Department of Microbiology & Immunology

Columbia University Medical Center
Uttiya Basu, Ph.D.
Associate 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?

Selected Publications

  1. Lim, J., Giri, P.K., Kazadi, D., Laffleur, B., Zhang, W., Grinstein, V., Pefanis, E., Brown, L.M., Ladewig, E., Martin, O., Chen, Y., Rabadan, R., Boyer, F., Rothschild, G., Cogne, M., Pinaud, E., Deng, H. and Basu, U. (2017) Nuclear proximity of Mtr4 to RNA exosome restricts DNA mutational asymmetry. Cell 169: 523-537 e515.
  2. Rialdi, A., Hultquist, J., Jimenez-Morales, D., Peralta, Z., Campisi, L., Fenouil, R., Moshkina, N., Wang, Z.Z., Laffleur, B., Kaake, R.M., McGregor, M.J., Haas, K., Pefanis, E., Albrecht, R.A., Pache, L., Chanda, S., Jen, J., Ochando, J., Byun, M., Basu, U., Garcia-Sastre, A., Krogan, N., van Bakel, H. and Marazzi, I. (2017) The RNA exosome syncs IAV-RNAPII transcription to promote viral ribogenesis and infectivity. Cell 169: 679-692 e614.
  3. Rothschild, G. and Basu, U. (2017) Lingering questions about enhancer RNA and enhancer transcription-coupled genomic instability. Trends Genet. 33: 143-154.
  4. Laffleur, B., Basu, U. and Lim, J. (2017) RNA exosome and non-coding RNA-coupled mechanisms in AID-mediated genomic alterations. J. Mol. Biol. pii: S0022-2836(17)30012-8. doi: 10.1016/j.jmb.2016.12.021. [Epub ahead of print]
  5. Casellas, R., Basu, U., Yewdell, W.T., Chaudhuri, J., Robbiani, D.F. and Di Noia, J.M. (2016) Mutations, kataegis and translocations in B cells: understanding AID promiscuous activity. Nature Rev. Immunol. 16: 164-176.
  6. Sun J., Wang J., Pefanis E., Chao J., Rothschild G., Tachibana I., Chen J., Ivanov I.I., Rabadan R., Takeda Y. and Basu U. (2015) Transcriptomics identify CD9 as a marker of murine IL-10 competent regulatory B cells. Cell Reports 13: 1110-1117.
  7. Rothschild G., Von Krusenstiern, A.N. and Basu U. (2015) Malaria-induced B cell genomic instability. Cell 162: 697-698.
  8. Pefanis E. and Basu U. (2015) RNA exosome regulates AID DNA mutator activity in the B cell genome. Advances in Immunology 127: 257-308.
  9. Pefanis E., Wang J., Rothschild G., Lim J., Kazadi D., Sun J., Federation A., Chao J., Elliot O., Liu Z-P., Economides A., Bradner J.E., Rabadan R. and Basu U. (2015) RNA exosome-regulated long non-coding RNA transcription controls super-enhancer activity. Cell 161: 774-789.
  10. Pefanis, E., Wang, J., Rothschild, G., Lim, J., Chao, J., Rabadan, R., Economides, A.N. and Basu, U. (2014) Noncoding RNA transcription targets AID to divergently transcribed loci in B cells. Nature 514: 389-393.
  11. Chao, J., Rothschild, G. and Basu, U. (2014) Ubiquitination events that regulate recombination of immunoglobulin Loci gene segments. Front. Immunol. 5: 100. doi: 10.3389/fimmu.2014.00100.
  12. Sun, J., Keim, C.D., Wang, J., Kazadi, D., Oliver, P.M., Rabadan, R., and Basu, U. (2013) E3-ubiquitin ligase Nedd4 determines the fate of AID-associated RNA polymerase II in B cells. Genes Dev. 27: 1821-1833.
  13. Sun, J., Rothschild, G., Pefanis, E., and Basu, U. (2013) Transcriptional stalling in B-lymphocytes: A mechanism for antibody diversification and maintenance of genomic integrity. Transcription. 4: 127-135.
  14. Keim, C., Kazadi, D., Rothschild, G. and Basu, U. (2013) Regulation of AID, the B-cell Genome Mutator. Genes Dev. 27: 1-17.
  15. 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. and 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)
  16. Ise, W., Kohyama, M., Schraml, B.U., Zhang, T., Schwer, B., Basu, U., Alt, F.W., Tang, J., Oltz, E.M., Murphy, T.L. and Murphy, K.M. (2011) The transcription factor BATF controls the global regulators of class-switch recombination in both B cells and T cells. Nature Immunology 12: 536-543.
  17. 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.
  18. 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.
  19. 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.
  20. Basu, U., Wang, Y., Alt, F.W. (2008) Evolution of phosphorylation-dependent regulation of Activation Induced cytidine Deaminase. Molecular Cell 32: 285-291.
  21. 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.
  22. 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.
  23. 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.
  24. 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.

Associate Professor Uttiya Basu
Phone: 212-305-1815
Lab Phone: 212-305-3744
Fax: 212-305-1468

Department of Microbiology & Immunology, Columbia University + 701 W. 168 St., HHSC 1208 New York, NY 10032 Tel. 212-305-3647