The Science of Immune Profiling

Innate versus Adaptive Immunity
video-how-tcrs-workThe immune system is comprised of innate and adaptive subsystems. Innate immunity provides an immediate and non-specific response to a variety of pathogens. The innate response is usually triggered when microbes are identified by pattern recognition receptors, which recognize components that are conserved among broad groups of microorganisms. The system does not confer long-lasting immunity against a pathogen.

In contrast, adaptive immunity adapts its response during the course of infection to improve its ability to recognize the pathogen. This improved response is then retained after the pathogen has been eliminated, in the form of immunological memory. This allows the adaptive immune system to mount faster and stronger attacks each time the pathogen is encountered. Adaptive immunity evolved in early vertebrates and allows for a stronger immune response than innate immunity. The adaptive immune response is antigen-specific and requires the recognition of specific “non-self” antigens during a process called antigen presentation. Antigen specificity allows for the generation of responses that are tailored to specific pathogens or pathogen-infected cells. The ability to mount these tailored responses is maintained in the body by “memory cells”.

The cells of the adaptive immune system are special types of leukocytes, called lymphocytes. B and T cells are the major types of lymphocytes and are derived from hematopoietic stem cells in the bone marrow. B cells are involved in the humoral immune response, whereas T cells are involved in the cell-mediated immune response.

Variable Region of Adaptive Immune Cells
Both B cells and T cells carry receptor molecules that recognize specific targets. T cells recognize non-self targets only after antigens (small fragments of the pathogen) have been processed and presented in combination with a major histocompatibility complex (MHC) molecule. There are two major subsets of T cells: killer T cells and helper T cells.

T cells express a T cell receptor (TCR) on the cell surface that determines specificity. There are over 100 million unique TCRs in the human body, forming an army of cells that enable the body to fight disease, each equipped with a single type of TCR. A TCR is created by selecting and splicing together a single V, D and J segment from a collection of available genomic segments. At the junctions between V-D and D-J segments, a varying number of nucleotides are deleted and a special enzyme inserts random nucleotides, creating a unique TCR. It is these inserted nucleotides that are responsible for the vast diversity found in the human TCR repertoire.

The immunoSEQ assay utilizes a multiplex PCR strategy to amplify the CDR3 region of the T cell receptor, spanning the variable region formed by the junction of the V, D and J segments and their associated non-templated insertions. In most cases, the identity of each segment is also captured. The resulting 60 base pair nucleotide sequence may be used as an identifier or “tag” for a particular clone across different samples. Combined with the quantitative property of the assay, this provides a useful way to track clonal expansions and contractions over time in the same patient. Applications of this technique include tracking a patient’s leukemia or lymphoma post-treatment, tracking the fate of novel T cell clones introduced into a patient, and studying the biology of T cell lineages and developmental processes.

Applications

Adaptive is in the process of developing assays for both clinical diagnosis and therapeutic monitoring for a variety of disorders and conditions.

Two possible mechanisms by which our technology leads to a clinically relevant diagnostic test include an analysis based upon the frequency distributions of TCR clonotypes, or upon the presence/absence of specific TCR clonotypes (or classes of clonotype).

Therapeutic Monitoring
Another application of our technology is the use of TCR profiling to monitor disease state or other conditions over the course of therapy. Adaptive is currently collaborating with the Fred Hutchinson Cancer Research Center to test the feasibility of this concept in patients who have undergone immune system ablation and reconstitution with cord blood stem cells.

Drug Discovery
Adaptive is concentrating its efforts on specific, prevalent auto-immune diseases. Autoimmune diseases result from a hyperactive immune system attacking normal tissues (TCRs mistakenly recognizing human proteins) as if they were foreign organisms. We believe a drug therapy targeting the specific TCR combinations associated with disease could pre-emptively block the relevant TCRs from mistakenly reacting to their own body tissues, thus preventing or ameliorating the autoimmune disease. In collaboration with Dr. Gerald Nepom, Director of the Benaroya Research Institute at Virginia Mason Hospital in Seattle, Adaptive is currently screening blood samples from patients with either Type 1 Diabetes or Multiple Sclerosis (“MS”) for public TCR sequences.