Overview
Our bodies have an amazing capacity to respond to a variety of pathogens - including those that we have never been exposed to. Such a feat is driven by a network of immune cells and programmed responses that lead to the development of humoral immunity. The incredible breadth that this system possesses is driven by a microscopic evolutionary process in which B cells rapidly mutate, divide, and are selected for their ability to bind to the offending pathogen. By repeating this cycle a multitude of times, the body can generate a high affinity antibody in a matter of weeks to a completely novel infectious agent.
A key component of this process, in addition to selection, is the process of generating diversity and mutations. Pathways to generating diversity include methods that produce new sequences that are otherwise not present anywhere in the genome (i.e. somatic hypermutation), as well as a templated process involving homologous recombination that duplicates short streches of nucleotides from elsewhere in the genome (i.e. gene conversion).
Somatic Hypermutation
Known canonically as the major driver of mutation in murine (mouse) and human B cells - this process relies on a specialized enzyme known as AID (Activation Induced Cytidine Deaminase) that specifically damages DNA at the antibody locus. This DNA damage is repaired in a variety of error-prone pathways that allow for a multitude of variants (i.e. mutations) to be used as the raw substrate for selection and ultimately, antibody maturation.
Gene Conversion
A pathway of DNA repair that allows a similar - but not identical - sequence to be used as a template for repair of a DNA lesion known as a double strand break (DSB). Use of this similar sequence allows repair of the DSB but in doing so also allows the differences between the sequences to be carried over as part of the repair. These changes are then the introduced mutations to this sequence. This pathway is unique because it is known to be a major contributor to antibody diversity in a multitude of species but is not considered to be a major driver in mice or humans.
Objectives & Methods
My research primarily examines the possibility that gene conversion is a process that is highly active in human and murine B cells. There are many challenges associated with identifying gene conversion events and thus we levy statistical approaches such as Monte Carlo Simulation and Support Vector Machines to identify such events. Experimentally, we levy new transgenic mouse models, CRISPR, next generation sequencing, ATAC-sequencing, and HI-C chromosome capture to evaluate hypotheses associated with such a process in human and murine B cells.
Some of our methods are described in the video below.