title: Estimating the ratio of CD4+ to CD8+ T cells using high-throughput sequence data.
abstract: Mature T cells express either CD8 or CD4, defining two physiologically distinct populations of T cells. CD8+ T cells, or killer T-cells, and CD4+ T cells, or helper T cells, effect different aspects of T cell mediated adaptive immunity. Currently, determining the ratio of CD4+ to CD8+ T cells requires flow cytometry or immunohistochemistry. The genomic T cell receptor locus is rearranged during T cell maturation, generating a highly variable T cell receptor locus in each mature T cell. As part of thymic maturation, T cells that will become CD4+ versus CD8+ are subjected to different selective pressures. In this study, we apply high-throughput next-generation sequencing to T cells from both a healthy cohort and a cohort with an autoimmune disease (multiple sclerosis) to identify sequence features in the variable CDR3 region of the rearranged T cell receptor gene that distinguish CD4+ from CD8+ T cells. We identify sequence features that differ between CD4+ and CD8+ T cells, including Variable gene usage and CDR3 region length. We implement a likelihood model to estimate relative proportions of CD4+ and CD8+ T cells using these features. Our model accurately estimates the proportion of CD4+ and CD8+ T cell sequences in samples from healthy and diseased immune systems, and simulations indicate that it can be applied to as few as 1000 T cell receptor sequences; we validate this model using in vitro mixtures of T cell sequences, and by comparing the results of our method to flow cytometry using peripheral blood samples. We believe our computational method for determining the CD4:CD8 ratio in T cell samples from sequence data will provide additional useful information for any samples on which high-throughput TCR sequencing is performed, potentially including some solid tumors.
authors: Adaptive Biotechnologies, 1551 Eastlake Ave E, Seattle, WA 98109, United States.
authors: Ryan
authors: R
authors: Emerson
authors: Anna
authors: A
authors: Sherwood
authors: Cindy
authors: C
authors: Desmarais
authors: Sachin
authors: S
authors: Malhotra
authors: Deborah
authors: D
authors: Phippard
authors: Harlan
authors: H
authors: Robins
mesh_terms: D016516:CD4-CD8 Ratio / Q000379:methods*; D015496:CD4-Positive T-Lymphocytes / Q000276:immunology*; D018414:CD8-Positive T-Lymphocytes / Q000276:immunology*; D016022:Case-Control Studies; D003198:Computer Simulation; D005434:Flow Cytometry; D015333:Gene Rearrangement, beta-Chain T-Cell Antigen Receptor; D019674:Genes, T-Cell Receptor beta; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D016013:Likelihood Functions; D008957:Models, Genetic; D009103:Multiple Sclerosis / Q000175:diagnosis* / Q000235:genetics / Q000276:immunology; D011237:Predictive Value of Tests; D015203:Reproducibility of Results