How Does the Immune System Work?

immune system, autoimmune disease

Your immune system protects your body from foreign germs and other substances. Through highly complex, and adaptive processes, the immune system identifies and protects you, even as it identifies and destroys, what is not you.

To do its job, the immune system must understand the difference between a foreign substance or molecule, called an antigen, and the cells and tissue of your own body, called self-antigens.

Always at work, your immune system spends your life surveying, sampling, remembering, and destroying antigens it considers destructive to the self.

T- and B-Cells

There are different kinds of white blood cells involved in protecting your body against disease or disorder. If you are ill, your doctor might suspect an infection, and order a blood panel to see if your body has mounted an immune response, increasing the number of white blood cells circulating throughout your body.

Some of those white blood cell types are lymphocytes. Two types of lymphocytes are T-cells and B-cells. While these are both lymphocytes—they have different jobs.

T-cells identify pathogens, or antigens, riding on the surface of your cells. When a cell is infected, it produces a chemical response that is carried to its surface by genes called the major histocompatibility complex (MHC). Once the chemical response emerges on the surface, passing T-cells are alerted to the presence of an antigen. Each T-cell has a vast number of receptor molecules on its surface, called a T-cell receptor, that work to identify and tag the infected cell.

With the help of T-cells, B-cells are largely responsible for creating specific antibodies that bind to the antigen and mark it for destruction by the immune system.

Two other types of white blood cells are macrophages and neutrophils.

Macrophages and Neutrophils

Invading germs and microorganisms enter the body in different places. When they do, they are met by some big eaters, literally. Macrophages surround, absorb, and eat antigens and cellular debris that do not bear the markers (and proteins) of healthy cells. Macrophages circulate throughout the bloodstream and body tissues. Other scavenging white blood cells are the neutrophils, which circulate in the blood, but not throughout tissues, performing a similar function.

One form of attack used by macrophages and neutrophils is the secretion of toxic molecules to damage or kill foreign microorganisms. Called reactive oxygen intermediate molecules, these chemicals are dangerous to surrounding tissue if too many are produced for too long.

An autoimmune disease called Wegener’s granulomatosis is condition worsened by overactive neutrophils and macrophages. Toxic secretions intended for antigens damage healthy blood vessels instead. With rheumatoid arthritis, white blood cells, and these reactive molecules migrate to joints, causing inflammation that leads to the swelling, warmth, and joint damage associated with RA.

MHC and Co-Stimulatory Molecules

Above, we talked about the function of genes that carry MHC molecules to the surface of an infected cell. These molecules are synthesized by the cell with fragments of the virus, or antigen, that has invaded the cell.

Like a red flag, the MHC response signals T-cells to respond. Communication takes place first when the antigen-presenting cell signals the presence of the antigen, and second when a signal is sent from the infected cell to a corresponding receptor on the T-cell. The molecules on the infected cell and the responding T-cell that mediate an immune response are called co-stimulatory molecules.

The elegant call and response of co-stimulatory molecules, when working correctly, readies each cell for action to destroy the antigen. The interaction of these molecules is rich research ground for studies on how to control, or stop, immune interaction when your healthy host cells and tissues are mistaken for invading antigens.

Cytokines and Chemokines

Upon interaction of co-stimulatory molecules, T-cells may secrete chemicals called cytokines and chemokines. Each of these compounds has a different immune function.

Cytokines are immune proteins that may call surrounding immune cells to action, and also affect nearby non-immune cells. One example of this is a thickening of the skin that occurs with the autoimmune disorder scleroderma.

A type of cytokine, chemokines attract the attention of additional cells of the immune system, oftentimes to produce an inflammatory response after an injury, or with infection. Too much of a good thing is damaging though. Overproduction of chemokines in RA, for example, results in pain and damage in joints as macrophages and neutrophils respond to a faulty signal.


Produced by B-cells, antibodies bind foreign antigens and assist in their destruction. T-cells chemically communicate with B-cells through cytokines. Upon receipt of instruction by the T-cell, B-cells are able to manufacture the specific antibody needed to target an infectious, or invading, antigen.


Problems occur when the immune system mistakenly manufactures autoantibodies—literally antibodies against the self. This hallmark problem of autoimmune diseases means that the immune system misidentifies self-antigens—your own cells, tissues, and organs—as foreign bodies.

For those that suffer the autoimmune disorder, myasthenia gravis, the characteristic muscle weakness of the disease is caused by autoantibodies that target specific nerves responsible for muscle movement.

Immune Complexes and the Complement System

Antibodies produced by B-cells bind to specific antigens. This latticing action is called an immune complex. Here again—too much of a good thing is damaging to the human body.​

When the body overproduces immune cells and complexes, this inflammatory response can block blood flow in vessels throughout the body, destroying tissue and organs. Kidney damage is a common result of an overactive immune response in those who suffer from lupus.

In a normal immune response, the body produces specialized molecules that form a complement system. The complement system scavenges tissues, and cell surfaces for immune complexes, working to make them soluble and slough off when no longer needed. This works to avoid the vascular and organ damage suffered by those with some autoimmune diseases.

Rarely, an individual inherits gene patterns that prevent the normal action of immune complement molecules. This disorder is not an autoimmune disease, but often mimics the damage suffered by those diagnosed with lupus.

Genetic Factors

As we talked about earlier, your genetic makeup can predispose you to development of an autoimmune disorder. Your genes are the blueprint for your immune cells, and function. That same blueprint patterns your T-cell receptors, the type of MHC molecules produced, and other features of your immune response. But genes alone do not predetermine your development of an autoimmune disease. Some people with autoimmune-related MHC molecule types never develop an autoimmune disorder.

Complicated, and ever-active, your immune system works hard to protect your health. It is easy to see how dysfunction at any stage of an immune response could lead to a troubling, damaging chronic autoimmune disease.