Zibo Zhao

I am an Assistant Professor at Northwestern University's Feinberg School of Medicine, where I specialize in the field of epigenetics, metabolism, and human cancers. My research focus is on discovering novel and effective ways of treating cancers with specific mutations, leveraging the concept of synthetic lethality. I have a strong passion for analyzing and visualizing next-generation sequencing data, and I am constantly working towards advancing the understanding of cancer biology through my research.

Experience

Education

Skills

• Cell culture at various scales (dishes and roller bottles) for multiple purposes, including various cancer cell lines, mouse embryonic cells and insect cells.
• Recombinant protein purification, antibody design and antigen purification.
• Large scale protein immunoprecipitation for Mass Spectrometry.
• CRISPR/Cas9 gene editing (knock-out, mutational knock-in and tagging knock-in).
• Genome-wide CRISPR screen including dropout and positive selection with Brenello and GeCKO v2 human libraries and Brie mouse library.
• ChIP-sequencing, RNA-sequencing and ATAC-sequencing.
• Cell cycle, intracellular protein staining, membrane protein labeling and apoptosis analysis with flow cytometry (BD FACS Calibur, BDFACSAria, FlowJo).
• High throughput screening of transcriptional regulators/small molecule inhibitors.
• Xenograft mouse models, IVIS spectrum in vivo imaging, immunohistochemistry (IHC).
• Seahorse live cell metabolic analyses.

• R, Python, Command Line, Git, Excel and VBA scripting
• SQL, MongoDB
• HTML, CSS, JavaScript

Publications

As an Assistant Professor

1. Aileen Szczepanski, Natsumi Tsuboyama, Huijue Lyu, Ping Wang, Oguzhan Beytullahoglu, Te Zhang, Benjamin David Singer, Feng Yue, Zibo Zhao* & Lu Wang A SWI/SNF-dependent transcriptional regulation mediated by POU2AF2/C11orf53 at enhancer. Nat Commun 15, 2067 (2024). https://doi.org/10.1038/s41467-024-46492-5(*co-corresponding author).
2. Zibo Zhao,Yuki Aoi, Cassandra N Philips, Khyati A Meghani, Sarah R Gold, Yanni Yu, Luke St John, Jun Qian, Jacob M Zeidner, Joshua J Meeks, Ali Shilatifard. Somatic mutations of MLL4/COMPASS induce cytoplasmic localization providing molecular insight into cancer prognosis and treatment. Proc Natl Acad Sci U S A. 2023 Dec 26;120(52):e2310063120. doi: 10.1073/pnas.2310063120. Epub 2023 Dec 19.
3. Shapiro JS, Chang HC, Tatekoshi Y, Zhao Z, Waxali ZS, Hong BJ, Chen H, Geier JA, Bartom ET, De Jesus A, Nejad FK, Mahmoodzadeh A, Sato T, Ramos-Alonso L, Romero AM, Martinez-Pastor MT, Jiang SC, Sah-Teli SK, Li L, Bentrem D, Lopaschuk G, Ben-Sahra I, O'Halloran TV, Shilatifard A, Puig S, Bergelson J, Koivunen P, Ardehali H. Iron drives anabolic metabolism through active histone demethylation and mTORC1. Nat Cell Biol. 2023 Oct;25(10):1478-1494. doi: 10.1038/s41556-023-01225-6. Epub 2023 Sep 25.
4. Zibo Zhao, Kaixiang Cao, Jun Watanabe, Cassandra N. Philips, Jacob M. Zeidner, Yukitomo Ishi, Qixuan Wang, Sarah R. Gold, Katherine Junkins, Elizabeth T. Bartom, Feng Yue, Navdeep S. Chandel, Rintaro Hashizume, Issam Ben-Sahra, & Ali Shilatifard. Therapeutic targeting of metabolic vulnerabilities in cancers with MLL3/4-COMPASS epigenetic regulator mutations. J Clin Invest. 2023 Jul 3;133(13):e169993. doi: 10.1172/JCI169993.



As a Postdoctoral Fellow and Research Assistant Professor

5. Aileen Patricia Szczepanski, Natsumi Tsuboyama, Jun Watanabe, Rintaro Hashizume, Zibo Zhao* & Lu Wang. POU2AF2/C11orf53 functions as a coactivator of POU2F3 by maintaining chromatin accessibility and enhancer activity Science Advances. 8, eabq2403 (2022) (*co-corresponding author).
6. Zibo Zhao, Emily Jane Rendleman, Aileen Patricia Szczepanski, Marc alard Morgan, Lu Wang* & Ali Shilatifard*. CARM1-mediated methylation of ASXL2 impairs tumor-suppressive function of MLL3/COMPASS Science Advances. 8, eadd3339 (2022)
7. Natsumi Tsuboyama, Aileen Patricia Szczepanski, Zibo Zhao & Lu Wang. MBD5 and MBD6 stabilize the BAP1 complex and promote BAP1-dependent cancer Genome Biology 23, 206 (2022). https://doi.org/10.1186/s13059-022-02776-x.
8. Natsumi Tsuboyama, Ru Wang, Aileen Patricia Szczepanski, Huanhuan Chen, Zibo Zhao, Lei Shi & Lu Wang. Therapeutic targeting of BAP1/ASXL3 sub-complex in ASCL1-dependent small cell lung cancer. Oncogene. 2022 Feb 22. doi: 10.1038/s41388-022-02240-x.
9. William K M Lai, Luca Mariani, Gerson Rothschild, Edwin R Smith, Bryan J Venters, Thomas R Blanda, Prashant K Kuntala, Kylie Bocklund, Joshua Mairose, Sarah N Dweikat, Katelyn Mistretta, Matthew J Rossi, Daniela James, James T Anderson, Sabrina K Phanor, Wanwei Zhang, Zibo Zhao, Avani P Shah, Katherine Novitzky, Eileen McAnarney, Michael-C Keogh, Ali Shilatifard, Uttiya Basu, Martha L Bulyk, B Franklin Pugh. A ChIP-exo screen of 887 Protein Capture Reagents Program transcription factor antibodies in human cells. Genome Research. 2021 Aug 23.
10. Zibo Zhao*, Aileen Patricia Szczepanski*, Tsuboyama N, Abdala-Valencia H, Goo YA, Singer BD, Bartom ET, Yue F, Wang L. PAX9 determines epigenetic state transition and cell fate in cancer. Cancer Research. 2021 Aug 2;. PubMed PMID: 34341073. (*co-first author).
11. Wang L, Birch NW, Zhao Z, Nestler CM, Kazmer A, Shilati A, Blake A, Ozark PA, Rendleman EJ, Zha D, Ryan CA, Morgan MA, Morgan J, Shilatifard A. Epigenetic targeted therapy of stabilized BAP1 in ASXL1 gain-of-function mutated leukemia. Nature cancer. 2021 May; 2:515-526.
12. Aileen Patricia Szczepanski*, Zibo Zhao*, Tori Sosnowski, Young Ah Goo, Elizabeth Thomas Bartom, Lu Wang. ASXL3 bridges BRD4 to BAP1 complex and governs enhancer activity in small cell lung cancer. Genome Medicine, 12 (1), 1-20. (*co-first author).
13. Delphine Douillet, Christie C Sze, Caila Ryan, Andrea Piunti, Avani P Shah, Michal Ugarenko, Stacy A Marshall, Emily J Rendleman, Didi Zha, Kathryn A Helmin, Zibo Zhao, Kaixiang Cao, Marc A Morgan, Benjamin D Singer, Elizabeth T Bartom, Edwin R Smith, Ali Shilatifard. Uncoupling histone H3K4 trimethylation from developmental gene expression via an equilibrium of COMPASS, Polycomb and DNA methylation. Nature Genetics volume 52, pages 615–625(2020).
14. Zibo Zhao, and Ali Shilatifard. Epigenetic modifications of histones in cancer. Genome Biology, 2019 Nov 20;20(1):245.
15. Zibo Zhao, Lu Wang, Elizabeth Bartom, Stacy Marshall, Emily Rendleman, Caila Ryan, Anthony Shilati, Jeffrey Savas, Navdeep Chandel, Ali Shilatifard. β-Catenin/Tcf7l2 dependent transcriptional regulation of GLUT1 gene expression by Zic family proteins in colon cancer. Science Advances, July 31, 2019. Vol. 5, no. 7, eaax0698. DOI: 10.1126/sciadv.aax0698.
16. Zibo Zhao, Lu Wang, Andrew G. Volk, Noah W. Birch, Kristen L. Stoltz, Elizabeth T. Bartom, Stacy A. Marshall, Emily J. Rendleman, Carson M. Nestler, Joseph Shilati, Gary E. Schiltz, John D. Crispino, and Ali Shilatifard. Regulation of MLL/COMPASS stability through its proteolytic cleavage by taspase1 as a possible approach for clinical therapy of leukemia. Genes & Development, December 20, 2018, doi:10.1101/gad.319830.118.
17. Lu Wang, Patrick A. Ozark, Edwin R. Smith, Zibo Zhao, Stacy A. Marshall, Emily J. Rendleman, Kathryn A. Helmin, Andrea Piunti, Caila Ryan, Anna L. Whelan, Marc Alard Morgan, Lihua Zou, Benjamin D. Singer, and Ali Shilatifard (2018). TET2 coactivates gene expression through demethylation of enhancers. Science Advances, 2018 Nov 7; 4(11):eaau6986.
18. Lu Wang, Zibo Zhao, Patrick Alexander Ozark, Damiano Fantini, Stacy A. Marshall, Emily J. Rendleman, Kira A. Cozzolina, Nundia Louis, Xingyao He, Marc A. Morgan, Yoh-hei Takahashi, Clayton K. Collings, Edwin R. Smith, Panagiotis Ntziachristos, Jeffrey N. Savas, Lihua Zou, Rintaro Hashizume, Joshua J. Meeks, and Ali Shilatifard (2018). Resetting the epigenetic balance of Polycomb/COMPASS function at enhancers for cancer therapy. Nature Medicine. 2018 Jun; 24(6):758-769.
    Highlighted by Cancer Discovery, MLL3 Mutations Disrupt COMPASS Recruitment to Enhancer Chromatin.
    Highlighted by Science Translational Medicine, Correcting COMPASS dysfunction in cancer. Recommended to Faculty of 1000.
19. Damiano Fantini, Alexander Glaser, Kalen Rimar, Yiduo Wang, Matthew Schipma, Nobish Varghese, Alfred Rademaker, Amir Behdad, Aparna Yellapa, Yanni Yu, Christie Sze, Lu Wang, Susan Crawford, Zibo Zhao, Deqing Hu, Jonathan Licht, Clayton Collings, Elizabeth Bartom, Dan Theodorescu, Ali Shilatifard and Joshua Meeks (2018). A Carcinogen-induced Mouse Model Recapitulates the Molecular Alterations of Human Muscle Invasive Bladder Cancer. Oncogene, 2018 Apr; 37(14):1911-1925. doi: 10.1038/s41388-017-0099-6. Epub 2018 Jan 25.
20. Lu Wang, Clayton K. Collings, Zibo Zhao, Kira Alia Cozzolino, Quanhong Ma, Kaiwei Liang, Stacy A. Marshall, Christie C. Sze, Rintaro Hashizume, Jeffrey Nicholas Savas and Ali Shilatifard (2017). A cytoplasmic COMPASS is necessary for cell survival and triple-negative breast cancer pathogenesis by regulating metabolism. Genes & Development, 31(20):2056-2066.



As a PhD Student

21. Zibo Zhao, Lu Wang, Taryn James, Youngeun Jung, Ikyon Kim, Renxiang Tan, F Michael Hoffmann and Wei Xu (2015). Reciprocal regulation of ERα and ERβ stability and activity by Diptoindonesin G. Chemistry & Biology, 22 (12): 1608-1621.
22. Yuzhi An*, Zibo Zhao*, Pengju Ou and Guangchuan Wang (2015). Expression of LRIG1 is associated with good prognosis for human non-small cell lung cancer. Medicine (Baltimore), 94(47):e2081. (*co-first author).
23. Lu Wang, Hao Zeng, Qiang Wang, Zibo Zhao, Thomas G. Boyer, Xiuwu Bian and Wei Xu (2015). MED12 methylation by CARM1 sensitizes human breast cancer cells to chemotherapy drugs. Science Advances, 1:e1500463.
24. David Shlensky, Jennifer Mirrielees, Zibo Zhao, Lu Wang, Aparna Mahajan, Menggang Yu, Nathan Sherer, Lee Wilke and Wei Xu (2015). Differential CARM1 isoform expression in subcellular compartments and among malignant and benign breast tumors. PLoS ONE, 10(6):e0128143.
25. Zibo Zhao, Lu Wang and Wei Xu (2015). IL-13Rα2 mediates PNR-induced migration and metastasis in ERα-negative breast cancer. Oncogene, 34(12): 1596–1607.
26. Lu Wang, Zibo Zhao, Mark Meyer, Sandeep Saha, Menggang Yu, Ailan Guo, Kari Wisinski, Wei Huang, Weibo Cai, Wesley Pike, Ming Yuan, Paul Ahlquist and Wei Xu (2014). CARM1 methylates chromatin remodeling factor BAF155 to enhance tumor progression and metastasis. Cancer Cell, 25(1): 21-36.
    Previewed in Cancer Cell, CARMA: CARM1 Methylation of SWI/SNF in Breast Cancer.
    Recommended to Faculty of 1000.
27. Erin K. Shanle, Zibo Zhao, John Hawse, Kari Wisinski, Sunduz Keles, Ming Yuan and Wei Xu (2013). Research Resource: Global identification of estrogen receptor beta target genes in triple negative breast cancer cells. Molecular Endocrinology, 27(10):1762-1775.
28. Lu Wang, Purin Charoensuksai, Nikole J. Watson, Xing Wang, Zibo Zhao, Carlos G. Coriano, Leslie R. Kerr and Wei Xu (2013). CARM1 automethylation is controlled at the level of alternative splicing. Nucleic Acids Research, 41(14): 6870-6880.
29. Zibo Zhao, Lu Wang, Zhi Wen, Serife Ayaz-guner, Yidan Wang, Paul Ahlquist and Wei Xu (2013). Systematic analyses of the cytotoxic effects of compound 11a, a putative synthetic agonist of photoreceptor-specific nuclear receptor (PNR), in cancer cell lines. PLoS ONE, 8(9): e75198.

Awards & Certifications

• Alex’s Lemonade Stand Foundation Young Investigator Award, ALSF and Northwestern Mutual
• Katten Muchin Rosenman Travel Scholarship, Lurie Cancer Center, Northwestern University
• T32 Training Program in Signal Transduction and Cancer, NIH
• Translational Bridge Program Award, Northwestern University
• National Outstanding Overseas Student Scholarship, Chinese government
• Vilas Conference Presentation funding, University of Wisconsin-Madison
• Academic Achievement Medal and Outstanding Student Award, HKUST
• Edward Wong & Company Limited Scholarship, HKUST
• University Scholarship, HKUST

• BD FACSAria II/BD FACSAria III Operation, BD at San Jose, 08/2016
• Data Scientist with R Track, Datacamp, 04/2020
• Statistician with R Track, Datacamp, 12/2020
• Genomic Data Science Specialization by Johns Hopkins University, Coursera, 09/2020 My certificate
• Data Science & visualization Bootcamp, Northwestern University, 12/2021 My certificate