Accurate immune repertoire sequencing reveals malaria infection driven antibody lineage diversification in young children

Ben S Wendel,Pengyu Ren,Ke-Yue Ma,Eugene W Liu,Keke Chen,Ning Jiang,Stefany M Hernandez,Di Wu,Peter D Crompton,Jun Xiao,Susan K Pierce,Mingjuan Qu,Chenfeng He

doi:10.1038/s41467-017-00645-x

Abstract

Accurately measuring antibody repertoire sequence composition in a small amount of blood is challenging yet important for understanding repertoire responses to infection and vaccination. We develop molecular identifier clustering-based immune repertoire sequencing (MIDCIRS) and use it to study age-related antibody repertoire development and diversification before and during acute malaria in infants (< 12 months old) and toddlers (12–47 months old) with 4−8 ml of blood. Here, we show this accurate and high-coverage repertoire-sequencing method can use as few as 1000 naive B cells. Unexpectedly, we discover high levels of somatic hypermutation in infants as young as 3 months old. Antibody clonal lineage analysis reveals that somatic hypermutation levels are increased in both infants and toddlers upon infection, and memory B cells isolated from individuals who previously experienced malaria continue to induce somatic hypermutations upon malaria rechallenge. These results highlight the potential of antibody repertoire diversification in infants and toddlers.

Highlights

Measuring antibody repertoire sequence composition in a small amount of blood is challenging yet important for understanding repertoire responses to infection and vaccination
Using naive B cells, we demonstrate that molecular identifier clustering-based immune repertoire sequencing (MIDCIRS) has a high coverage of the diversity estimate, or different types of antibody sequences, that is consistent with the input cell number and a large dynamic range of three orders of magnitude compared to other molecular identifiers (MID)-based immune repertoire-sequencing methods[10, 11]
Using peripheral blood mononuclear cells (PBMC) from 13 children aged 3–47 months old before and during acute malaria, with two of the children followed for a second year and nine additional pre-malaria individuals we show that infants and toddlers use the same V, D, and J combination frequencies and have similar complementarity determining region 3 (CDR3) length distributions

Summary

Introduction

Measuring antibody repertoire sequence composition in a small amount of blood is challenging yet important for understanding repertoire responses to infection and vaccination. We develop molecular identifier clustering-based immune repertoire sequencing (MIDCIRS) and use it to study age-related antibody repertoire development and diversification before and during acute malaria in infants (< 12 months old) and toddlers (12–47 months old) with 4−8 ml of blood. We show this accurate and high-coverage repertoire-sequencing method can use as few as 1000 naive B cells. Infants have a lower level of average SHM than a Step[1]: FACS-sort bulk naive B cells

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