerebellar autoantibodies, and glutamate receptor autoimmunity. Multiple EBV markers were elevated (EBNA1: 29.0, p18: >30), indicating past infection with active immune memory and likely ongoing neuroimmune drive.

What this meant for her: The brain fog wasn't psychological. The mood swings weren't personality. Her immune system was targeting her own dopamine receptors — the architecture of motivation, focus, and emotional regulation.
04
Estrogen Dominance & Environmental Toxic Load
Clinical mechanism: Total estrogen was nearly double the reference range (14.94, ref 1.73–7.54). BPA elevated (7.84, ref ≤5.09). Skewed estrogen detox pathway with excess 2-OH estrone production. Prior OCP use for six years likely primed the estrogen–histamine–immune loop. Poor glucuronidation capacity compounding the toxic load.

What this meant for her: Her detox pathways couldn't keep up. Estrogen was recycling instead of clearing. Combined with a compromised gut microbiome, this created a hormonal environment that actively inflamed her immune system.
05
Nutrient Insufficiency Across Key Immune & Hair Pathways
Clinical mechanism: Neutrophils critically low (1.4, range 2–7.5). Vitamin D suboptimal at functional levels (61 nmol/L). Omega-6:3 ratio elevated at 10.9 (desirable ≤11). MCH slightly elevated — B12/folate flag. Ferritin previously low. Zinc insufficient.

What this meant for her: The immune system, hair follicles, and mucosal barriers all require the same raw materials — and none of them were getting enough. This wasn't a supplement problem. It was a system that couldn't heal because it lacked the building blocks to do so.
Clinical Pattern
"This is the gut–immune–stress cascade I see in a significant proportion of women in their late twenties under sustained professional and emotional pressure. The alopecia is the most visible signal. But it's the last thing to appear — not the first thing to address."
Recognise This Pattern?
Multiple symptoms. One system.
Root causes — not management.
Book a Clarity Call
What the tests actually showed.
The hidden pattern behind the hair loss,
the skin flares, and the brain fog.
Zone 1
Gut & Immune — Root Cause
Optimal
Out of range
Borderline
Result
Critical S100A12 — Gut Inflammation
116mcg/ml
Ref ≤50 · 2.3× the limit · Neutrophil-driven
Elevated Secretory IgA — Immune Load
1652mcg/g
Ref 426–1450 · Immune system in battle mode
Low Pancreatic Elastase — Digestion
124.7mcg/g
Ref ≥200 · Critically low — poor food breakdown
Depleted Total SCFAs — Gut Repair Fuel
37.4µmol/g
Ref 45–210 · Below floor — barrier repair blocked
Elevated EPX — Eosinophil Inflammation
10.5mcg/g
Ref ≤4.8 · 2.2× over limit
Low Lactobacillus — Protective Flora
8.2
Ref ≥10 · Protective strains depleted
Leaky, inflamed, under-digested gut. Immune system in battle mode — with no fuel left to repair itself.
Zone 2
Hormonal & Stress — Amplifiers
Optimal
Out of range
Borderline
Result
4× Limit Night Cortisol — HPA Axis
4.28nmol/L
Ref 0.5–1.1 · HPA axis — no off-switch
3× Limit Daily Cortisone Output
288nmol/L
Ref 35–102 · Chronic adrenal overdrive
2× Limit Total Estrogen — Clearance
14.94pg/mg
Ref 1.73–7.54 · Recycling instead of clearing
Elevated BPA — Endocrine Disruptor
7.84µg/g
Ref ≤5.09 · Driving estrogen load
Skewed 2-OH Estrone — Detox Path
5.90pg/mg
Ref 0.65–2.98 · Detox pathway overwhelmed
Chronic adrenal overdrive. HPA axis with no off-switch. Estrogen recycling instead of clearing — amplified by environmental toxic load.
Zone 3
Neuroimmune — Downstream Consequence
Normal
Elevated
Result
High EBV Reactivation — EBNA1
29.0
Active viral immune memory — driving neuroinflammation
Elevated Anti-Dopamine Receptor 1
17.1
Autoimmunity targeting dopamine — mood, focus, motivation
Elevated Anti-Dopamine Receptor 2
13.1
Dopamine receptor autoimmunity — mood instability explained
Elevated Anti-Purkinje — Cerebellar IgM
14.4
Cerebellar autoimmunity — processing speed, coordination
Stressed Blood-Brain Barrier — GRP78
11.6
BBB under stress — cognitive load, neuroinflammation
The brain fog and mood swings were not psychological. The immune system was attacking its own dopamine architecture.
Zone 4
System Capacity — Foundation
Optimal
Out of range
Borderline
Result
Below Range Neutrophils — Immune Resilience
1.4×10⁹/L
Ref 2–7.5 · Immune resilience critically low
Low Vitamin D — Immune Regulator
61nmol/L
Ref 50–250 · Low functional level
Sub-optimal Omega-3 Index — Anti-Inflammatory
7.74%
Optimal 8–12% · Below threshold
Borderline Omega 6:3 Ratio — Inflammation
10.9
Ref ≤11 · Borderline — inflammatory bias
Flagged MCH — B12 / Folate Pathway
32.4pg
Ref 27–32 · Slightly above — B12/folate flagged
The building blocks for immune regulation, hair, and skin repair were simply insufficient. The system lacked the capacity to heal itself.
How It All Connected
Trigger
EBV Reactivation
+ Chronic Stress
Root Cause
Gut Permeability
+ Dysbiosis
Amplifier
HPA Overdrive
+ Estrogen Load
Consequence
Dopamine Receptor
Autoimmunity
Outcome
Fatigue · Brain Fog
Hair Loss · Skin
Chronic viral activation + gut immune dysregulation + neuroinflammation = a system that had run out of capacity to hold itself together.
Phase by phase — what shifted and when.
OCT
Phase 1 — October 2025 · Baseline & Investigation
The full picture emerges
Initial consultation mapped the full timeline — childhood blepharitis, years of digestive sensitivity, six years of OCP use, and the acute stress escalation of summer 2024 that preceded every major flare. MSQ score: 55. Testing commissioned: stool, hormone, neural zoomer, Medichecks blood panel. AIP diet initiated immediately. Core supplement protocol established — omega-3, zinc, vitamin D, magnesium, collagen, sea buckthorn oil. Gupta Programme introduced for limbic system regulation.
NOV
Phase 2 — November 2025 · First Results & Protocol Deepening
Gut data lands. The protocol sharpens.
MSQ score dropped to 38 — stress levels lower, gut noticeably better, rosacea calming slightly. Test results confirmed the full picture: severely inflamed gut, HPA overdrive, neuroimmune activation, EBV reactivation, estrogen dominance. Protocol expanded significantly: Berberine and Allimed for dysbiosis, sodium butyrate for SCFA deficit, GI-Restore for mucosal repair, LDN added for immune modulation. Bowel markers confirmed the strategy was directionally correct.
JAN
Phase 3 — January 2026 · Recalibration
A temporary setback — and what it revealed.
MSQ score moved back up to 49 — a reminder that autoimmune recovery is rarely linear. Clinical review identified the likely causes: adherence gaps during the holiday period and an increase in external stressors. The January session was used to reinforce the nervous system and limbic regulation components of the protocol, recognise progress made (hair shedding reduced, ear flushing reduced, inflammatory tone softened), and re-anchor the approach. Counselling and CBT formally commenced this month — a significant step in addressing the emotional dimension of the stress load.
FEB
Phase 4 — February 2026 · Final Session
Back to work. Brain fog gone. The system holds.
MSQ score: 30 — best recorded across the programme. Brain fog completely cleared. Energy significantly and consistently better. Feeling considerably calmer — not managing calm, genuinely experiencing it. Gupta Programme actively contributing to nervous system regulation. CBT helping. B12 injections added for neurological support. Estrogen detox protocol formalised with DIM and Calcium D-Glucarate.

The defining outcome of this case: she returned to full-time work. The role that had contributed to her collapse was no longer incompatible with her health. That is the measure that matters — not a score on a questionnaire, but a life reclaimed.
Three pillars.
One direction.
01
Diet — AIP Framework
  • Autoimmune Paleo protocol — removing all common antigenic triggers (gluten, dairy, nightshades, grains, legumes, eggs, nuts)
  • Emphasis on grass-fed meats, organ meats 2–4x weekly, bone broth for gut-lining glycine and collagen
  • All vegetables cooked — reducing raw fibre load on compromised digestive capacity
  • Animal fats prioritised — tallow, duck fat, fatty cuts — for fat-soluble vitamin delivery and immune support
  • Later phases: rice and buckwheat reintroduced carefully as gut stabilised
02
Nervous System & Lifestyle
  • Gupta Programme — neuroplasticity-based limbic system retraining to reduce central threat signalling
  • CBT and IFS-based counselling commenced — addressing the emotional and relational roots of the chronic stress load
  • Buteyko breathing for parasympathetic activation and autonomic recalibration
  • Structured morning protocol: natural light, salt water rehydration, cold shower, movement before stimulants
  • Magnesium at night for nervous system downregulation and sleep architecture
03
Targeted Supplementation
  • Gut repair: sodium butyrate (SCFA replacement), GI-Restore, digestive enzymes, Allimed and Berberine (dysbiosis)
  • Immune modulation: Low Dose Naltrexone (LDN), quercetin, curcumin, sea buckthorn oil (omega-7 for mucosal support)
  • Foundational: Vitamin ADK (5000 IU D3), zinc chelate, high-dose omega-3, collagen with hyaluronic acid
  • Neurological: B12 injections (hydroxocobalamin), creatine for mitochondrial and cognitive energy stability
  • Estrogen detox: DIM, Calcium D-Glucarate — supporting phase II glucuronidation and clearance
Five levers.
Each one necessary.
1
Removing dietary antigens — immediately and completely
With secretory IgA at more than three times the upper limit, the immune system was in constant battle mode. Every food antigen crossing a permeable gut lining was adding fuel. This was not a gentle dietary adjustment — it was an emergency brake. → Strict AIP removed the single largest daily driver of immune activation. Without this, nothing else could have worked.
2
Addressing dysbiosis and rebuilding gut repair capacity
Inflammatory bacteria cleared with botanical antimicrobials. Butyrate supplemented directly — the microbiome was producing almost none, and the gut lining cannot repair without it. → Barrier integrity began to recover. The immune system's primary point of activation started to calm.
3
Treating the nervous system as a primary clinical target — not an afterthought
Dopamine receptor autoantibodies confirmed. Cortisol output nearly three times the reference range. Night cortisol four times the upper limit. The HPA axis had no functional off-switch. In this context, gut repair and supplementation alone would have been structurally incomplete — like fixing the wiring while the fuse box is still overloaded. Gupta Programme, CBT, and IFS-based counselling were as clinically necessary as anything in the supplement protocol. → Nervous system regulation created the physiological conditions that allowed every other intervention to take effect.
4
Clearing the estrogen burden
Total estrogen nearly double the reference range, driven by BPA exposure, impaired gut detox, and years of OCP use. DIM and Calcium D-Glucarate opened the glucuronidation clearance pathway that had been compromised. → Reduced a persistent hormonal driver of immune dysregulation and inflammatory load.
5
Restoring the nutrient foundations the system needed to heal itself
Neutrophils below range. Vitamin D suboptimal. Omega-3 index insufficient. Zinc depleted. With these gaps in place, the immune system lacked the basic raw materials for self-regulation — regardless of what else was being done. → Foundational repletion gave the biology what it needed to respond.
What changed — in numbers and in life.
Long-term sick leave
Returned to work full-time
Primary outcome
MSQ Score: 55
Score: 30
Symptom burden score — a clinically validated measure of overall toxic and inflammatory load across all body systems
Persistent brain fog
Brain fog cleared
Cognitive function
Active daily shedding
Hair falling out — slowing
Alopecia areata
Key Lab Markers
S100A12116 → target ≤50
sIgA1652 → target 426–1450
Elastase124.7 → target ≥200
Night cortisol4.28 → target 0.5–1.1
Total estrogen14.94 → target 1.73–7.54
Neutrophils1.4 → target 2–7.5
Anti-Dopamine R117.1 elevated
EBV EBNA129.0 elevated
Total SCFAs37.4 → target 45–210
The stark contrast — in her own experience.
Before
Off work on long-term sick leave
Unable to sustain the role she'd spent years building toward
Watching her hairline disappear
A defined band of loss — impossible to ignore, impossible to conceal
Skin that flared without warning
Burning, flushing, rosacea — especially around the ears and cheeks
Heavy, persistent brain fog
Dulling everything — impossible to push through at work
Mood swings she couldn't explain
Not situational. Not psychological. Immune and neurological.
Her body making her life smaller
Every symptom narrowing what was possible
After
Back to full-time work
Returned to her career — the life her symptoms had taken offline
Hair shedding reduced
The loss has slowed — and the conditions for regrowth are now in place
Rosacea considerably calmed
Skin settling as immune and gut load reduced
Brain fog gone
Thinking clearly — the neurological pressure has lifted
Feeling considerably calmer
Not managing stress — genuinely less reactive to it
Energy that can be relied on
Consistent, better than it's been since this all started
What this case teaches.
1
Alopecia areata is an immune condition, not a hair condition
Treating the scalp is treating the symptom. The driver — immune dysregulation, gut permeability, viral reactivation, stress physiology — lives elsewhere. Address the root and the hair follicle environment changes with it.
2
Multiple symptoms from one system — not multiple diseases
Hair loss, rosacea, dry eye, brain fog, mood swings, bloating — these appeared to be separate problems. They shared one root: a gut-immune-stress cascade expressing itself across every surface barrier simultaneously.
3
Normal blood tests do not mean optimal function
Her GP panels were unremarkable. The stool test, neural zoomer, hormone panel, and detailed blood analysis told a completely different story. Functional medicine tests for sufficiency — not just the absence of disease.
4
EBV reactivation is an underdiagnosed driver of autoimmunity
Elevated EBV markers — not a distant history, but active immune engagement — were contributing to neuroimmune activation, dopamine receptor autoimmunity, and sustained inflammatory tone. Post-viral immune patterns deserve direct clinical attention.
5
The nervous system is not a soft add-on — it's a primary driver
With dopamine receptor autoantibodies confirmed and cortisol chronically elevated, nervous system regulation was as clinically necessary as any supplement or dietary intervention. Gupta Programme and counselling were not optional extras.
6
Autoimmune conditions can take people out of their lives entirely — root-cause resolution can bring them back
She went from long-term sick leave to full-time work in six months. Not by managing her condition — by resolving the drivers behind it. That is the practical ceiling of functional medicine: not symptom suppression, but restored capacity for life. It is achievable more often than conventional medicine suggests.
7
Autoimmune recovery is non-linear — and that is expected
The January score rising back to 49 after reaching 38 was not a failure. It was a response to real-world stressors and a temporary break in protocol consistency. The system that learns to recover from setbacks is building resilience — not losing ground.

Sound Familiar?

You're not broken.
You're not lazy.

You're running a depleted system. There are root causes. There are answers. This is solvable.

Book a Clarity Call →

PFoley Clinic · Functional Medicine