Role of chromatin topology in antibody somatic hypermutation

Damage to the genome is generally not desirable since it can lead to cancer and other diseases. Consequently, cells have equipped themselves with an arsenal of defense mechanisms to restrict DNA damage. In some cases, however, mutations in the genome are necessary and beneficial for health. One of the best examples of this is the process of somatic hypermutation (SHM) of antibody- encoding genes in B lymphocytes or B cells. SHM alters the shape of the antibodies thereby generating enormous diversity in the antibody repertoire. This diversity ensures that protective antibodies are made against any kind of pathogen or vaccine and is thus the very foundation of a long-term, robust immune response. However, this system is not perfect and SHM can have detrimental consequences. For example, SHM is responsible for generating self-reactive antibodies (autoantibodies) that are directly involved in causing autoimmune diseases like rheumatoid arthritis and Lupus disease. Moreover, the enzyme responsible for SHM, activation induced deaminase (AID), can also occasionally target other genes, including cancer-causing oncogenes, wherein the resulting mutations can drive cancer progression. Thus, B cells have apparently developed the means to targ et SHM to the desired location i.e. the antibody genes, while minimizing the off-target SHM at other genes. This proposal aims to study key aspects of the SHM reaction to gain a deeper understanding of how this critical process works.

Antibodies are the sole basis for all long-term immunity against pathogens and vaccines. Different parts of the antibody are encoded by different DNA fragments that are spread over large genomic distances. To make an antibody, these fragments need to be stitched together, a process called recombination. Moreover, antibody genes must be mutated in order to change the shape of the antibody and allow it to bind different pathogenic targets called antigens. To make all this possible, the DNA must fold in 3-D space to bring all these fragments into proximity where specialised mutational and recombination enzymes can perform their functions. In this grant proposal, we aimed to understand this folding process by studying the 3D architecture of the DNA encoding the antibody genes using specialised cutting edge techniques. We have successfully identified this 3D architecture and made important discoveries regarding how this architectural state is maintained and how it supports the mutation and recombination processes.