Liu Lab

Liu Lab

"The function of the immune system is well-balanced, with one arm defending invading pathogens, and the other arm protecting from self attack. Loss of control can cause disastrous consequences such as the development of autoimmune diseases. My mission is to investigate the molecular events in lymphocytes in both normal and dysregulated states." — Yun-Cai Liu, Ph.D. // Professor
Division of Cellular Biology

Overview

Yun-Cai Liu, Ph.D and his team study the regulation of lymphocyte function by tagging a small peptide ubiquitin to protein targets and the implication of the ubiquitin system in abnormal immune responses such as autoimmune diseases or allergic asthma.

The process of ubiquitin conjugation to a protein substrate is carried out by sequential enzymatic reactions. When a protein is tagged with ubiquitin, it sends a signal for destruction by the garbage disposal machinery inside the cell. Timely removal of harmful or excessive proteins is critical to maintain normal cell function. Dysfunction in this system can result in a disease state such as cancer, or immunological diseases.

Work from Dr. Liu’s team has established that Cbl family of adaptor proteins acts as E3 ubiquitin ligases, which facilitate the transfer of ubiquitin to a specific protein target. More recent work identified that one of this family proteins, Cbl-b, is essential to keep T cells under control. Loss of Cbl-b results in excessive T cell activation, which leads to the attack of self-tissues or organs such as the joints or pancreas, and the development of arthritis and diabetes.

Dr. Liu’s team also discovered that another E3 ubiquitin ligase, Itch, is a critical regulator for the development of a specific subset of T cells, called T cell helper type 2, which are responsible for the production of allergic mediators. Loss of Itch results in abnormal excessive function of these cells, and in the development of allergic asthma. Further understanding of the ubiquitin system may add in designing therapeutic inventions for human diseases such as arthritis, diabetes, and asthma.

From The Lab

Jun 20, 2018

Genetic Deletion of Two Protein-Modifying Enzymes Predisposes Mice to Asthma

Feb 13, 2018 // Immunity

LJI researchers reveal how to undermine immune cell mobilization in allergic inflammation.

Feb 2, 2016 // Science Codex

Sharpin emerges from the pack as a regulator of inflammation

Feb 2, 2016

Sharpin emerges from the pack as a regulator of inflammation

Liu Lab

Publications

Nat Immunol

The E3 ligases Itch and WWP2 cooperate to limit TH2 differentiation by enhancing signaling through the TCR

2018-06
Immunity

E3 ligase VHL promotes group 2 innate lymphoid cell maturation and function via glycolysis inhibition and induction of interleukin-33 receptor

2018-02
Curr Top Microbiol Immunol

Immune regulation by ubiquitin tagging as checkpoint code

2017-01
Zeng P, Ma J, Yang R, Liu YC
Int Immunol

T follicular helper cells, T follicular regulatory cells and autoimmunity

2016-04
Zhu Y, Zhou L, Liu YC
Nat Immunol

SHARPIN controls regulatory T cells by negatively modulating the T cell antigen receptor complex

2016-03
Park Y, Jin HS, Lopez J, Lee J, Liao L, Elly C, Liu YC
Arthritis Rheumatol

Receptor protein tyrosine phosphatase _-mediated enhancement of rheumatoid synovial fibroblast signaling and promotion of arthritis in mice

2016-02
Stanford SM, Svensson MN, Sacchetti C, Pilo CA, Wu DJ, Kiosses WB, Hellvard A, bergum B, Muench GR, Elly C, Liu YC, den…
Immunological Reviews

The E3 ligase itch in immune regulation and beyond

2015-07
Aki D, Zhang W, Liu YC
Immunity

E3 ubiquitin ligase VHL regulates hypoxia-inducible factor-1α to maintain regulatory T cell stability and suppressive capacity

2015-06
Lee JH, Elly C, Park Y, Liu YC
Nature Communications

IL-10-producing intestinal macrophages prevent excessive antibacterial innate immunity by limiting IL-23 synthesis

2015-05
Krause P, Morris V, Greenbaum JA, Park Y, Bjoerheden U, Mikulski Z, Muffley T, Shui JW, Kim G, Cheroutre H, Liu YC,…
Immunity

In vivo RNA interference screens identify regulators of antiviral CD4(+) and CD8(+) T cell differentiation

2014-08
Chen R, Bélanger S, Frederick MA, Li B, Johnston RJ, Xiao N, Liu YC, Sharma S, Peters B, Rao A, Crotty S, Pipkin ME
Nature Immunology

The E3 ubiquitin ligase Itch is required for the differentiation of follicular helper T cells

2014-07
Xiao N, Eto D, Elly C, Peng G, Crotty S, Liu YC
FEBS Letters

Ubiquitin ligase cbl-b acts as a negative regulator in discoidin domain receptor 2 signaling via modulation of its stability

2014-05
Yu J, Zhao H, Zhang Y, Liu YC, Yao L, Li X, Su J
Advances in Immunology

The ubiquitin system in immune regulation

2014-01
Park Y, Jin HS, Aki D, Lee J, Liu YC
Journal of Clinical Investigation

TSC1 regulates the balance between effector and regulatory T cells

2013-12
Park Y, Jin HS, Lopez J, Elly C, Murai M, Kronenberg M, Liu YC
Journal of Clinical Investigation

Itch expression by treg cells controls th2 inflammatory responses

2013-11
Jin HS, Park Y, Elly C, Liu YC
EMBO Molecular Medicine

Usp18 deficient mammary epithelial cells create an antitumour environment driven by hypersensitivity to IFN-λ and elevated secretion of Cxcl10

2013-07
Burkart C, Arimoto K, Tang T, Cong X, Ziao N, Liu YC, Kotenko SV, Ellies LG, Zhang DE
Proceedings of the National Academy of Sciences of the United States of America

Regulation of T cell function by the ubiquitin-specific protease USP9X via modulating the Carma1-Bcl10-Malt1 complex

2013-06
Park Y, Jin HS, Liu YC
Proceedings of the National Academy of Sciences of the United States of America

Neddylation pathway regulates T-cell function by targeting an adaptor protein Shc and a protein kinase Erk signaling

2013-01
Jin HS, Liao L, Park Y, Liu YC
Cell Research

To go or not to go: the "itchy" effect on the destiny of hematopoietic stem cells

2011-08
Aki DC, Liu YC

Principal Investigator

Yun-Cai Liu, Ph.D.

Professor

Dr. Liu is currently a Professor in the Division of Cell Biology at LIAI. Dr. Liu’s research focuses on analyzing signaling molecules in biochemical events that are triggered by receptors on lymphocytes.

Dr. Liu received his Ph.D. in Cell Biology from Gunma University in Japan. Following his doctorate, Dr. Liu did research at the Kirin Brewery Co., Ltd. before coming to LIAI in 1993 for his postdoctoral training. In 1997 he became a research scientist at LIAI, and in 1999 he was appointed to the faculty as an Assistant Professor.

Lab Members

Sarah El Baghdady

Research Tech I

I graduated from the University of East Anglia in England in the summer of 2015 with a BSc in Biomedicine and shortly started an internship at the institute a few months later. I am currently working in Cell Biology in the Liu lab.

I hope to gain more practical experience and through this develop a more specific focus that I can obtain through a PhD.

Shirley Cheung

Intern (non-paid)

Christian Elly

Research Tech IV

Shannon Geels

Lab Assistant

Biosketch:
I am currently in my third year of undergrad at the University of California, San Diego studying towards a bachelor of science in General Biology. In June 2017 I started working as a Lab Assistant for the Liu Lab at the La Jolla Institute for Allergy and Immunology.

Research Focus:
In the Liu Lab I assist with various cell biology experiments and genotype mice. Through this position I hope to gain valuable experience and knowledge that will help me focus my field of interest and further my scientific career.

Jihye Han

Postdoctoral researcher

Biosketch:
I graduated from Korea University in 2009 with a B.S. degree in school of Life Sciences and Biotechnology. I then obtained my Ph.D. in Immunology from Korea University in 2015. I started working as a postdoc in the Liu laboratory at the La Jolla Institute for Allergy and Immunology in February 2016.

Research Focus:
My research projects are focused on the roles of E3 ubiquitin ligases in allergic asthma. I am interested in understanding how loss of E3 ubiquitin ligases can affect lung inflammation and in identifying their specific roles and mechanisms in allergic asthma.

Hyung Seung Jin

Visiting Scientist

Jee Ho Lee, Ph.D.

Instructor

Biosketch:
I received my BS and MS degree in Biology at Yonsei University, South Korea. Then, I had worked as a research scientist at ChoongWae Pharmaceutical Research Institute. I earned PhD degree in Immunology at Purdue University in 2011. I joined in Liu Lab at La Jolla Institute for Allergy and Immunology as a postdoc in 2012 and promoted to the instructor in 2015.

Research Focus:
Our research is focusing on the role of ubiquitin systems in immune cells. Regulatory T cell (Treg) is one of important T cell subsets, which play an important role in immune suppression and tolerance. By utilizing conditional knockout mice and mouse disease models, I am studying the role of E3 ubiquitin ligase or deubiquitinase in Treg development as well as function.

Diana Li

Lab Assistant

Yoon Park

Visiting Scientists

Qingqing Wan

Visiting Graduate Student

Liu Lab

Research Projects

The major focus of research in this laboratory is to analyze the function of signaling molecules in intracellular biochemical events initiated by the T cell receptor (TCR) and cytokine receptors, with particular emphasis on the mechanisms that turn off signal transduction through protein ubiquitination. Ubiquitin (Ub)-dependent proteolysis has been implicated in a variety of cellular processes, including cell-cycle control, signal transduction, transcriptional regulation, DNA repair, receptor down-regulation, antigen presentation, and apoptosis. Abnormalities in the Ub system have been shown to cause pathological responses, including malignant transformation, and several genetic diseases. Ubiquitination of protein substrates involves a cascade of enzymatic reactions: first, Ub, a highly conserved 76-amino acid polypeptide, is activated by Ub-activating enzyme, or E1, leading to a ATP-dependent formation of high energy thiol-ester bond between the C-terminus of Ub and E1; the activated Ub is then transferred to E2s (Ub-conjugating enzymes or Ubcs). Ub-protein ligases, or E3s, are responsible for substrate recognition and for promoting Ub ligation to the substrate. A substrate may be multiply ubiquitinated by sequential linkage of additional Ub molecules to form a poly-Ub chain, which marks the protein substrate for the recognition and consequent degradation by the 26S proteasome. Based on amino acid sequences for E2 binding, E3 ligases are generally classified into two families: RING (really interesting new gene)-type E3 ligases, and HECT (homologous to the E6-associated protein C-terminus)-type E3 ligases. We are currently studying Cbl and Cbl-b RING-type E3s and Itch HECT-type E3.

Although protein ubiquitination has been considered to be a means of garbage disposal, i.e., protein degradation, works from many labs including my own have convincingly demonstrated that it also represents a novel means of protein modification, such as affecting protein-protein interaction, or protein phosphorylation.

Functional analysis of Cbl proteins in T cell activation and tolerance

We originally discovered that Cbl acts as RING-type E3 by recruiting Ubc E2 conjugating enzyme via its RING-finger domain and at the same time, binds to the activated receptor tyrosine kinases via its N-terminal tyrosine kinase binding domain, which results in the Ub transfer from E2 to the substrate (in this case, the tyrosine kinase) and the subsequent downmodulation of the receptor. We then shifted our efforts from biochemical studies to more physiologically relevant analysis using gene-targted T cells. Particularly, we showed that Cbl-b interacts with, and induces Ub conjugation to, the p85 regulatory subunit of PI-3 kinase. More importantly, we showed that ubiquitination of p85 does not lead to its degradation, but affects its association with upstream molecules such as CD28. This study presented a novel concept on protein ubiquitination in the functional modification of protein substrates.

We then focused on the study of an essential role of Cbl-b in T cell anergy induction. The Cbl-b E3 Ub ligase is implicated in setting the activation threshold of mature T cell and in regulating the autoimmune response. However, the exact mechanisms underlying Cbl-b-mediated T cell tolerance were unclear. Here we used mouse models of autoimmune diseases to investigate the effect of Cbl-b deficiency on T cell tolerance induction and the development of autoimmunity. Ablation of Cbl-b resulted in exacerbated diseases, which were accompanied by the hyper-responsiveness and augmented transcriptional activation of Cbl-b-/- T cells. Mechanistically, it was found that loss of Cbl-b resulted in resistance to T cell anergy induction, whereas the other potential tolerance mechanisms like the generation of natural killer T or T regulatory cells, and the peripheral T cell deletion, were relatively normal. Moreover, loss of Cbl-b largely rescued the reduced calcium mobilization of anergic T cells. In conclusion, our results point out a critical role for Cbl-b in regulating the peripheral tolerance by contributing to T cell anergy induction.

The E3 ligase Itch in T cell differentiation

Itch, a novel E3 Ub ligase, is absent in the non-agouti-lethal 18H, or Itchy, mice. These mutated mice develop immunological and inflammatory diseases, including inflammation in the lung and stomach, hyperplasia of lymphoid organs, and constant itching in the skin, suggesting that Itch is involved in the regulation of immune responses. Itch contains an amino-terminal protein kinase C-related C2 domain, four WW protein-interaction domains and carboxy-terminal HECT ligase domain. However, the biological pathways regulated by Itch E3 ligase remained unclear. We proposed that, first, Itch targets protein substrates for degradation through the interaction of the four WW domains; second, Itch regulates signal transduction pathways via the ubiquitination of its protein substrates; and, third, Itch-deficient mice have a dysregulation of protein ubiquitination and of intracellular signal transduction.
We examined the T cell function in Itchy mice and found that Itch-/- T cells display increased cell proliferation and express cell surface activation markers in aging mice. More interestingly, these T cells tend to differentiate into T cell helper type 2 (Th2) cells, with enhanced IL-4 and IL-5 cytokine production in both in vitro and in vivo. Consistent with this notion, there are more IgG1 and IgE antibodies in the sera of Itchy mice. Molecularly, we identified that Jun-B/c-Jun is the target molecule for Itch E3 ligase. Itch-/- T cells have more Jun-B in the nuclear fraction as well as increased Jun-B DNA-binding activity. Since it was previously shown that T cells harboring Jun-B transgene preferentially produce Th2 cytokines, we conclude that Itch regulates T cell differentiation via promoting Jun-B ubiquitination.
Protein ubiquitination has been implicated in the regulation of transforming growth factor (TGF)-β signaling, particularly via the Ub conjugation to and subsequent degradation of, the Smad signaling mediators or their binding proteins. We examined the involvement of Itch in TGF-β signaling, and found that Itch-/- fibroblasts display reduced response to TGF-β treatment. Instead of the proteasome-dependent degradation as previously demonstrated in transient transfection studies, we observed that Itch in fact modulates the interaction between Smad2 and the TGF-β receptor and the subsequent Samd2 phosphorylation. The study points out a novel function of Itch in the regulation of TGF-β signaling via modulating protein-protein interactions.
Although those studies suggest that Itch is important in modulating critical signaling pathways by targeting specific substrates for ubiquitination, the mechanisms by which Itch-induced protein ubiquitination is regulated remain largely unclear. A recent study may shed light on this aspect, in which a MEKK1-JNK-mediated signaling pathway controls the turnover of Jun proteins via the phosphorylation of Itch and its subsequent activation. This new finding distinguishes from previous observations, in that the upstream kinases do not induce the phosphorylation of the substrates, rather they directly modulate the E3 Ub ligases for the substrates.

We continued the study of the regulation of Itch E3 ligase by tyrosine phosphorylation. It was found that Fyn kinase induces the tyrosine phosphorylation of Itch at tyrosine residue 371. Strikingly, unlike JNK-induced serine/threonine phosphorylation, Fyn-mediated tyrosine phosphorylation does not affect Itch ligase activity. Rather, it negatively modulates the association between Itch and its substrate JunB. The results suggest that Itch function is tightly controlled by upstream kinases via counterbalancing serine/threonine vs. tyrosine phosphorylation.