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Research Overview

Research Overview

We are working at the intersection of genomics and infectious diseases to gain a better understanding of viral pathogenesis and immune cell biology in the context of antiretroviral therapy. Using systems biology tools, we investigate cellular and viral dynamics at the single-cell or single-virus level using various high-throughput sequencing techniques. Our data reveal previously unseen diversities of HSC and T-cell functions compared to population-based studies.

HIV-1 genomics and epitranscriptomics: We develop various genomics and high-throughput sequencing tools to address challenging questions in retroviral pathogenesis at the single-cell and single-virus levels.

  1. Sanggu Kim, Namshin Kim, Angela P. Presson, Mark E. Metzger, Aylin C. Bonifacino, Mary Sehl, Samson A. Chow, Gay M. Crooks, Cynthia E. Dunbar, Dong Sung An, Robert E. Donahue and Irvin S.Y. Chen, “Dynamics of HSPC Repopulation in Non-human Primates Revealed by a Decade-long Clonal-Tracking Study”, 2014, Cell Stem Cell, 14 (4), p419–420. PMID:24702996; PMCID:PMC4009343
  2. Gajendra W. Suryawanshi, Song Xu, Yiming Xie, Tom Chou, Namshin Kim, Irvin S.Y. Chen, and Sanggu Kim*, “Bidirectional Retroviral Integration Site PCR Methodolgy and Quantitative Data Analysis Workflow”, 2017, Journal of Visualized Experiments, 14;(124). doi: 10.3791/55812., PMID: 28654067. *Senior corresponding author
  3. Gajendra W. Suryawanshi; Wannisa Khamaikawin; Jing Wen; Saki Shimizu; Hubert Arokium; Yiming Xie; Eugene Wang; Shihyoung Kim; Hyewon Choi; Chong Zhang; Angela P. Presson; Namshin Kim; Dong-Sung An; Irvin S. Y. Chen; Sanggu Kim*, “The clonal repopulation of HSPC gene-modified with anti-HIV-1 RNAi is not impacted by pre-existing HIV-1 infection”, Science Advances (IF:13.116), 22 Jul 2020: Vol. 6, no. 30, eaay9206; PMID: 32766447. *Senior corresponding author
  4. Gajendra W Suryawanshi, Hubert Arokium, Sanggu Kim, Wannisa Khamaikawin, Samantha Lin, Saki Shimizu, Koollawat Chupradit, YooJin Lee, Yiming Xie, Xin Guan, Vasantika Suryawanshi, Angela P Presson, Dong Sung An, Irvin S Y Chen. Longitudinal clonal tracking in humanized mice reveals sustained polyclonal repopulation of gene-modified human-HSPC despite vector integration bias. +Stem Cell Res Ther. 2021 Oct 7;12(1):528. doi: 10.1186/s13287-021-02601-5. PubMed PMID: 34620229; PubMed Central PMCID: PMC8499514.
  5. Stacia Phillips, Alice Baek, Sanggu Kim, Shuliang Chen, and Li Wu, “Protocol for the generation of HIV-1 genomic RNA with altered levels of N6-methyladenosine (m6A)STAR*Protocols (Cell press), 2022, Aug 10;3(3):101616. doi: 10.1016/j.xpro.2022.101616. eCollection 2022 Sep 16.

Polyclonal hematopoietic reconstitution in HIV-1 and T-cell depletion therapy settings: We investigate hematopoietic stem cell (HSC) and T-cell dynamics using retroviral tagging (cellular barcoding) methods we developed.

  1. Sidhartha Goyal*, Sanggu Kim*, Irvin SY Chen and Tom Chou, “Mechanisms of blood homeostasis: lineage tracking and a neutral model of cell populations in rhesus macaque”, 2015, BMC Biology, 20;13:85, PMCID: PMC4615871. *equal contribution
  2. Song Xu, Sanggu Kim, Irvin SY Chen, and Tom Chou, “Modeling large fluctuations of thousands of clones during hematopoiesis: the role of stem cell self-renewal and bursty progenitor dynamics in rhesus macaque,” 2018, PLoS Computational Biology, 14 (10): e1006489, PMID: 30335762
  3. Shihyoung Kim, Rajni Kant Shukla, Eunsoo Kim,Sophie G. Cressman, Hannah Yu, Alice Baek, Hyewon Choi, Alan Kim, Amit Sharma, Zhirui Wang, Christene A. Huang, John C. Reneau, Prosper N. Boyaka, Namal P. M. Liyanage, and Sanggu Kim* “Comparison of CD3e Antibody and CD3e-sZAP Immunotoxin Treatment in Mice Identifies sZAP as the Main Driver of Vascular LeakageBiomedicines 2022, 10, 1221. *Senior corresponding author
  4. 4. Chi-Ling Chiang; Eileen Hu; Lingqian Chang; Kevan Zapolnik; Xiaokui Mo; Jadwiga Labanowska; Junfeng Shi; Tzyy-Jye doong; Arletta Lozanski; Pearlly Yan; Ralf bundschuh; Logan A. Walker; Daniel Gallegoperez; Wu lu; Meixiao long; Sanggu Kim; Nyla heerema; Gerard lozanski; Jennifer Woyach; John C. Byrd; L. James Lee; Natarajan Muthusamy, “Leukemia Initiating HSCs in Chronic Lymphocytic Leukemia Reveal Clonal leukemogenesis and Differential Drug SensitivityCell Reports, 2022, 40 (3) 19;
  5. Shihyoung Kim, Alice Baek, Rajni Kant Shukla, Sophie G Cressman, Hannah Yu, Sarah Golconda, Hye Won Choi, John C Reneau, Zhirui Wang, Christene A. Huang, Namal P. M. Liyanage and Sanggu Kim*, “CD3e immunotoxin spares CD62Llo effector Tregs and reshapes organ-specific tissue-resident T-cell composition via preferential depletion of CD3ehi T cells.” Frontiers in Immunology, 2022 Oct 26;13:1011190. doi: 10.3389/fimmu.2022.1011190. eCollection 2022. PMID: 36389741. *Senior corresponding author