HIV's Impact on the Immune Repertoire: New Analytic Methods
Creators: name: University Of California Office Of The President
Publisher: name: University of California Office of the President
publisherIdentifier: https://ror.org/00dmfq477
publisherIdentifierScheme: ROR
Year: 2024

description: Our body’s immune system is able to protect us from a wide variety of germs. Cells of the immune system called lymphocytes use receptor molecules on their surfaces to recognize germs as foreign invaders and fight them off. Although each lymphocyte only uses a single type of receptor that is able to recognize only one specific germ, each person has millions of different lymphocyte receptors. This collection of receptors is known as the immune repertoire. The diversity of the immune repertoire is crucial to the functioning of the immune system. We need to have enough different lymphocyte receptors so that, when our immune system encounters a germ for the first time, there will be a lymphocyte that has a receptor that can recognize the germ. Patients with AIDS usually have decreased numbers of lymphocytes, and it has been thought that their immune repertoire is not as diverse as normal, increasing their susceptibility to infections. This unproven idea is known as the “holes in the repertoire” hypothesis. While it is straightforward to measure the number of lymphocytes in a person’s blood, until now there has been no simple way to measure the diversity of receptors of these cells. I have invented a new method, called AmpliCot, to measure the diversity of lymphocyte receptors. This method is relatively inexpensive and can be performed on many samples at a time. Starting with a sample of cells to study, I use a chemical process called the polymerase chain reaction (or PCR) to make many copies of the genes that encode the lymphocyte receptors. Each of the gene copies made in the PCR reaction is made of DNA in its familiar structure of two matching strands paired together in a double helix. To measure the diversity of receptors in the sample, I briefly heat the DNA so that the two strands come apart and then I measure how long it takes for the DNA strands to pair back together. The experiment is done under special conditions that only allow perfectly matched DNA pairs to re-form. The length of time it takes the pairs to re-form is directly proportional to the number of different receptor genes that were in the original sample. This measurement, therefore, provides an estimate of the diversity of the immune repertoire. Although I have figured out the best way to perform AmpliCot in the laboratory, we do not yet know the best way to analyze the data produced by AmpliCot. In the project proposed here, I will work closely with a statistician to answer several questions. First, which measurement methods should be used to make the measurements as reliable as possible, and also as sensitive as possible for rare cell types in the sample? Second, can we develop ways to compare the relative diversity of two samples if we cannot collect equal amounts of cells from each sample? Third, do AIDS patients show evidence of a loss of lymphocyte specificities, or “holes in the repertoire”? AmpliCot will open the door to measuring the normal size of the immune repertoire and to understanding how the repertoire is affected in AIDS patients. My long-term goal is to understand how much immune receptor diversity is required for good health, and to evaluate therapeutic strategies that might be able to restore receptor diversity in AIDS patients.