Autoimmune Disease, Nervous System Regulation, and the Conditions for Healing

Emma Toms
Jan 7
5 min read

Autoimmune disease is most often framed as immune dysfunction — a body that has somehow lost the ability to distinguish self from non-self. While this description is not biologically incorrect, it is incomplete.

Increasingly, research across psychoneuroimmunology, endocrinology, and lifestyle medicine points toward a more nuanced understanding: autoimmune disease reflects dysregulation across interconnected systems, rather than an isolated immune failure.

This distinction matters, because how we conceptualise illness shapes clinical care, patient experience, and long-term outcomes.

When illness is framed as a body “attacking itself,” the response tends to focus on suppression and control. When it is understood as a system under prolonged strain, the focus shifts toward regulation, recovery, and capacity.

Immune function is inseparable from nervous system state

The immune system does not operate independently.

It is continuously regulated by:

the autonomic nervous system
the hypothalamic–pituitary–adrenal (HPA) axis
circadian rhythms
metabolic and inflammatory signalling

Together, these systems constantly assess whether the body is safe enough to repair or whether it must remain vigilant.

Under conditions of chronic stress, this balance shifts.

Prolonged activation of stress pathways alters cortisol signalling, increases sympathetic nervous system dominance, disrupts sleep architecture, and promotes low-grade systemic inflammation. Over time, immune tolerance narrows, inflammatory thresholds change, and tissue repair becomes compromised.

Large population studies now demonstrate associations between stress-related disorders and subsequent autoimmune disease, as well as significantly higher rates of anxiety and depression among people already living with autoimmune conditions. These findings support a bidirectional relationship between nervous system load and immune dysregulation — not a one-way story of immune malfunction.

This does not imply simplistic causation. It highlights shared biological pathways that increase vulnerability over time.

Autoimmunity as adaptation, not attack

From a systems perspective, many autoimmune processes can be understood as adaptive responses that have become maladaptive.

Inflammation, immune activation, and heightened vigilance are protective in the short term. They mobilise energy, defend against threat, and support survival.

The problem is not activation — it is duration.

When the body remains in a prolonged state of threat detection, whether due to psychological stress, physical illness, social adversity, or cumulative life strain, these same protective mechanisms begin to generate damage and persistent symptoms.

This reframing challenges the language of the body “turning against itself.” Instead, it suggests a body that has been responding appropriately to sustained pressure, without sufficient opportunity to return to baseline.

For many people, this shift alone is regulating. It replaces blame with context — and opens the door to care aimed at restoring balance rather than silencing signals.

Why nervous system therapies matter in autoimmune disease

If autoimmune disease reflects long-term systems dysregulation, education alone is rarely enough to create change.

Understanding stress physiology does not automatically shift it. Much of nervous system organisation occurs below conscious awareness, shaped by implicit memory, emotional imprinting, and repeated physiological responses to stress. These patterns are often established long before diagnosis. This is where nervous system–focused therapies become essential.

Integral Eye Movement Therapy (IEMT)

IEMT works directly with emotional imprinting and identity-linked nervous system responses.

Rather than analysing events, it focuses on:

how emotional responses were learned
how they are stored neurologically
how identity-level stress patterns are maintained

By using eye movements and spatial processing, IEMT supports the nervous system to decouple emotional charge from memory and identity — often without prolonged exposure or re-traumatisation.

For people living with autoimmune disease, this can reduce:

chronic emotional vigilance
identity-based stress patterns (“this is just who I am”)
persistent autonomic activation linked to past experiences

This is not about reliving the past. It is about allowing the nervous system to update its responses so it no longer behaves as though past threat is still present.

The Safe and Sound Protocol (SSP)

The Safe and Sound Protocol works through the auditory system to support vagal regulation and felt safety.

The nervous system uses sound — particularly frequencies associated with the human voice — to assess whether it is safe to connect or necessary to defend. When this system is compromised, people may experience hypervigilance, sound sensitivity, social withdrawal, or chronic stress activation.

SSP is designed to:

support ventral vagal activation
improve autonomic flexibility
reduce sensory and social defensiveness
increase capacity for connection and regulation

For individuals with autoimmune disease, SSP offers a gentle, non-verbal pathway back toward safety. This matters because immune regulation improves when the body experiences felt safety, not simply intellectual reassurance.

The Pillars of Health: infrastructure, not advice

Lifestyle medicine is sometimes misunderstood as behavioural guidance layered on top of illness. In reality, it addresses the biological terrain in which immune processes occur.

Each pillar influences immune regulation through established mechanisms:

Sleep

Sleep is not passive rest. It is an active period of immune recalibration. Sleep disruption is associated with increased inflammatory cytokines, altered pain perception, impaired glucose metabolism, and reduced immune resilience.

Nutrition (food-first approach)

Whole-food dietary patterns rich in fibre, phytonutrients, and healthy fats support gut-immune signalling and reduce inflammatory burden. This is not about restriction or perfection, but about adequacy and consistency.

Movement

Appropriately dosed movement supports mitochondrial function and immune modulation. Both over-exertion and prolonged inactivity can worsen symptoms, highlighting the importance of pacing and individualisation.

Stress regulation

Chronic stress alters autonomic balance and HPA axis function. Regulation strategies work physiologically, not through willpower or positive thinking.

Social connection and meaning

Isolation and lack of purpose are associated with increased morbidity and mortality. Immune health is shaped by relational and environmental context, not individual effort alone.

Crucially, these pillars work best after regulatory capacity is supported. Without nervous system safety, lifestyle change can become another source of pressure.

Capacity, not compliance

A central issue in autoimmune care is not what changes are recommended, but how they are supported.

Fatigue, pain, cognitive impairment, financial strain, and social isolation all affect capacity. When lifestyle guidance ignores this, it risks increasing shame rather than health.

Evidence from behavioural science consistently shows that small, supported, person-centred changes are more sustainable than large, unsupervised overhauls. This is why coaching, group work, and nervous system-informed support matter — not as motivation tools, but as scaffolding for real change.

Lived experience as clinical insight

My own experience of autoimmune disease mirrors what the science increasingly reflects.

In hindsight, my diagnosis was preceded by years of heightened stress, poor recovery, emotional suppression, and nervous system overactivation. Medication was essential and stabilising. Long-term improvement came from addressing the conditions that shaped my immune responses in the first place.

This is not a rejection of medical care. It is an argument for integration.

Lived experience adds depth to clinical understanding, particularly in conditions where symptoms fluctuate and recovery is non-linear.