Our research is focused on understanding how RNA helicases control the molecular and cellular changes underpinning antibody gene diversification in B cells.
Age-related defects in humoral immunity often result from the inability to generate a diverse repertoire of antibodies, and pathological outcomes associated with antibody gene diversification, such as autoimmunity and B cell lymphoma, show increased prevalence in older individuals. We envisage RNA helicases and RNA structure to constitute ideal therapeutic targets to modulate B cell function in the elderly, and this will require a better understanding of their fundamental roles in B cell biology.
Defining RNA-protein interactions controlling B cell developmental transitions
B cells are crucial to immune defence by producing large quantities of antibodies with pathogen neutralizing capacities. Antibody responses can be made to target a limitless range of antigens with exquisite specificity and affinity, while eliciting different effector functions. This remarkable ability of the adaptive immune system relies on DNA mutation and recombination events occurring at immunoglobulin (Ig) loci, that encode for antibody heavy and light chains.
The first steps of antibody gene diversification occur at the early stages of B cell development in the bone marrow. Here, precursor (pre-) B cells undergo V(D)J recombination at Ig loci, resulting in the generation of a vast repertoire of antibodies with different antigen specificities. Key to successful V(D)J recombination and the maintenance of B cell genome stability, is the coordination of cell proliferation with the induction of DNA double-strand breaks (DSBs) by RAG endonucleases at the pre-B cell stage. One main line of research in our lab aims to understand the dynamic changes in the RNA-bound proteome underpinning the developmental transition between large and small pre-B cells.
Characterizing RNA helicase roles during antibody immune responses
Once a mature B cell encounters its cognate antigen in peripheral lymphoid organs such as the spleen, antibody responses can be further refined through processes known as class switch recombination (CSR) and somatic hypermutation (SHM). As a result, mature B cells differentiating into plasma cells change antibody isotype (or class, which determines different effector functions and the neutralizing capacity of antibodies) and increase antibody affinity towards antigen. Both CSR and SHM are catalysed by the DNA mutator enzyme activation-induced cytidine deaminase (AID), but only SHM is reliant on the formation of specialized microanatomical structures known as germinal centres (GCs).
Using novel mouse genetic tools, we are investigating how RNA helicases regulate B cell immune responses, impacting on the quality and quantity of antibody that is produced. We have uncovered a role for DDX1 in the remodelling of G-quadruplex (G4) RNA structures that target AID to the Ig heavy-chain (IgH) locus during CSR (Ribeiro de Almeida et al, Mol Cell 2018). This has prompt us to seek further mechanistic understanding of how RNA helicase function controls the antibody response. Our current work aims to explore whether DDX1 and other RNA helicases participate in GC selection mechanisms that improve antibody affinity for antigen and direct B cell differentiation towards antibody secreting plasma cells and memory-B cells. Preliminary analyses highlight RNA helicase activity is required for the formation and/or maintenance of GC structures.
Investigating how RNA helicase activity remodels RNA structure in B cells
RNA helicases operate inside the cell as traffic controllers, instructing various steps of the mRNA life cycle from its biogenesis in the nucleus to translation in the cytoplasm. RNA helicases also determine mRNA fate decisions such as storage for later translation or degradation, and therefore subtle changes in their activity can significantly impact gene expression. It is anticipated that RNA helicase function inside living cells is, at least in part, promoted by changes in mRNA secondary structure.
There is a significant knowledge gap on how flexible RNA structural conformations are inside living B cells; and how RNA helicases instruct RNA structural modification to relay cellular cues into changes in gene expression. Together with Yiliang Ding, we are employing state-of-the-art methodology to profile RNA structure in B cells (press release). These studies will be key to understand the functional relevance of RNA helicase鈥檚 remodelling activity for gene expression and inform future RNA-based therapeutics.