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

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.

The receptor repertoire and functional profile of follicular T cells in HIV-infected lymph nodes

“…For bulk cell analyses, TCR library generation and raw sequence processing were performed using MIDs with primers listed in Table S1. (18, 19). …”

COLT-Viz: Interactive Visualization of Antibody Lineage Trees

“…We visually encode multiple properties of nodes and edges into the lineage tree visualization, so users can understand these properties intuitively. Figure 1 shows an antibody lineage we found in a young African child who experienced acute malaria twice in two consecutive malaria seasons from our previous study (19). There are a total of 23 unique sequences obtained from 4 timepoints in this lineage.…”

IgEvolution: clonal analysis of antibody repertoires

“…Many studies have analyzed the distributions of the number of SHMs across all individual antibodies (Wendel et al, 2017;Lee et al, 2019) or across all clonal lineages (Ellebedy et al, 2016;Nielsen et al, 2019;Horns et al, 2019) in an antibody repertoire. These approaches, while valuable, face the difficulty of finding the closest D genes and identifying non-genomic insertions, leading to complications in deriving SHMs in CDR3s.…”

“…The usage of a germline gene is defined as the fraction of reads in a repertoire aligned to this gene. Although this concept (that we refer to as the simple usage) proved to be useful (Wendel et al, 2017;Lee et al, 2019), it does not accurately estimate the number of VDJ recombinations that include a given germline gene, particularly for stimulated repertoires with expanded clonal lineages. Since each clonal lineage reveals a single VDJ recombination, we define the clonal usage of a germline gene as the fraction of clonal graphs derived from this gene (Figure 7).…”