Research Topics

Ig Diversification

Rebecca Delker
Paul Hakimpour
Eric Fritz
Jan Davidson-Moncada
Deaminases in Antiviral Defence

Brad Rosenberg
Claire Hamilton
Xenia Gourzi
Deaminases and VSG Gene Conversion

Catharine Boothroyd
Galadriel Hovel-Miner
Tanya Leonova
Oliver Dreesen

Ig Diversification

One of the unique features of the immune system is that it has evolved to raise antibodies against an unlimited number of antigens, a number too large to be encoded in the genome. This flexibility is made possible by the evolution of specific mechanisms that create a large number of diverse antibody specificities from a limited amount of genetic material. Our research focuses on the different processes that are employed by immune cells to generate this diversity.

Using a combination of biochemistry, cell and molecular biology, we are establishing new assays to study the molecular basis of somatic hypermutation, the mutagenic process that, in B lymphocytes, is essential for their ability to recognize diverse antigens. When B cells, specialized cells that produce antibodies against foreign molecules, encounter an antigen, mutations are introduced in the genes of their B cell receptors that recognize that antigen. This process helps some of those B cells to acquire a higher affinity for the antigen, and those cells then become selected for survival -- the immune system is selecting the B cells that are the best candidates for long-term memory against the antigen. Without somatic hypermutation, individuals may become immunocompromised in their ability to deal with antigens. However, unregulated hypermutation can also lead to cancer.

Hypermutation in B cells is dependent upon a protein called AID (for activation-induced cytidine deaminase). AID is exclusively expressed in B cells and acts by changing cytidine residuces in the DNA to uracil, which is then recognized as DNA damage. When the base pair is repaired, the uridine is replaced by a thymidine. We have demonstrated that AID belongs to a novel class of cytidine deaminases that act exclusively on single stranded DNA. A number of processes in the cell can transiently generate single stranded DNA, and we have shown that it is the process of gene transcription that generates the proper substrate for AID; we have developed biochemical assays with purified protein components that recapitulate the Ig reaction in the test tube. The mechanism by which AID engages and mutagenizes only the transcribed specific gene sequences for antibody production, sparing the rest of the genome where mutations would be dangerous, remains a mystery and an active area of research.

Deaminases in Antiviral Defence

The role of AID and of related deaminases in the innate anti-viral response is a second active area of interest in the lab. We are trying to understand how hypermutation evolved. It turns out that several organisms use hypermutation as a weapon against viruses. We hypothesized that AID was co-opted from an innate anti-viral response and we have recently shown that AID, aside from its role in antibody gene hypermutation is also active in protecting the organism from infection by viruses that cause cancer. For example, when the Ab-MLV retrovirus infects a cell, AID acts by damaging the DNA of the infected cell which then stops proliferating. At the same time, AID-mediated DNA damage results in expression of certain markers on the surface of the damaged cells which target them for clearance. Thus AID expression after viral infection leads to the demise of the infected cell and of the virus that infected it.

Abelson-MLV Infection & response

Illustration by: Brad Rosenberg

Deaminases and VSG Gene Conversion

In vertebrate immune systems, AID deaminates transcribed antibody genes resulting either in hypermutation or in gene conversion, depending on the DNA repair pathway used to repair the uridine lesion. Recent evidence suggests that gene conversion may be the real driving force behind the generation of adaptive immunity in jawless vertebrates, and it is still used to generate antigen receptor diversity in most organisms (cattle, rabbits, sheep etc). Gene conversion is also used by many pathogens to evade immune recognition by diversifying their surface receptors. For instance, surface antigen variation in parasites such as Plasmodium falciparum (the causative agent of malaria) and Trypanosoma brucei (the causative agent of sleeping sickness) is generated by gene conversion between silent cassettes and one expression site. In collaboration with the G. Cross lab, we are very interested in understanding whether targeted gene conversion in these parasites is mediated by ancestral cytidine deaminases. Hence the role of cytidine deamination in gene conversion in parasites is a third area of interest in the lab.