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Any organism or substance that causes an immune system reaction is considered an antigen. These commonly include pathogens (viruses, bacteria, fungi and parasites), toxins, and body cells that become cancerous. Transplanted cells or tissues are also foreign to the immune system and may cause a response. Immune system reactions are aimed at turning the antigen into a less dangerous substance or removing it from the body entirely.

When functioning properly, the immune system is able to differentiate between the body’s own cells and foreign substances. It recognizes certain protein molecules on the surface of every healthy cell in the human body. These molecules are part of the major histocompatibility complex (MHC) that occurs in specific patterns and differs from person to person, with the exception of identical twins. These surface molecules are either absent or unrecognizable in foreign substances.

Thus, organisms or substances that penetrate body tissues and do not have the proper MHC are identified as foreign by the immune system, provoking an immune system response. During an immune system response, foreign invaders are typically surrounded and bound by proteins called antibodies that are produced by white blood cells in the body. This prevents the invading substances from reproducing or being transported throughout the body. These foreign substances are then removed from the body or killed.

Some pathogens, such as viruses and some bacteria, invade the body’s cells to reproduce and spread. When this occurs, body cells will often change their MHC surface proteins. This signals to the immune system that the cell is infected and needs to be removed. Cells of the immune system may also use part of the antigen to signal other immune cells that an infection is occurring, thus triggering a larger scale response.

Cancer cells are mutated body cells that begin to uncontrollably reproduce. This frequently causes a change in the MHC surface proteins, similar to what happens when a pathogen infects a cell. The immune system response typically removes the cancer cells to prevent further spread. The immune system can become weakened or overwhelmed and allow cancer cells to continue to reproduce. This is one route that can lead to disease.

Toxins and other foreign molecules are often far smaller than cells. After they are recognized by the immune system as potentially harmful substances, they are engulfed and removed from tissues.

Transplanted cells and organs also have external molecules that differ from those the immune system recognizes as part of its body. The immune system reacts to these transplanted tissues much like it does to pathogens and will attempt to reject the transplanted organ. Immunosuppressant medications are often used to reduce the body’s efforts to kill and remove these tissues.