The production of antibodies by B cells is an important component of adaptive immunity. While antibodies often afford protection against pathogens such as viruses and bacteria, one class of antibodies, known as IgE, is involved in the pathogenesis of allergies and mediates the symptoms of allergic reactions. This role of IgE has long been known, but the B cells that produce these antibodies are extremely rare, even in allergic individuals. Consequently, the transcriptional programs of these cells and the functional attributes of their antibodies have remained poorly understood.

In a paper published Dec. 14 in Science, Stanford researchers led by Bioengineering professor Stephen Quake developed an approach that leveraged single-cell RNA sequencing (scRNA-seq) to better understand these rare IgE B cells and their antibodies. Starting with blood from individuals with food allergies, the researchers performed fluorescence activated cell sorting (FACS) prior to single-cell transcriptome amplification using the “full-length” Smart-seq2 chemistry. Consequently, the full length heavy and light chains that comprise each individual antibody could be bioinformatically reassembled from short sequencing reads. The researchers were then able to cluster B cells with similar antibodies into clonal families, where one clonal family in particular stood out; it contained B cells belonging to two unrelated peanut-allergic individuals. After cloning and expressing the antibodies from these B cells, the researchers found that they bound two separate peanut allergens with high affinity and propose that

“either these antibodies or engineered variants could be used as therapeutic agents.”

The researchers also compared the transcriptomes of IgE B cells with B cells producing antibodies of other classes. Within the subset of B cells known as plasmablasts, which are non-terminally differentiated antibody secreting cells, IgE plasmablasts expressed a relatively immature gene expression program that also appeared deficient in activation, proliferation, and survival capacity. Furthermore, differences in antibody heavy chain mRNA splicing between IgE B cells and B cells of other classes pointed to compromised signaling as a mechanism for regulating the number of circulating IgE B cells.

Asked about the research, lead author Derek Croote notes:

“Our study focused on B cells producing peanut-specific IgE antibodies, but the approach we developed to isolate these rare cells applies equally to other allergies as well.”

Availability – Workflows for alignment and antibody assembly are available at https://github.com/dcroote/singlecell-ige

Croote D, Darmanis S, Nadeau KC, Quake SR. (2018) High-affinity allergen-specific human antibodies cloned from single IgE B cell transcriptomes. Science 362(6420): 1306-1309. [abstract]