Phylogenetic analysis of migration, differentiation, and class switching in B cells

• Published in: PLoS computational biology Vol. 18; no. 4; p. e1009885
• Main Authors: Hoehn, Kenneth B., Pybus, Oliver G., Kleinstein, Steven H.
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 01.04.2022; Public Library of Science (PLoS)
• Subjects: Algorithms; Allergies; Antibodies; B cells; B-cell receptor; B-Lymphocytes; Biological research; Biology and Life Sciences; Biology, Experimental; Cell adhesion & migration; Cell Differentiation - genetics; Class switching; Computer and Information Sciences; Differentiation (biology); Evolution; Food allergies; Food hypersensitivity; Genetic aspects; HIV; HIV Infections; Human immunodeficiency virus; Humans; Hypotheses; Immunoglobulin Class Switching; Information processing; Isotypes; Lymphocytes B; Medicine and Health Sciences; Mutation; Phylogenetics; Phylogeny; Phylogeography; Physical Sciences; Physiological aspects; Receptors, Antigen, B-Cell - genetics; Research and Analysis Methods; Statistical analysis; Statistics; Switching; United States
• ISSN: 1553-7358; 1553-734X; 1553-7358
• DOI: 10.1371/journal.pcbi.1009885

B cells undergo rapid mutation and selection for antibody binding affinity when producing antibodies capable of neutralizing pathogens. This evolutionary process can be intermixed with migration between tissues, differentiation between cellular subsets, and switching between functional isotypes. B cell receptor (BCR) sequence data has the potential to elucidate important information about these processes. However, there is currently no robust, generalizable framework for making such inferences from BCR sequence data. To address this, we develop three parsimony-based summary statistics to characterize migration, differentiation, and isotype switching along B cell phylogenetic trees. We use simulations to demonstrate the effectiveness of this approach. We then use this framework to infer patterns of cellular differentiation and isotype switching from high throughput BCR sequence datasets obtained from patients in a study of HIV infection and a study of food allergy. These methods are implemented in the R package dowser , available at https://dowser.readthedocs.io .