Research Summary

The Shu lab believes in what Richard Feynman said "If you're not having fun, you are not learning. There's a pleasure in finding things out." Thus, having fun is an essential part of our research life. Our students and postdoc trainees and the PI always find unexpected fun in their biological adventures because we are an interdisciplinary lab, focusing on visualizing inner life of living cells and animals. The cells' inner life is like a glowing beautiful world of Avatar, after we label many proteins in the cell with multicolor fluorescent reporters.

Our research interests span the fields of Physical Biology, Chemical Biology, Structural Biology, Protein Engineering, Cell & Molecular Biology, Developmental Biology, and Drug Discovery. We apply Physics, Chemistry and Engineering to design biological tools for visualizing and manipulating dynamic cell signaling in vivo in order to understand animal development and homeostasis, because dynamical features of signaling are the essence of living organisms. Effector proteins such as proteases and kinases regulate almost every major signaling pathways, and protein-protein interactions (PPIs) define specificity of signal transduction from extracellular cues to the appropriate intracellular effector proteins. We have developed new classes of fluorescent reporters of proteases, kinases, and PPIs. These reporters achieve large dynamic range, high brightness and fast kinetics, in addition being genetically encoded requiring no exogenous cofactor for non-invasive imaging. Our reporters enable robust and rapid imaging of dynamic signaling in living cells and animals with unexpected fun, identifying small molecules that inhibit dysregulated signaling in disease such as cancer. Other biological tools we are developing include: chemogenetic tools for manipulating protein interaction and liquid-liquid phase separation; a genetically encoded photosensitizer for activating caspase and apoptosis signaling and ablating single cells in live animals; singlet oxygen-mediated proximity labeling technologies for identifying weak and transient PPIs by mass spectrometry. We are applying these novel technologies to explore exciting biology and therapeutics. We also collaborate with many biologists and chemists. We have shared our tools by depositing them to not-for-profit organizations, e.g. Addgene, Bloomington Stock Center.

Together let's explore fascinating biology and discover life-saving therapeutics while having fun in the biological adventures!

Research Funding

  • April 1, 2021 - March 31, 2026 - Imaging and manipulating oncoprotein phase separation and compartmentalization , Principal Investigator . Sponsor: NIH, Sponsor Award ID: R01CA258327
  • September 15, 2020 - June 30, 2025 - Modulation and functional characterization of protein condensation in chromatin organization , Co-Principal Investigator . Sponsor: NIH, Sponsor Award ID: U01DK127421
  • June 1, 2019 - May 31, 2024 - Designing a new class of fluorescent reporters for imaging dynamic cell signaling in live animals , Principal Investigator . Sponsor: NIH, Sponsor Award ID: R35GM131766
  • May 4, 2018 - March 31, 2022 - Rational design of fluorescent kinase reporters for visualizing dynamic kinase signaling in vivo , Principal Investigator . Sponsor: NIH, Sponsor Award ID: R01GM127664
  • August 1, 2015 - July 31, 2019 - Rational design of a genetically encoded infrared fluorescent protease reporter , Principal Investigator . Sponsor: NIH, Sponsor Award ID: R01GM115399
  • September 30, 2012 - June 30, 2017 - New principle-based technologies for identifying transient protein interactions , Principal Investigator . Sponsor: NIH, Sponsor Award ID: DP2GM105446

Education

Sichuan University, Chengdu, China, B.S., 2000, Theoretical Physics
Fudan University, Shanghai, China, M.S., 2003, Condensed Matter Physics
University of Oregon, Eugene, OR, Ph.D., 2007, Biophysics
University of California-San Diego, San Diego, CA, Postdoc, 2010, Biochemistry

Honors & Awards

  • 2012
    NIH Director’s New Innovator Award
  • 2018-2020
    Dean’s Apple Award for Excellence in Teaching (UCSF)
  • 2019
    Maximizing Investigators’ Research Award (NIGMS)

Selected Publications

  1. Chan-I Chung, Junjiao Yang, Xiaokun Shu. Chemogenetic Minitool for Dissecting the Roles of Protein Phase Separation. ACS Central Science. 2023 Jul 7.  View on PubMed
  2. Dekker J, Alber F, Aufmkolk S, Beliveau BJ, Bruneau BG, Belmont AS, Bintu L, Boettiger A, Calandrelli R, Disteche CM, Gilbert DM, Gregor T, Hansen AS, Huang B, Huangfu D, Kalhor R, Leslie CS, Li W, Li Y, Ma J, Noble WS, Park PJ, Phillips-Cremins JE, Pollard KS, Rafelski SM, Ren B, Ruan Y, Shav-Tal Y, Shen Y, Shendure J, Shu X, Strambio-De-Castillia C, Vertii A, Zhang H, Zhong S. Spatial and temporal organization of the genome: Current state and future aims of the 4D nucleome project. Mol Cell. 2023 08 03; 83(15):2624-2640.  View on PubMed
  3. Li X, Combs JD, Salaita K, Shu X. Polarized focal adhesion kinase activity within a focal adhesion during cell migration. Nat Chem Biol. 2023 Jun 22.  View on PubMed
  4. Li X, Chung CI, Yang J, Chaudhuri S, Munster PN, Shu X. ATM-SPARK: A GFP phase separation-based activity reporter of ATM. Sci Adv. 2023 03; 9(9):eade3760.  View on PubMed
  5. Yang J, Xiao Y, Lidsky PV, Wu CT, Bonser LR, Peng S, Garcia-Knight MA, Tassetto M, Chung CI, Li X, Nakayama T, Lee IT, Nayak JV, Ghias K, Hargett KL, Shoichet BK, Erle DJ, Jackson PK, Andino R, Shu X. Fluorogenic reporter enables identification of compounds that inhibit SARS-CoV-2. Nat Microbiol. 2023 01; 8(1):121-134.  View on PubMed
  6. Lafaye C, Aumonier S, Torra J, Signor L, von Stetten D, Noirclerc-Savoye M, Shu X, Ruiz-González R, Gotthard G, Royant A, Nonell S. Riboflavin-binding proteins for singlet oxygen production. Photochem Photobiol Sci. 2022 Sep; 21(9):1545-1555.  View on PubMed
  7. Tsz-Leung To, Xiaokun Shu. Chapter 4 Major methods and technologies for assessing cell death. . 2022 Jan 1; 93-118.  View on PubMed
  8. Li X, Lidsky PV, Xiao Y, Wu CT, Garcia-Knight M, Yang J, Nakayama T, Nayak JV, Jackson PK, Andino R, Shu X. Ethacridine inhibits SARS-CoV-2 by inactivating viral particles. PLoS Pathog. 2021 09; 17(9):e1009898.  View on PubMed
  9. Li X, Lidsky P, Xiao Y, Wu CT, GarciaKnight M, Yang J, Nakayama T, Nayak JV, Jackson PK, Andino R, Shu X. Ethacridine inhibits SARS-CoV-2 by inactivating viral particles in cellular models. bioRxiv. 2020 Nov 02.  View on PubMed
  10. Guo WH, Qi X, Yu X, Liu Y, Chung CI, Bai F, Lin X, Lu D, Wang L, Chen J, Su LH, Nomie KJ, Li F, Wang MC, Shu X, Onuchic JN, Woyach JA, Wang ML, Wang J. Enhancing intracellular accumulation and target engagement of PROTACs with reversible covalent chemistry. Nat Commun. 2020 08 26; 11(1):4268.  View on PubMed
  11. Shu X. Imaging dynamic cell signaling in vivo with new classes of fluorescent reporters. Curr Opin Chem Biol. 2020 02; 54:1-9.  View on PubMed
  12. Zhang Q, Schepis A, Huang H, Yang J, Ma W, Torra J, Zhang SQ, Yang L, Wu H, Nonell S, Dong Z, Kornberg TB, Coughlin SR, Shu X. Designing a Green Fluorogenic Protease Reporter by Flipping a Beta Strand of GFP for Imaging Apoptosis in Animals. J Am Chem Soc. 2019 03 20; 141(11):4526-4530.  View on PubMed
  13. Torra J, Lafaye C, Signor L, Aumonier S, Flors C, Shu X, Nonell S, Gotthard G, Royant A. Tailing miniSOG: structural bases of the complex photophysics of a flavin-binding singlet oxygen photosensitizing protein. Sci Rep. 2019 02 20; 9(1):2428.  View on PubMed
  14. Chung CI, Zhang Q, Shu X. Dynamic Imaging of Small Molecule Induced Protein-Protein Interactions in Living Cells with a Fluorophore Phase Transition Based Approach. Anal Chem. 2018 12 18; 90(24):14287-14293.  View on PubMed
  15. Zhang SQ, Huang H, Yang J, Kratochvil HT, Lolicato M, Liu Y, Shu X, Liu L, DeGrado WF. Designed peptides that assemble into cross-α amyloid-like structures. Nat Chem Biol. 2018 09; 14(9):870-875.  View on PubMed
  16. Zhang Q, Zheng YW, Coughlin SR, Shu X. A rapid fluorogenic GPCR-β-arrestin interaction assay. Protein Sci. 2018 04; 27(4):874-879.  View on PubMed
  17. Shao-Qing Zhang, Lijun Liu, Junjiao Yang, Marco Lolicato, Huong Kratochvil, Xiaokun Shu, William F. DeGrado. De Novo Design of Cross-a Amyloid-Like Fibrils with Cellular Activity. Biophysical Journal. 2018 Feb 1; 114(3):410a.  View on PubMed
  18. Zhang Q, Huang H, Zhang L, Wu R, Chung CI, Zhang SQ, Torra J, Schepis A, Coughlin SR, Kornberg TB, Shu X. Visualizing Dynamics of Cell Signaling In Vivo with a Phase Separation-Based Kinase Reporter. Mol Cell. 2018 01 18; 69(2):347.  View on PubMed
  19. Zhang Q, Huang H, Zhang L, Wu R, Chung CI, Zhang SQ, Torra J, Schepis A, Coughlin SR, Kornberg TB, Shu X. Visualizing Dynamics of Cell Signaling In Vivo with a Phase Separation-Based Kinase Reporter. Mol Cell. 2018 01 18; 69(2):334-346.e4.  View on PubMed
  20. To TL, Shu X. Detecting Activity at Different Length Scales: From Subdiffraction to Whole-Animal Activity. Biochemistry. 2017 10 03; 56(39):5163-5164.  View on PubMed

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