The Laboratory of Yan Shi
Yan Shi, Ph.D.
1982-1988 Bachelor of Medicine, Shanghai Medical University, China
1992-1998 Ph.D., University of Iowa, Iowa City, USA
1997-2003 University of Massachusetts Medical School, USA Postdoctoral Fellow
2003-2006 Research Assistant Professor, Univ. of Massachusetts Medical School, USA
2006-2010 Assistant Professor, University of Calgary, Canada
2010-2013 Associate Professor, University of Calgary, Canada
2013-present Professor, School of Medicine, Tsinghua University, China
2014-present Professor, Institute for Immunology, Tsinghua University, China
Recognitions and Awards
2006-2011 Canada Research Chair in Immune Regulation
2006-2012 Canadian Heritage Foundation Scholar
2013 Young Investigator Award, Canadian Society for Immunology
Tie (Ted) Xia
2005-09 – 2010-03 Ph.D. in Physics Leiden University, The Netherlands
2003-09 – 2005-08 M.Sc. in Chemistry Utrecht University, The Netherlands
1995-09 – 2000-07 B.Sc. in Medicine Beijing University of Chinese Medicine
2016-09 – now Associate Researcher, School of Medicine, Tsinghua University
2013-05 – 2016-08 Contract Researcher, School of Medicine, Tsinghua University
2010-05 – 2013-04 Postdoc （supervisor：Fang xiaohong）Institute of Chemistry, CAS
2001-12 – 2003-09 Technical support, Pel-Freez Biotechnology (Beijing) Ltd.
2000-12 – 2000-11 Technical support, Beijing PUSRY Biotechnology Ltd.
2010-12 Chinese Academy of Sciences K. C. Wong Post-doctoral Fellowships
1. Understand the entanglement between lipid molecules and receptor proteins on eukaryotic cell membranes and its influence on the cell signaling across the plasma membrane.The classical view of receptor activation on the cell surface is based on ligand-receptor recognition, which is protein-centered. However, a growing body of experimental evidence shows that in the absence of ligand molecules, receptors can be activated autonomously. Such ligand-independent receptor activation usually occurs when the surrounding lipid microenvironment alters, which suggests that lipid molecules play an important role in the process of receptor activation. Therefore, the classical protein-centered receptor activation theory needs to be revised and supplemented, and the involvement of membrane lipids should be considered in order to see a full picture of receptor activation on the cell membrane.
2. Develop and apply biophysical techniques such as single-molecule/cell fluorescence and forces to characterize the dynamics of lipid domains and its influence on the oligomeric status and mobility of receptor proteins on the live-cell membrane.
3. Investigate the dynamics of lipid molecules and protein sorting/partition on the model membrane systems such as supported lipid-bilayer (SBL), giant unilamellar vesicles (GUVs), and giant plasmamembrane vesicles (GPMVs).
• Chen, Jiahuan; Xu, Ying; Shi, Yan; Xia, Tie*; Functionalization of Atomic Force Microscope Cantilevers with Single-T Cells or Single-Particle for Immunological Single-Cell Force Spectroscopy, JOURNAL OF VISUALIZED EXPERIMENTS, 2019, (149): 0-e59609.
• Mu L; Tu Z; Miao L; Ruan H; Kang N; Hei Y; Chen J; Wei W; Gong F; Wang B; Du Y; Ma G; Amerein M W; Xia T*; Shi Y*; A phosphatidylinositol 4,5-bisphosphate redistribution-based sensing mechanism initiates a phagocytosis programing , Nature Communications, 2018, 9(1): 0-4259.
• Xia T.; Li N.; Fang X. H. ; Single-Molecule Fluorescence Imaging in Living Cells , Annual Review of Physical Chemistry, Vol 64, 2013, 64: 459-480.
• Xia, T, N. Li, and X. Fang*；Conformational dynamics of an ATP-binding DNA aptamer: A single molecule study. J. Phys. Chem. B 2013, 117, 14994–15003
• Chapter: Other Modern methods for Studying Biomembrane, Mathhias Amrein*, Tie Xia, Yan Shi* Membrane Biophysics pp 393-421, Edit by Hongda Wang, Guohui Li, Springer, 2018, ISBN:978-981-10-6822-5
Link for a full list of publications：
I received my PhD from Institute of Chemistry Chinese Academy of Sciences in July 2017. Then I came to Shilab for postdoctoral training on the recommendation of my supervisor. My research interests focus on membrane biophysical properties, cell membrane structure and receptor signal transduction, super resolution fluorescence imaging, and single molecule fluorescence imaging.
Yanni Xu got her BSc in Biology from Northwest A&F University at 2011. After that, she started her MD-PhD track in Northwest A&F University and Center for Excellence in Molecular Cell Science, CAS (Joint-PhD program) and was focused on the oncolytic virotherapy of pancreatic cancer. In April 2019, Dr. Xu joined Professor Shi’s lab as a postdoctoral researcher. Now, her research interest is the perception of signals by immune receptors, such as TNFR1 and TCR. She wants to do impressive researches which are important to human welfare.
Rui Yu obtained her Ph. D. degree in China Agricultural University and focused on the immunoregulatory effect of Bifidobacterium adolescentis strains. She joined Shi lab as postdoctoral fellow in 2020 and studied on memory T cells development machenisms.
I'm a postdoctoral researcher at Shi lab. I got my master degree at Beijing Forestry University, and Ph.D degree at Sorbonne University. Currently, my research focuses on the origin of adaptive immune system and its early evolution. The main purpose of this topic is to use some methods of comparative immunology and evolutionary biology to retrospect how the components of the adaptive immune system of higher vertebrates, especially humans, have evolved from the initial simple state to today's complex and fine state in the long evolutionary history.
Xiaobo Wang obtained his bachelor's degree from Inner Mongolia University. In 2016, he entered into Institute for Immunology Tsinghua University and started his PhD trip in Professor Yan Shi's group. Here, he focused on research on mechanisms of the suppressive function Regulatory T cell from the view of calcium signaling based on Atomic Force Microscope.
Huiyun Lv, Ph. D student in CLS from 2016, Bachelor’s degree from Nanchang University. Research Focus: Calcium influx induced nuclear import of NFAT regulate Treg stability
Ying Xu，Ph. D student (from 2016) in School of Medicine, Bachelor’s degree from Beijing Forestry University, research focus: inhibitory Mechanism of Clec12a during MSU-induced dendritic cell activation
Nuerdida Nuerbulati, Ph. D student (from 2018) in the School of Medicine,Tsinghua University. Bachelor’s degree from Peking University Health Science Center. Research focus : Human Treg biology and calcium channels.
Di Zhai，Ph. D student (from 2017) in School of Medicine. Master’s degree from Peking Union Medical College.
Mingke Zheng, Ph. D student in school of medicine, Bachelor’s degree from Yantai University, master’s degree from Henan University, research focus: Pseudomonas aeruginosa quorum-sensing molecular and host defense.
Xin Wang, Ph.D student (from 2018) in CLS, Bachelor's degree from Shandong University, research focus: lipid rafts and membrane receptor activation.
Xinyi Liu, Ph.D student (from 2019) in School of Medicine, Bachelor’s degree from Shandong University, research focus: Treg function mechanism.
Xun Xu, received bachelor's degree from Sichuan University.
Chunlin Zou，Ph. D student (from 2020) in CLS, Bachelor’s degree from Tianjin University.
Xinrong Song, Ph.D student of grade 2020, received her Bachelor's degree from Northwest A&F University. Research focus: Regulatory T cells. Hobbies: Table tennis and photography.
Jialin Li，Ph. D student (from 2020) in School of Medicine, Bachelor‘s degree from Jilin university
Ze Zhang, student from medical experimental class of 2017.
Detailed Research Summary
Area 1. Biophysics and membrane dynamics in immunology
a. Regulatory T cell-mediated dendritic cell paralysis via membrane binding
Dendritic cells (DC) are targeted by regulatory T (Treg) cells, in a manner that operates as an indirect mode of T cell suppression. Using a combination of single-cell force spectroscopy and structured illumination microscopy, we analyze individual Treg cell-DC interaction events and show that Treg cells exhibit strong intrinsic adhesiveness to DCs. This increased DC adhesion reduces the ability of contacted DCs to engage other antigen-specific cells. We show that this unusually strong LFA-1-dependent adhesiveness of Treg cells is caused in part by their low calpain activities, which normally release integrin–cytoskeleton linkage, and thereby reduce adhesion. Super resolution imaging reveals that such Treg cell adhesion causes sequestration of Fascin-1, an actin-bundling protein essential for immunological synapse formation, and skews Fascin-1-dependent actin polarization in DCs toward the Treg cell adhesion zone. Although it is reversible upon Treg cell disengagement, this sequestration of essential cytoskeletal components causes a lethargic state of DCs, leading to reduced T cell priming. Our results reveal a dynamic cytoskeletal component underlying Treg cell-mediated DC suppression in a contact-dependent manner.
We plan to continue to expand on a key aspect of Treg contact-dependent suppression: reduced calpain activity. Tregs bind to DCs tightly, unlike regular T cells which release their binding partners in due course. During the release phase of cellular binding, the main effector protease is m-Calpain. We have identified a key regulator of Ca2+ signaling for m-Calpain in Tregs. This signal fully controls the suppressive activity of Tregs, and remarkably is under the tight control of FoxP3 transcription factor. We have fully established the essential role of this Ca2+ regulator in Treg functions via a series of biophysical, biochemical, imaging, and genetic analyses. We are currently testing several mouse models with deficiency in or unsuppressible expression of this molecule. These studies may eventually reveal a fundamental factor in the Treg-mediated physical suppression of DC activation.
b. ERM proteins as a primordial and universal adaptor in membrane sensing of solid particles
Traditionally, phagocytosis has been regarded as a receptor mediated event. This notion however is evolutionarily difficult to reconcile. Receptor expression is an event occurs in complex organisms such as multicellular life forms. Phagocytosis as the means of energy uptake, started at the eukaryogenesis 2 billion years ago. In addition, because modern day phagocytes can take up most solid structures, some of them came after the industrial revolution (such as latex beads and hydrocarbon particles), and by definition should not have pre-formed receptors. In addition, a host genome cannot encode so many different membrane molecules to recognize large variations of phagocytic targets.
Our previous studies show that lipid redistribution upregulates a phagocytic program recapitulating FcR-based phagocytosis with complete dependence on Src family kinases, Syk, and phosphoinositide 3-kinases (PI3K). We reported recently that in phagocytes, an atypical ITAM sequence in the ancient membrane anchor protein Moesin transduces signal without receptor activation. Plasma membrane deformation created by solid structure binding generates phosphatidylinositol 4,5-bisphosphate (PIP2) accumulation at the contact site, which binds the Moesin FERM domain and relocalizes Syk to the membrane via the ITAM motif. Phylogenic analysis traces this signaling using PI3K and Syk to 0.8 billion years ago, earlier than immune receptor signaling. The proposed general model of solid structure phagocytosis implies a preexisting lipid redistribution-based activation platform collecting intracellular signaling components for the emergence of immune receptors.
c. Membrane lipid domain stability and immune signaling
Lipid domains are an important part of eukaryotic cell membrane and have been implicated in essentially all the cell surface receptor signaling. How this structure is targeted by microbial factors is unknown. Bacterial quorum sensing autoinducers are small chemicals released to control microbial community behaviors. N-(3-oxo-dodecanoyl) homoserine lactone (3oc), the autoinducer of aeruginosaLasI/R circuitry, triggers significant cell death in lymphocytes. We found that this molecule is incorporated into mammalian plasma membrane and induces dissolution of eukaryotic lipid domains. This event expels TNFR1 into the disordered lipid phase for its spontaneous trimerization without its ligand, and drives caspase3/caspase8-mediated apoptosis. In vivo, P. aeruginosareleases 3oc to suppress host immunity for its own better survival; conversely, blockage of caspases strongly reduces the severity of the infection. This work reveals an unknown communication method between microbes and mammalian host, and suggests interventions of bacterial infections by intercepting quorum sensing signaling.
Area 2. Gut dendritic cells shape secondary lymphoid organs
Lymphocyte homing to draining lymph nodes is critical for the initiation of immune responses. Germ-free mice have normal bone marrow and thymic output, yet their secondary lymphoid organs, including peripheral lymph nodes, are underdeveloped. How gut commensal microbes remotely regulate cellularity and volume of secondary lymphoid organs (SLO) remains unknown. We have found that driven by commensal fungi, a wave of CD45+CD103+ RALDH+ cells migrates to the peripheral lymph nodes after birth. The arrival of these cells introduces high amounts of retinoic acid, mediates the neonatal to adult addressin switch on endothelial cells, and directs the homing of lymphocytes to both gut-associated lymphoid tissues and peripheral lymph nodes. In adult mice, a small number of these RALDH+ cells might serve to maintain the volume of secondary lymphoid organs.
The key missing link in the published study above is the regulatory factor in the commensal fungi that drives lymphoid development. With a sequential fractions of a fungal extracts containing thousands of individual lipid species, we have identified a group of fungal lipids that have the ability to activate several host hormone receptors. These lipids and their host receptors are critically needed for the CD45+CD103+ RALDH+ cell migration to the peripheral lymph nodes. These lipids exert strong effects on several key immune regulations. This work, arguably for the first time, uses direct molecular isolation to identify a group of previously unknown microbial molecules that interact with host immune system with clearly defined receptors. This approach should pave the way for the focus switch from the microbial species-confined observations to molecularly definitive receptor-ligand interactions that lie underneath the broad spectrum of host/commensal interactions.
1. Tong D, Zhang L, Ning F, Xu Y, Hu X, Shi Y*. Contact-dependent delivery of IL-2 by dendritic cells to CD4 T cells in the contraction phase promotes their long-term survival. Protein Cell. 2020 11(2):108-123
2. Zhou X, Zhao S, He Y, Geng S, Shi Y* and Wang B*. Precise spatio-temporal interruption of regulatory T cell-mediated CD8+ T cell suppression leads to tumor immunity. Cancer Res. 2019 79(3):585-597）
3. Song D, Meng J, Cheng J, Fan Z, Chen P, Ruan H, Tu Z, Kang N, Li N, Xu Y, Wang X, Shu F, Mu L , Li T, Ren W, Lin X, Zhu J , Fang X, Matthias W. Amrein, Wu W, Yan L, Lü J, Xia T* and Shi Y*. Pseudomonas aeruginosa quorum-sensing metabolite induces host immune cell death through cell surface lipid domain dissolution. Nat Microbiol. 2019 4(1):97-111
4. Yu W, Geng S, Suo Y, Wei X, Cai Q, Wu B, Zhou X, Shi Y*, and Wang B* Critical role of regulatory T cells in the latency and stress-induced reactivation of HSV-1. Cell Rep. 2018 ;25(9):2379-2389.e3
5. Mu L, Tu Z, Miao L, Ruan H, Kang N, Hei Y, Chen J, Wei W, Gong F, Wang B, Du Y, Ma G, Amerein MW, Xia T*, Shi Y*. A phosphatidylinositol 4,5-bisphosphate redistribution-based sensing mechanism initiates a phagocytosis programing. Nat Commun. 2018 9(1):4259.
6. Zhang Y, Rong H, Zhang FX, Wu K, Mu L, Meng J, Xiao B, Zamponi GW, Shi Y*. A Membrane Potential- and Calpain-Dependent Reversal of Caspase-1 Inhibition Regulates Canonical NLRP3 Inflammasome. Cell Rep. 2018 24(9):2356-69 e5.
7. Xia Y, Xie Y, Yu Z, Xiao H, Jiang G, Zhou X, Yang Y, Li X, Zhao M, Li L, Zheng M, Han S, Zong Z, Meng X, Deng H, Ye H, Fa Y, Wu H, Oldfield E, Hu X, Liu W*, Shi Y*, Zhang Y*. The Mevalonate Pathway Is a Druggable Target for Vaccine Adjuvant Discovery. Cell. 2018 175(4):1059-1073
9.Shu F, Chen J, Ma X, Fan Y, Yu L, Zheng W, Amrein MW, Xia T, Shi Y*. Cholesterol Crystal-Mediated Inflammation Is Driven by Plasma Membrane Destabilization. Front Immunol. 2018;9:1163.
10. Chen J, Ganguly A, Mucsi AD, Meng J, Yan J, Detampel P, Munro F, Zhang Z, Wu M, Hari A, Stenner MD, Zheng W, Kubes P, Xia T, Amrein MW, Qi H, Shi Y*. Strong adhesion by regulatory T cells induces dendritic cell cytoskeletal polarization and contact-dependent lethargy. J Exp Med. 2017 Feb;214(2):327-38.
11. Zhang Z, Li J, Zheng W, Zhao G, Zhang H, Wang X, Guo Y, Qin C, Shi Y*. Peripheral Lymphoid Volume Expansion and Maintenance Are Controlled by Gut Microbiota via RALDH+ Dendritic Cells. Immunity. 2016 Feb 16;44(2):330-42.
12. Flach TL, Ng G, Hari A, Desrosiers MD, Zhang P, Ward SM, Seamone ME, Vilaysane A, Mucsi AD, Fong Y, Prenner E, Ling CC, Tschopp J, Muruve DA, Amrein MW, Shi Y*. Alum interaction with dendritic cell membrane lipids is essential for its adjuvanticity. Nat Med, 2011 7(4):479-87.
13. Ng G, Sharma K, Ward SM, Desrosiers MD, Stephens LA, Schoel WM, Li T, Lowell CA, Ling C-C, Amrein MW, Shi Y*. Receptor-independent, direct membrane cholesterol binding leads to cell surface lipid sorting and dendritic cell activation. Immunity,2008 Nov 29:807-818.
14. Shi Y, Evans JE, Rock KL. Molecular identification of a danger signal that alerts the immune system to dying cells. Nature, 2003 425:516-521,.
Copyright © 2017 Institute for Immunology Tsinghua University
Contact Address: Room D302, Medical Science Building, Tsinghua University, Beijing 100084, China
Tel: (86) 10-62776420 Fax: (86) 10-62776420