Shan Zha, M.D., Ph.D.

James A. Wolff Professor of Pediatrics, Pathology & Cell Biology and Microbiology & Immunology
M.D., Ph.D., Peking University, Johns Hopkins University

The molecular mechanisms of DNA damage response and their roles in lymphocyte gene-rearrangement

Research
The diversity and specificity of the adaptive immune system is achieved through somatic assembly and subsequent modification of antigen receptor genes in developing lymphocytes. Specifically, functional immunoglobulin and T cell receptor genes are assembled from germline variable, diversity and joining gene fragments through V(D)J recombination. In peripheral lymphoid organs, the immunoglobulin heavy chain gene is further modified through class switch recombination to achieve different effector functions. While V(D)J recombination and class switch recombination are initiated by a lymphocyte-specific cleavage mechanism, the repair of DNA double-strand break intermediates is mediated by the ubiquitously expressed non-homologous end-joining pathway. Moreover, like other DNA damage events, physiological DNA breaks activate DNA damage responses to enforce cell cycle arrest and achieve efficient and precise repair. Not surprisingly, defects in the DNA repair pathways can block lymphocyte development, leading to congenital primary immunodeficiency. Reducing the fidelity of DNA repair increases the risk of chromosomal translocations that can cause leukemia and lymphoma. The clinical treatment of human lymphomas and leukemias often induces additional DNA damage, which needs to be repaired by the non-homologous end-joining pathway with the help of DNA damage response factors. Therefore, elucidating the cellular pathways that mediate DNA repair, understanding their molecular mechanisms of action, and evaluating their in vivo functions in animal models will yield critical information for the clinical management of both immunodeficiencies and lymphoid malignancies.

Our research is focused on understanding the fundamental mechanisms by which cells respond to DNA damage, especially DNA double-strand breaks, and how these responses impact normal lymphocyte development, lymphomagenesis, and cancer therapy. We have developed over 20 new animal models to study the molecular regulation of DNA double-strand break repair, especially the mechanism of non-homologous end-joining (NHEJ) and its interaction with DNA damage response orchestrated primarily by three PI3 kinase-related protein kinases (PI3KKs): ATM, DNA-PK, and ATR. In this context, we have characterized the mouse model for three new NHEJ factors, established a series of mouse models expressing the kinase-dead forms of ATM, ATR and DNA-PKcs, uncovered critical structural functions of the kinases in DNA repair, and highlighted the clear difference between kinase deletion vs kinase inhibition, with implication for the development and use of specific kinase inhibitors.

Some ongoing projects include: (1) ascertaining how the PI3 kinase-related protein kinases implicated in DNA repair, namely ATM, DNA-PKcs, and ATR, are regulated by phosphorylation; (2) identifying new NHEJ factors and their roles in primary immunodeficiency; (3) dissecting how chromatin-bound DNA damage response factors promote chromosomal end-ligation and limit end-resection and chromosomal translocations; (4) elucidating the mechanisms by which pathogenic chromosome translocations elicit human lymphoid malignancies, and generating new mouse models of these diseases; (5) understanding PARylation-dependent regulation of poly-[ADP-ribose] polymerases (PARPs) during DNA repair; and (6) the metabolic impact and regulation of DNA damage response.

Selected Publications

1. Langelier, M.F., Lin, X., Zha, S. and Pascal, J. M. (2023) Clinical PARP inhibitors allosterically induce PARP2 retention on DNA. Science Adv. 9: eadf7175. https://doi.org/10.1126/sciadv.adf7175

2. Zagelbaum, J., Schooley, A., Zhao, J., Schrank, B.R., Callen, E., Zha, S., Gottesman, M.E., Nussenzweig, A., Rabadan, R., Dekker, J. and Gautier, J. (2023) Multiscale reorganization of the genome following DNA damage facilitates chromosome translocations via nuclear actin polymerization. Nature Struct. Mol. Biol. 30: 99–106. https://doi.org/10.1038/s41594-022-00893-6

3. Lin, X., Jiang, W., Rudolph, J., Lee, B.J., Luger, K. and Zha, S. (2022) PARP inhibitors trap PARP2 and alter the mode of recruitment of PARP2 at DNA damage sites. Nucleic Acids Res. 50: 3958–3973. https://doi.org/10.1093/nar/gkac188

4. Wang, X.S., Menolfi, D., Wu-Baer, F., Fangazio, M., Meyer, S.N., Shao, Z., Wang, Y., Zhu, Y., Lee, B.J., Estes, V.M., Cupo, O.M., Gautier, J., Pasqualucci, L., Dalla-Favera, R., Baer, R. and Zha, S. (2021) DNA damage-induced phosphorylation of CtIP at a conserved ATM/ATR site T855 promotes lymphomagenesis in mice. Proc. Natl. Acad. Sci. U.S.A. 118: e2105440118. https://doi.org/10.1073/pnas.2105440118

5. Milanovic, M., Shao, Z., Estes, V.M., Wang, X.S., Menolfi, D., Lin, X., Lee, B.J., Xu, J., Cupo, O.M., Wang, D. and Zha, S. (2021) FATC domain deletion compromises ATM protein stability, blocks lymphocyte development, and promotes lymphomagenesis. J. Immunol. 206: 1228–1239. https://doi.org/10.4049/jimmunol.2000967

6. Milanovic, M., Houghton, L.M., Menolfi, D., Lee, J.H., Yamamoto, K., Li, Y., Lee, B.J., Xu, J., Estes, V.M., Wang, D., Mckinnon, P.J., Paull, T.T. and Zha, S. (2021) The cancer-associated ATM R3008H mutation reveals the link between ATM activation and its exchange. Cancer Res. 81: 426–437. https://doi.org/10.1158/0008-5472.CAN-20-2447

7. Wang, X.S., Zhao, J., Wu-Baer, F., Shao, Z., Lee, B.J., Cupo, O.M., Rabadan, R., Gautier, J., Baer, R. and Zha, S. (2020) CtIP-mediated DNA resection is dispensable for IgH class switch recombination by alternative end-joining. Proc. Natl. Acad. Sci. U.S.A. 117: 25700–25711. https://doi.org/10.1073/pnas.2010972117

8. Crowe, J.L., Wang, X.S., Shao, Z., Lee, B.J., Estes, V.M. and Zha, S. (2020) DNA-PKcs phosphorylation at the T2609 cluster alters the repair pathway choice during immunoglobulin class switch recombination. Proc. Natl. Acad. Sci. U.S.A. 117: 22953–22961. https://doi.org/10.1073/pnas.2007455117

9. Shao, Z., Flynn, R.A., Crowe, J.L., Zhu, Y., Liang, J., Jiang, W., Aryan, F., Aoude, P., Bertozzi, C.R., Estes, V.M., Lee, B.J., Bhagat, G., Zha, S. and Calo, E. (2020) DNA-PKcs has KU-dependent function in rRNA processing and haematopoiesis. Nature 579: 291–296. https://doi.org/10.1038/s41586-020-2041-2

10. Jiang, W., Estes, V.M., Wang, X.S., Shao, Z., Lee, B.J., Lin, X., Crowe, J.L. and Zha, S. (2019) Phosphorylation at S2053 in murine (S2056 in human) DNA-PKcs is dispensable for lymphocyte development and class switch recombination. J. Immunol. 203: 178–187. https://doi.org/10.4049/jimmunol.1801657

11. Liu X., Wang X.S.,  Lee B.J., Wu-Baer F.K., Lin X., Shao S., Estes V.M., Gautier J., Baer R.J., and Zha S. (2019) CtIP is essential for early B cell proliferation and development in mice. J. Exp. Med. 216: 1648-1663. doi: 10.1084/jem.20181139. Epub 2019 May 16. PMID:31097467

12. Menolfi, D., Jiang W., Lee B.J., Moiseeva T., Shao Z., Estes V., Frattini M.G., Bakkenist C.J. and Zha S. (2018) ATR inhibition differs from ATR loss by limiting the dynamic exchange of ATR and RPA on ssDNA filaments. Nature Communication 9: 5351. doi: 10.1038/s41467-018-07798-3. PMID: 30559436

13. Crowe J.L., Shao Z., Wang X.S., Wei P.C., Jiang W., Lee B.J., Estes V.M., Alt F.W. and Zha S. (2018) Kinase-dependent structural role of DNA-PKcs during immunoglobulin class switch recombination. Proc. Natl. Acad. Sci. U.S.A. 115: 8615-8620. doi: 10.1073/pnas.1808490115. Epub 2018 Aug 2.PMID: 30072430

14. Liu X., Shao Z., Jiang W., Lee B.J. and Zha S. (2017) PAXX promotes Ku-accumulation at DNA breaks and is essential for end-joining in XLF-deficient mice.  Nature Communication 8: 13816. PMID: 28051062 

15. Yamamoto K., Wang J., Sprinzen L., Xu J., Haddock C.J., Li C., Lee B.J., Loredan D.G., Jiang W., Vindigni A., Wang D., Rabadan R. and Zha S. (2016) Kinase-dead ATM protein is highly oncogenic and can be preferentially targeted by Topo-isomerase I inhibitors. Elife 5: e14709. doi: 10.7554/eLife.14709. PMID: 27304073

16. Jiang W., Crowe J., Liu X., Nakajima S., Wang Y., Li C., Lee B.J., Dubois R.L., Liu C., Yu X., Lan L. and Zha S. (2015) Differential phosphorylation of DNA-PKcs regulates the interplay between end-processing and end-ligation during non-homologous end-joining. Molecular Cell 58: 172-185 PMID:25818648

17. Avagyan S., Churchill M., Yamamoto K., Crowe J.L., Li C., Lee B.J., Zheng T., Mukherjee S. and Zha S. (2014) Hematopoietic stem cell dysfunction underlies the progressive lymphocytopenia in XLF/Cernunnos deficiency. Blood 124: 1622-1625. PMID: 25075129

18. Liu X., Jiang W., Dubois R.L., Yamamoto K., Wolner Z. and Zha S. (2012) Overlapping functions between XLF repair protein and 53BP1 DNA damage response factor in end joining and lymphocyte development. Proc. Natl. Acad. Sci. U.S.A. 109: 3903-3908. PMID:22413262

19. Zha S., Guo C., Boboila C., Oksenych V., Cheng H., Zhang Y., Wesemann D.R., Yuen G., Patel H., Goff  P.H., Dubois R.L. and Alt F.W. (2011) XLF has functional redundancy with ATM and H2AX in non-homologous DNA end-joining. Nature 469: 250-254. PMID:21160472

20. Li G., Alt F.W., Cheng H.L., Brush J.W., Goff P.H., Murphy M.M., Franco S., Zhang Y. and Zha S. (2008) Lymphocyte-specific compensation for XLF/Cernunnos end-joining functions in V(D)J recombination. Mol. Cell. 31: 631-640. PMID:18775323