Zhaoqing Ba, Ph.D.

Assistant Professor, TIMBR, Assistant Investigator, NIBS, Beijing, China

Education

2013    Ph.D. in Biochemistry and Molecular Biology, National Institute of Biological Science (TIMBR/NIBS), Beijing & Beijing Normal University, Beijing, China

2008    B.S. in Biotechnology (National Base of Life Science & Biotechnology Education Program), Jiangnan University, Wuxi, Jiangsu, China

Experience

2021-    Assistant Professor, TIMBR, Assistant Investigator, NIBS, Beijing, China

2019-2021    Instructor/Research Associate, Harvard Medical School/Boston Children’s Hospital, Boston, USA

2014-2019    Postdoctoral Research Fellow, Harvard Medical School/Boston Children’s Hospital, Boston, USA

2013-2014    Postdoctoral Research Fellow, Tsinghua University, Beijing, China

Research

As an integral part of adaptive immunity, B lymphocytes play fundamental roles in defensing against infection and illness. During B cell differentiation and antigen activation, extremely diversified antibody repertoires are generated through a highly coordinated spatio-temporal regulation with each B cell expressing a unique antibody, which is pivotal for the immune system to be “adaptable” to the numerous antigens. Moreover, B cells contribute to the establishment of advanced lymphoid structures and are involved in antigen presenting, tissue homeostasis, and immune responses to tumors. B cell dysfunction is associated with various types of diseases including immunodeficiency, autoimmunity, and tumorigenesis. We have devoted major efforts to the development of several innovative high-throughput sequencing-based approaches and addressed the major long-standing enigma of how antibody genes are diversified at the molecular level. We have also developed a rapid mouse model for B-cell lymphomas and provided a new general approach for the generation of genetically complex mouse disease models. In the future, we will continue to develop and employ multidisciplinary state-of-the-art technologies and take multi-scale approaches to further elucidate mechanisms that orchestrate B cell differentiation and function, and antibody diversification, and mechanisms that underlie the related immunological disorders and cancer. Based on the new understanding from the basic research, we will ultimately generate innovative platforms and strategies to develop vaccines and therapeutic antibodies to fight against human diseases.

Publications

(*Equal contribution; #Co-correspondence)

Original Articles

1. Liang, Z.*#, Zhao, L.*, Ye, A.Y.*, Lin, S.G.*, Zhang, Y., Guo, C., Dai, H.Q., Ba, Z.#, Alt, F.W.# (2023). Contribution of the IGCR1 regulatory element and the 3'Igh CTCF-binding elements to regulation of Igh V(D)J recombination. Proc. Natl. Acad. Sci. USA 120(26), e2306564120. doi: 10.1073/pnas.2306564120.

2. Ba, Z.*#, Lou, J.*, Ye, A.Y., Dai, H.-Q., Dring, E.W., Lin, S.G., Jain, S., Kyritsis, N., Kieffer-Kwon, K.-R., Casellas, R.#, and Alt, F.W.# (2020). CTCF orchestrates long-range cohesin-driven V(D)J recombinational scanning. Nature 586, 305–310.

3. Jain, S.*, Ba, Z.*, Zhang, Y., Dai, H.-Q., and Alt, F.W.# (2018). CTCF-Binding Elements Mediate Accessibility of RAG Substrates During Chromatin Scanning. Cell 174, 102-116. (Recommended as ‘Exceptional’ by Faculty of 1000)

4. Lin, S.G.*, Ba, Z.*, Du, Z.*, Zhang, Y., Hu, J.#, and Alt, F.W.# (2016). Highly Sensitive and Unbiased Approach for Elucidating Antibody Repertoires. Proc. Natl. Acad. Sci. USA 113, 7846-7851. (Recommended by Faculty of 1000)

5. Ba, Z.*, Meng, F.-L.*, Gostissa, M.*, Huang, P.-Y., Ke, Q., Wang, Z., Dao, M.N., Fujiwara, Y., Rajewsky, K., Zhang, B.#, and Alt, F.W.# (2015). A Rapid Embryonic Stem Cell-Based Mouse Model for B-cell Lymphomas Driven by Epstein-Barr Virus Protein LMP1. Cancer Immunol. Res. 3, 641-649.

6. Wei, W.*, Ba, Z.*, Gao, M., Wu, Y., Ma, Y., Amiard, S., White, C.I., Rendtlew Danielsen, J.M., Yang, Y.-G., and Qi, Y.# (2012). A Role for Small RNAs in DNA Double-Strand Break Repair. Cell 149, 101-112. (Selected as Best of Cell in 2012, also featured and highlighted in Nat. Rev. Mol. Cell Biol., 2012, Nat. Rev. Gen., 2012, Nat. Struct. & Mol. Biol., 2012, and Faculty of 1000)

7. Dai, H.-Q.*#, Hu, H.*, Lou, J., Ye, A.Y., Ba, Z., Zhang, X., Zhang, Y., Zhao, L., Yoon, H.S., Chapdelaine-Williams, A.M., Kyritsis, N., Chen, H., Johnson, K., Lin, S., Conte, A., Casellas, R., Lee, C.-S.# and Alt, F.W.# (2021). Loop extrusion mediates physiological Igh locus contraction for RAG scanning. Nature 590, 338–343.

8. Chen, H.*, Zhang, Y.*, Ye, A.Y.*, Du, Z., Xu, M., Lee, C.-S., Hwang, J.K., Kyritsis, N., Ba, Z., Neuberg, D., Littman, D.R., and Alt, F.W.# (2020). BCR selection and affinity maturation in Peyer’s patch germinal centres. Nature 582, 421-425.

9. Zhang, X., Zhang, Y., Ba, Z., Kyritsis, N., Casellas, R., and Alt, F.W.# (2019). Fundamental roles of chromatin loop extrusion in antibody class switching. Nature 575, 385-389.

10. Zhang, Y.*, Zhang, X.*, Ba, Z., Liang, Z., Dring, E.W., Hu, H., Lou, J., Kyritsis, N., Zurita, J., Shamim, M.S., Presser Aiden, A., Lieberman Aiden E., and Alt, F.W.# (2019). The fundamental role of chromatin loop extrusion in physiological V(D)J recombination. Nature 573, 600-604.

11. Liu, M., Ba, Z., Costa-Nunes, P., Wei, W., Li, L., Kong, F., Li, Y., Chai, J., Pontes, O., and Qi, Y.# (2017). IDN2 Interacts with RPA and Facilitates DNA Double-Strand Break Repair by Homologous Recombination in Arabidopsis. Plant Cell 29, 589-599.

12. Gao, M.*, Wei, W.*, Li, M.-M.*, Wu, Y.-S.*, Ba, Z., Jin, K.-X., Li, M.-M., Liao, Y.-Q., Adhikari, S., Chong, Z., et al. (2014). Ago2 Facilitates Rad51 Recruitment and DNA Double-Strand Break Repair by Homologous Recombination. Cell Research 24, 532-541. (Featured by “Research Highlight”)

Invited Review and Book Chapter

1. Lin, S.G.*, Ba, Z.*, Alt, F.W.#, and Zhang, Y. (2018). RAG Chromatin Scanning During V(D)JRecombination and Chromatin Loop Extrusion Are Related Processes. Adv. Immunol. 139, 93-135.

2. Ba, Z., and Qi, Y.# (2013). Small RNAs: Emerging Key Players in DNA Double-Strand Break Repair.Science China Life Sciences 56, 933-936.

Patents

1. Alt, F.W., Jain, S., Ba, Z., Tian, M. Methods and compositions relating to high-throughput models for antibody discovery and/or optimization. PCT/US2019/036321. Application filed 2019-06-10.

2. Alt, F.W., Meng, F.-L., Ba, Z., Gostissa, M., Zhang, B., Wei, P.-C., Schwer, B. Methods and compositions relating to an embryonic stem cell-based tumor model. US15/564,647. Application filed 2016-04-07.