The human cellular adaptive immune system identifies and destroys cells expressing aberrant proteins or protein fragments. The source of the abnormal protein fragments can include intracellular pathogenic infection, genomic mutations, or deregulation of gene expression. Cancerous cells often express such aberrant peptides, prompting a cellular adaptive immune response. These peptides are presented on the surface of cells by human leukocyte antigen molecules for binding by T cell receptors (TCRs) on the surface of T-lymphocytes, the primary mediators of the cellular adaptive immune response.
Tumor-infiltrating lymphocytes (TILs) have been shown to directly attack tumor cells in a variety of types of cancer, and multiple independent studies have demonstrated that the presence of TILs is strongly correlated with increased survival. For both colorectal and ovarian carcinoma patients, the presence or absence of TILs provides a strong prognostic marker for survival independent of current staging methods. However, existing assays and pathology tests to measure TILs are cumbersome, have inherent variability, are mostly restricted to research studies, and thus are not used for clinical decision-making.
As the importance of TILs gains appreciation, particularly given their potential utility for cancer prognostication and their role in immunotherapeutic response, new technologies to quantitatively measure TILs are needed. Fortunately, adaptive immune cells have a molecular signature that can be exploited for direct measurement. T cells have gene rearrangements in their TCR loci. The nucleotide sequences that encode the TCR regions are generated by somatic rearrangement of noncontiguous variable (V), diversity (D), and joining (J) region gene segments for the β chain, and V and J segments for the α chain. The existence of multiple V, D, and J gene segments in germline DNA permits substantial combinatorial diversity in receptor composition, and receptor diversity is further increased by the deletion of nucleotides adjacent to the recombination signal sequences (RSSs) of the V, D, and J segments, and template-independent insertion of nucleotides at the Vβ-Dβ, Dβ-Jβ, and Vα-Jα junctions.
We have developed QuanTILfy to measure the number of T-lymphocytes and assess clonality in a tissue using droplet digital polymerase chain reaction (ddPCR) technology. The massive sample partitioning is a key aspect of the ddPCR technique and a vital component of the QuanTILfy assay. ddPCR surpasses the performance of earlier techniques by introducing a scalable implementation of digital PCR, where the creation of tens of thousands of droplets allows for the generation of tens of thousands of data points, bringing the power of statistical analysis inherent to digital PCR into practical application.