Assistant Professor of Microbiology & Immunology
Ph.D., Albert Einstein College of Medicine

Genomic alterations and the generation of adaptive immunity

Antibodies are polypeptide complexes produced by B-lymphocytes of the immune system that identify and neutralize pathogens, such as bacteria and viruses. Antibodies are comprised of immunoglobulin (Ig) heavy (IgH) and light (IgL) chain polypeptides. Each polypeptide has an N-terminal variable region that facilitates its binding to antigen, whereas the C-terminal constant region of the IgH chain is necessary for downstream effector functions. There are three DNA alteration events that allow mammalian B lymphocytes to achieve enormous antibody diversification: V(D)J recombination, class switch recombination and somatic hypermutation. Developing B cells, in the bone marrow, undergo V(D)J recombination to assemble exons encoding the IgH and IgL variable (V) regions upstream of the corresponding constant region exons. Thereafter, the newly generated B cells migrate to secondary lymphoid organs where they encounter antigens, and are stimulated to further undergo two additional Ig gene alterations, class switch recombination (CSR) and somatic hypermutation (SHM). CSR is a B cell-specific DNA rearrangement reaction that replaces the initial Ig heavy chain constant region gene exon Cmu with other downstream constant region exons so that secondary isotypes (IgG, IgA etc) with different effector functions are generated. SHM, on the other hand, introduces point mutations into V genes at a very high rate, ultimately leading to increased antibody affinity. Although CSR and SHM are distinct processes, they both require transcription through the relevant Ig loci, and activity of the enzyme activation induced cytidine deaminase (AID). Human patients with inactivating mutations in the AID gene suffer from severe immunodeficiency leading to Hyper-IgM syndrome (HIGM2), whereas hyperactivity of AID leads to various B and T cell malignancies.

The discovery of the DNA mutagenic properties of AID has opened up many questions. Four important questions that we wish to pursue are: (a) How is AID predominantly targeted to V genes and switch sequences? (b) What are the mechanisms by which physiological targets of AID are repaired in a mutagenic fashion in B cells? (c) How is AID prevented from acting as a pleiotropic cellular mutagen? and (d) What is the physiological role of AID in non-B cells?

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1. Basu, U.*, Meng, F.L., Keim, C., Grinstein, V., Pefanis, E., Eccleston, J., Zhang, T., Myers, D., Wasserman, C.R., Wesemann, D.R., Januszyk, K., Gregory, R.I., Deng, H., Lima, C.D., Alt. F.W.*. (2011) The RNA Exosome Targets the AID Cytidine Deaminase to Both Strands of Transcribed Duplex DNA Substrates. Cell 144: 353-363. (*corresponding authors)
2. Basu, U., Franklin, A., Schwer, B., Cheng, H-L, Chaudhuri, J. and Alt, F.W. (2009) Regulation of Activation-Induced Cytidine Deaminse DNA Deamination Activity in B cell by Serine-38 phosphorylation. Biochem. Soc. Trans. 37: 561-568.
3. Cheng, H.L., Vuong, B., Basu, U., Franklin, A., Schwer, B., Phan, R., Datta, A., Manis, J., Alt, F.W. and Chaudhuri, J. (2009) Integrity of the AID Serine-38 Phosphorylation Site is Critical for Class Switch Recombination and Somatic Hypermutation in Mice. Proc. Natl. Acad. Sci. U.S.A. 106: 2717-2722.
4. Basu, U., Franklin, A. and Alt, F.W. Post-translational regulation of activation induced deaminase. (2009) Philosophical Transactions of the Royal Society of Sciences 364: 667-673.
5. Basu, U., Wang, Y., Alt, F.W. (2008) Evolution of phosphorylation-dependent regulation of Activation Induced cytidine Deaminase. Molecular Cell 32: 285-291.
6. Chaudhuri, J., Basu, U., Zarrin, A., Yan, C., Franco, S., Perlot, T., Vuong, B., Wang, J., Phan, R.T., Datta, A., Manis, J., and Alt, F.W. (2007) Evolution of the Immunoglobin Heavy Chain Class Switch Recombination Mechanism. Advances in Immunology 94: 157-214.
7. Basu, U., Chaudhuri, J., Phan, R.T., Datta, A. and Alt, F.W. (2007) Regulation of activation induced deaminase via phosphorylation In: Mechanisms of Lymphocyte Activation and Immune Regulation XI, Gupta, S., Cooper, M., Rajewsky, K., Alt, F.W., Melchers, F., Eds. New York, Springer, 129-137.
8. Longerich, S., Basu, U., Alt, F.W. and Storb, U. (2006) AID in somatic hypermutation and class switch recombination. Curr. Op. In Immunology 18: 1-11.
9. Basu, U., Chaudhuri, J., Alpert, C., Dutt, S., Rangananth, S., Li, G., Schrum, J.P., Manis, J.P. and Alt, F.W. (2005) The AID antibody diversification enzme is regulated by protein kinase A phosphorylation. Nature 438: 508-511.