Understanding Autoimmune Diseases: Causes, Symptoms & Treatments Explained

By Dr. Jane B. Ayala, FACR and Dr. Thomas A. Rennie, FCR Board Certified in Internal Medicine and Rheumatology

Note to Readers:
Some content in this article is written at a professional, scientific level, intended for healthcare providers. If you have any questions about the information here, please contact us at support@rheumthera.com and we will respond as soon as possible.

What Is an Autoimmune Disease?

Autoimmune diseases are conditions in which the immune system — normally your defense against infections — mistakenly attacks healthy tissues.

The immune system’s job is to tell the difference between “self” and “non-self.” It should attack harmful pathogens like viruses and bacteria while leaving your own cells alone. In autoimmune disease, that system of discrimination breaks down.

Key features include:

• Autoreactive immune cells – T cells and B cells that react against the body’s own proteins

• Autoantibodies – antibodies that target healthy tissue

• Chronic inflammation – persistent, self-sustaining immune activity even without infection

How the Immune System Breaks Down

Several mechanisms contribute to autoimmunity:

• Molecular mimicry – a virus or bacteria resembles a normal human protein, confusing the immune system

• Loss of immune tolerance – autoreactive immune cells are not eliminated as they should be

• Cytokine imbalance – excessive inflammatory messengers (TNF-α, IL-6, interferons) fuel tissue damage

• Genetic susceptibility – certain HLA (human leukocyte antigen) genes increase risk

• Environmental triggers – UV light, viral infections, stress, smoking, or medications can set off disease in susceptible people

The Role of Dysregulated Inflammation

Autoimmune inflammation isn’t like the temporary swelling from a cold or cut. It is chronic, persistent, and often self-sustaining.

Immune cells such as macrophages, T cells, and neutrophils infiltrate tissues where they don’t belong — and they don’t stop. Over time, this leads to:

• Swelling and warmth in joints or organs

• Pain from cytokines activating nerve endings

• Tissue damage from oxidative stress and enzymes

• Fibrosis (scarring) that can permanently impair function

For patients, this often starts as fatigue, joint pain, rashes, or low-grade fevers, but may progress to serious organ involvement if untreated.

Why Do Joints and Muscles Often Suffer?

1. Synovial tissue is vulnerable
   The lining of joints (the synovium) contains proteins easily recognized as antigens. In rheumatoid arthritis, this tissue becomes inflamed, thickened, and flooded with destructive immune cells.

2. Mechanical stress exposes proteins
   Daily wear and tear may “unmask” hidden proteins. If the immune system is already dysregulated, it may attack these proteins as invaders.

3. Molecular similarity with pathogens
   Joint proteins like collagen resemble viral or bacterial proteins. The immune system, trained to fight infection, cross-reacts with self-proteins.

Systemic vs Organ-Specific Autoimmune Diseases

Not all autoimmune diseases behave the same. Some affect many organs (systemic), while others remain confined to one organ (organ-specific).

Systemic Autoimmune Diseases (Managed by Rheumatologists)

• Rheumatoid Arthritis (RA) – joints, lungs, heart, blood vessels, eyes

• Systemic Lupus Erythematosus (SLE) – skin, kidneys, brain, joints, blood system

• Systemic Sclerosis (Scleroderma) – skin, lungs, GI tract, heart, blood vessels

• Sjögren’s Syndrome – salivary glands, tear glands, joints, lungs, kidneys

These conditions often require immunosuppressive therapy and close monitoring of organ function.

Organ-Specific Autoimmune Diseases (Managed by Organ Specialists)

• Hashimoto’s Thyroiditis / Graves’ Disease – thyroid (endocrinologist)

• Type 1 Diabetes Mellitus – pancreas β-cells (endocrinologist)

• Autoimmune Hepatitis – liver (hepatologist or gastroenterologist)

• Celiac Disease / Inflammatory Bowel Disease – intestines (gastroenterologist)

• Multiple Sclerosis (MS) – brain and spinal cord (neurologist)

• Autoimmune Uveitis – eyes (ophthalmologist or ophthalmology/rheumatology team)

What Triggers Autoimmunity?

Factors that increase risk include:

• Genetics – HLA-DR4, HLA-B27, and other HLA types; family history matters

• Infections – viruses such as EBV, parvovirus, or CMV may trigger disease

• Medications – some drugs can cause lupus-like syndromes or reactive arthritis

• Smoking and environmental exposures – especially in RA and lupus

• Hormonal and sex differences – women are affected up to 9x more than men; estrogen and pregnancy play a role

Are Autoimmune Diseases Always Progressive?

Not necessarily. Outcomes vary:

• Some patients experience flares and remissions

• Others remain in long-term low disease activity

• Many respond dramatically to treatment, especially when started early

Modern therapies such as DMARDs, biologics, and JAK inhibitors have transformed long-term outcomes, preventing much of the irreversible damage that once occurred.

Key Takeaways for Patients and Caregivers

• Autoimmune diseases result from loss of immune tolerance, causing the body to attack its own tissues

• They may be systemic (affecting many organs) or organ-specific (affecting one system)

• Rheumatologists manage systemic autoimmune diseases such as RA, lupus, scleroderma, and Sjögren’s

• Inflammation is measurable, treatable, and modifiable with modern therapies

• Early intervention can prevent long-term complications and improve outcomes

If you or a loved one are experiencing unexplained fatigue, joint pain, or chronic inflammation, speak with a rheumatologist. Early diagnosis and treatment can make all the difference.