Team:CPU CHINA/Demonstrate
Demonstrate
Abstract
FOXP3 + regulatory T cells (Treg) are a class of T lymphocyte subsets that play an immunosuppressive and regulatory function. The dysfunction of FOXP3 + Treg is closely related to the development of autoimmune diseases, such as rheumatoid arthritis. FOXP3, a transcription factor in Forkhead family, whose functional stability is regulated by post-translational modification enzymes, is a key transcription factor for Treg cells’ specific expression. The ubiquitinase USP7 was able to specifically modify the FOXP3 protein by specific ubiquitination to enhance the functional stability of FOXP3, thereby enhancing the immunosuppressive function of Treg cells.
In our design, first, we designed a SynNotch system that contains a modified Notch protein capable of specifically activating the gene expression of USP7 in inflammatory conditions with the presence of IL17A. USP7 proteins can lead to de-ubiquitination of the FOXP3 protein, so that enhance the stability of FOXP3 protein in the inflammation environment by protecting FOXP3 from degradation via ubiquitination. As a result, Treg cells can maintain their immunosuppressive function. Meantime, we designed a CAR system that enables Treg cells to target CD20+ B lymph Cell specifically to play an immunosuppressive function and thus play an anti-inflammatory effect.
Given our design and purpose, we call the system a Human Engineered Anti-Autoimmune-Disease Regulatory T Cells System (HEAD-Treg).
Introduction and Background
People are exposed to billions of pathogens every day. In the meantime, billions of cells within our body undergo a complicated process from generation, aging to apoptosis, together with injuries and mutations. Our immune system identifies and eliminates the threat within and from outside of our body with precision and efficacy, just like an elaborate network.
In accordance with the Chinese Yin-Yang theory and the western critical thinking, our immune system is under a dynamic equilibrium at all times. The immune network consisting immune organs, immune tissues and immune cells rely on each other and promote each other, which is a both unified and varying state that we call as immune homeostasis, with immune response and immune tolerance as two most critical features. On one hand, immune response helps us get rid of antigens, eradicating harmful factors against human body; while on the other hand, immune tolerance helps us distinguishing the enemies from our own, avoiding any harm from overreaction and indiscriminate destruction. Thus, the immune homeostasis is a prerequisite for our healthy life, once the balance is no longer maintained a series of diseases will occur and physical functions may fail. If immune tolerance shows more potency than immune response, the human body will be in an immune inhibited state, where pathogens and cancer cells are left uncontrolled leading to the onset of severe infection and malignancy. If immune response gains the upper hand over immune tolerance, normal cells will be targeted for elimination leading to diseases we call as autoimmune diseases, for example rheumatoid arthritis (RA), systematic lupus erythromatosis, autoimmune type I diabetes, etc. In this way, finding a way to recover the immune homeostasis becomes an essential strategy in dealing with these two types of diseases.
Figure1. Therapeutic targets and interference strategies of rheumatoid arthritis
An imbalance in immune cell’s function is often found in them. Sometime the immune system cannot recognize the target cell, sometime a certain type of immune cell may proliferate. Thus, remodeling the function of a crucial type of immune cell turns into a key point. Cytotherapy has, therefore, become a rising star against these diseases, with CAR-T and TCR-T as the representatives in this technology. The trick in these therapies lies in transforming T cells with synthetic biology approaches, inserting and expressing artificial genes of chimeric antigen receptor into T cell genome and enabling them to recognize and eradicate target cells precisely. Obviously, such strategy has achieved a certain success. This year, the CAR-T product from Novartis was officially approved by FDA to treat acute lymphoblastic leukemia(ALL) in enfants and young adults, which has shown high efficacy in the treatment of non-solid tumors.
Figure2. The design of CAR-T system
Two subtypes of immune cells are of great significance with respect to the onset of autoimmune diseases like RA, one is the incendiary of inflammation which is called Th17 cell, and one is the firefighter of inflammation which is called regulatory T cell(Treg). In normal human body, the ratio of Th17 to Treg is in a dynamic equilibrium, while in rheumatoid arthritis patients Th17 greatly outnumbers Treg in the focus of a lesion. Inflammatory cytokines secreted by Th17, including IL-17, IL-6, TNF-α, will trigger a cascade of reaction causing severe inflammation locally together with B lymphocytes which may further lead to organ dysfunction and could be fatal.
Figure3. The dynamic balance and mutual transformation between Regulatory T cells and Th17 cells
FOXP3 is the most important transcription factor in Treg, taking part in most of the transcription and expression of Treg structural genes. We can assume that the expression and stability of FOXP3 protein determines the function level of Treg. Under inflammation environment, a series of cytokines, such as IL-6, will activate a ubiquitinase Stub1 which will ubiquitinate FOXP3, thus leading to its deactivation and degradation. Consequently, Treg loses its immune inhibitory function, which is mainly why Treg cannot function properly in RA patients. In this way, how to engineer Treg cell to maintain its FOXP3 stability under inflammation conditions and how to direct Treg to target RA specific inflammatory cells to exert its immune inhibitory function becomes a new strategy against RA.
Figure4. Post-translational modification and interference targets of FOXP3 protein
Mathematical Model Analysis
In different tissues, the proportion of different types of CD4+ lymphocytes, to a large extent, is determined by various cytokines that can induce the differentiation of CD4+ CD45RA+ naive T cells. For example, IL-12 leads to Th1 cells, Il-4 leads to Th2 cells and TGF-β leads to Treg cells. Many studies have also shown that subgroups of helper T cells such as Th1, Th2, Th17, and Treg, which have been differentiated into functional subpopulations, can also be transdifferentiated into other subgroups of helper T cells under the action of certain cytokines. Their original functions may decline if transdifferentiation does not happen in some conditions.
In order to theoretically demonstrate that regulatory T cells are dysfunctional or transdifferentiated in the cell microenvironment of rheumatoid arthritis patients imbued with a large number of inflammatory factors, and to describe the necessity of intervening the corresponding regulatory pathway of Treg cells in the clinical treatment of rheumatoid arthritis, we established the mathematical model of T cell differentiation and transdifferentiation (see more from Model section).
In order to theoretically demonstrate that regulatory T cells are dysfunctional or transdifferentiated in the cell microenvironment of rheumatoid arthritis patients imbued with a large number of inflammatory factors, and to describe the necessity of intervening the corresponding regulatory pathway of Treg cells in the clinical treatment of rheumatoid arthritis, we established the mathematical model of T cell differentiation and transdifferentiation (see more from Model section).
Figure5. The ubiquitination mechanism of FOXP3 in regulatory T cells under inflammatory conditions and our intervention strategy
Syn-Notch System
In order to deal with RA, we need to arm Treg with a sharp spear as well as a solid shield. With no doubt, a solid shield is the premise of survival in a difficult situation. That is why we try to activate a pathway to protect FOXP3 under inflammatory conditions in our design. We choose to focus on USP7, a protein that can promote FOXP3 stability by deubiquitinating FOXP3 specifically. An up-regulation in USP7 expression can result in an enhanced immune inhibitory function of Treg. Thus, we decide to express a SynNotch system in Treg, which can specifically activate the transcription of USP7 after receiving an inflammatory stimulus.
SynNotch, as you can tell from its name, is a synthetic biologically engineered Notch protein. Notch protein is a transmembrane protein, which can be divided into three domains: extracellular domain, transmembrane domain and intracellular domain. There is a cleavage site within its intracellular domain at which the Notch protein will be cleaved under stimulus, releasing its C-terminal peptide from the membrane to bind with a downstream protein and carrying out the signal transduction. Apparently, this is a non-specific signal transduction system. In our SynNotch system, we retain the transmembrane domain as well as its cleavage site, while on the N-terminal we fuse the extracellular domain of IL-17AR with Notch1 so that it can specifically recognize IL-17A, a cytokine secreted by Th17. In this way, our Treg is capable of sensing the presence of IL-17A. The next question is how to enable the protein cleaved by SynNotch to recognize and activate the transcription of USP7. That is where we introduce our next system, the Gal4-UAS system in yeast.
In yeast cells, Gal4 protein can specifically recognize the UAS sequence in its genome. If we attach an artificial transcription factor VP64 to Gal4 and insert UAS sequence before the promoter of target gene, we can presume that the transcription of target gene will be specifically activated. Thus, we add a Gal4-VP64 fusion protein sequence after the cleavage site in SynNotch system, meanwhile we add the UAS sequence before USP7 promoter. Now with the presence of the inflammatory cytokine IL-17A, SynNotch system will be activated and the cleavage will take place. Gal4-VP64 will be freed from cell membrane before entering the cell nucleus and binding with the UAS sequence before USP7 promoter. Then USP7 protein will be expressed and will deubiquitinate FOXP3, stabilizing FOXP3 under inflammation conditions, making it possible for Treg to survive the inflammatory environment and to exert its immune inhibitory function. Above is the shield we equip Treg with.
Figure5. Design of SynNotch system and CAR system
The functioning validation of SynNotch and CAR system
To test SynNotch’s stabilization function on FOXP3 in Treg cells under inflammatory conditions, inflammatory factor IL-6 was added into the culture medium to simulate the microenvironment in RA patients, then western blot and quantitative real-time PCR were performed. Without IL-17A, the expression of FOXP3 was significantly reduced compared to normal one due to the inactivation of SynNotch. However, with the addition of IL-17A, the FOXP3 level was greatly uplifted (Figure 2), indicating that the SynNotch system stabilized FOXP3 in Treg cells with the presence of IL-6.
To explore the effect of IL-17A concentration on the function of SynNotch with the presence of IL-6, various concentrations of IL-17A were given and the expression of USP7 and FOXP3 was tested. With a higher concentration of IL-17A, a higher expression of USP7 and FOXP3 was detected, indicating that the concentration of IL-17A played an important role in the expression level of SynNotch.
Figure2. The SynNotch system stabilizing FOXP3 in Treg under inflammatory conditions
Reference:
1.Roybal KT, Williams JZ, et al. Engineering T Cells with Customized Therapeutic Response Programs Using Synthetic Notch Receptors. Cell 2016. doi: 10.1016/j.cell.2016.09.011.
2.Klebanoff CA, Restifo NP. Customizing Functionality and Payload Delivery for Receptor-Engineered T Cells. Cell 2016. doi: 10.1016/j.cell.2016.09.033.
3.Ellebrecht CT, Bhoj VG, et al. Reengineering chimeric antigen receptor T cells for targeted therapy of autoimmune disease. Science 2016. doi: 10.1126/science.aaf6756.
4.Fransson M, Piras E, et al. CAR/FoxP3-engineered T regulatory cells target the CNS and suppress EAE upon intranasal delivery. J Neuroinflammation. 2012. doi: 10.1186/1742-2094-9-112.
5.MacDonald KG, Hoeppli RE, et al. Alloantigen-specific regulatory T cells generated with a chimeric antigen receptor. J Clin Invest. 2016. doi: 10.1172/JCI82771. Epub 2016 Mar 21.
6.Roybal KT, Rupp LJ. et al. Precision Tumor Recognition by T Cells With Combinatorial Antigen-Sensing Circuits. Cell. 2016. doi: 10.1016/j.cell.2016.01.011.
7.Kononenko AV, Lee NC. et al. Generation of a conditionally self-eliminating HAC gene delivery vector through incorporation of a tTAVP64 expression cassette. Nucleic Acids Res. 2015. doi: 10.1093/nar/gkv124.
8.Müller K, Zurbriggen MD, Weber W. An optogenetic upgrade for the Tet-OFF system. Biotechnol Bioeng. 2015. doi: 10.1002/bit.25562.
9.Khalil DN, Smith EL, et al. The future of cancer treatment: immunomodulation, CARs and combination immunotherapy. Nat Rev Clin Oncol. 2016 May. doi: 10.1038/nrclinonc.2016.25.
10.Chen Z, Barbi J, et al. The ubiquitin ligase Stub1 negatively modulates regulatory T cell suppressive activity by promoting degradation of the transcription factor Foxp3. Immunity. 2013. doi: 10.1016/j.immuni.2013.08.006.
11.Van Loosdregt J, Fleskens V, et al. Stabilization of the transcription factor Foxp3 by the deubiquitinase USP7 increases Treg-cell-suppressive capacity. Immunity. 2013. doi: 10.1016/j.immuni.2013.05.018.
12.Wang L, Kumar S, et al. Ubiquitin-specific Protease-7 Inhibition Impairs Tip60-dependent Foxp3+ T-regulatory Cell Function and Promotes Antitumor Immunity. EBioMedicine. 2016. doi: 10.1016/j.ebiom.2016.10.018.
13.Chen X, Oppenheim JJ. Th17 cells and Tregs: unlikely allies. J Leukoc Biol. 2014 May;95(5):723-731. Epub 2014 Feb 21
14. Ren J, Li B. The Functional Stability of FOXP3 and RORγt in Treg and Th17 and Their Therapeutic Applications. Adv Protein Chem Struct Biol.2017;107:155-189. doi: 10.1016/ bs.apcsb.2016.10.002. Epub 2016 Dec 15.
15. Chen X, Oppenheim JJ. Th17 cells and Tregs: unlikely allies. J Leukoc Biol. 2014 May;95(5):723-731. Epub 2014 Feb 21.
16.Brudno JN, Kochenderfer JN. Chimeric antigen receptor T-cell therapies for lymphoma. Nat Rev Clin Oncol. 2017 Aug 31. doi: 10.1038/nrclinonc.2017.128.
17.Miossec P, Kolls JK. Targeting IL-17 and TH17 cells in chronic inflammation. Nat Rev Drug Discov. 2012 Oct;11(10):763-76. doi: 10.1038/nrd3794.
18.Mills KH. TLR-dependent T cell activation in autoimmunity. Nat Rev Immunol. 2011 Nov 18;11(12):807-22. doi: 10.1038/nri3095.
19.Burzyn D, Benoist C, Mathis D. Regulatory T cells in nonlymphoid tissues. Nat Immunol. 2013 Oct;14(10):1007-13. doi: 10.1038/ni.2683. Epub 2013 Sep 18.
20.Sakaguchi S, Yamaguchi T, Nomura T, Ono M. Regulatory T cells and immune tolerance. Cell. 2008 May 30;133(5):775-87. doi: 10.1016/j.cell.2008.05.009.
In order to theoretically demonstrate that regulatory T cells are dysfunctional or transdifferentiated in the cell microenvironment of rheumatoid arthritis patients imbued with a large number of inflammatory factors, and to describe the necessity of intervening the corresponding regulatory pathway of Treg cells in the clinical treatment of rheumatoid arthritis, we established the mathematical model of T cell differentiation and transdifferentiation (see more from Model section).
In order to theoretically demonstrate that regulatory T cells are dysfunctional or transdifferentiated in the cell microenvironment of rheumatoid arthritis patients imbued with a large number of inflammatory factors, and to describe the necessity of intervening the corresponding regulatory pathway of Treg cells in the clinical treatment of rheumatoid arthritis, we established the mathematical model of T cell differentiation and transdifferentiation (see more from Model section).
Figure5. The ubiquitination mechanism of FOXP3 in regulatory T cells under inflammatory conditions and our intervention strategy
Syn-Notch System
In order to deal with RA, we need to arm Treg with a sharp spear as well as a solid shield. With no doubt, a solid shield is the premise of survival in a difficult situation. That is why we try to activate a pathway to protect FOXP3 under inflammatory conditions in our design. We choose to focus on USP7, a protein that can promote FOXP3 stability by deubiquitinating FOXP3 specifically. An up-regulation in USP7 expression can result in an enhanced immune inhibitory function of Treg. Thus, we decide to express a SynNotch system in Treg, which can specifically activate the transcription of USP7 after receiving an inflammatory stimulus.
SynNotch, as you can tell from its name, is a synthetic biologically engineered Notch protein. Notch protein is a transmembrane protein, which can be divided into three domains: extracellular domain, transmembrane domain and intracellular domain. There is a cleavage site within its intracellular domain at which the Notch protein will be cleaved under stimulus, releasing its C-terminal peptide from the membrane to bind with a downstream protein and carrying out the signal transduction. Apparently, this is a non-specific signal transduction system. In our SynNotch system, we retain the transmembrane domain as well as its cleavage site, while on the N-terminal we fuse the extracellular domain of IL-17AR with Notch1 so that it can specifically recognize IL-17A, a cytokine secreted by Th17. In this way, our Treg is capable of sensing the presence of IL-17A. The next question is how to enable the protein cleaved by SynNotch to recognize and activate the transcription of USP7. That is where we introduce our next system, the Gal4-UAS system in yeast.
In yeast cells, Gal4 protein can specifically recognize the UAS sequence in its genome. If we attach an artificial transcription factor VP64 to Gal4 and insert UAS sequence before the promoter of target gene, we can presume that the transcription of target gene will be specifically activated. Thus, we add a Gal4-VP64 fusion protein sequence after the cleavage site in SynNotch system, meanwhile we add the UAS sequence before USP7 promoter. Now with the presence of the inflammatory cytokine IL-17A, SynNotch system will be activated and the cleavage will take place. Gal4-VP64 will be freed from cell membrane before entering the cell nucleus and binding with the UAS sequence before USP7 promoter. Then USP7 protein will be expressed and will deubiquitinate FOXP3, stabilizing FOXP3 under inflammation conditions, making it possible for Treg to survive the inflammatory environment and to exert its immune inhibitory function. Above is the shield we equip Treg with.
Figure5. Design of SynNotch system and CAR system
The functioning validation of SynNotch and CAR system
To test SynNotch’s stabilization function on FOXP3 in Treg cells under inflammatory conditions, inflammatory factor IL-6 was added into the culture medium to simulate the microenvironment in RA patients, then western blot and quantitative real-time PCR were performed. Without IL-17A, the expression of FOXP3 was significantly reduced compared to normal one due to the inactivation of SynNotch. However, with the addition of IL-17A, the FOXP3 level was greatly uplifted (Figure 2), indicating that the SynNotch system stabilized FOXP3 in Treg cells with the presence of IL-6.
To explore the effect of IL-17A concentration on the function of SynNotch with the presence of IL-6, various concentrations of IL-17A were given and the expression of USP7 and FOXP3 was tested. With a higher concentration of IL-17A, a higher expression of USP7 and FOXP3 was detected, indicating that the concentration of IL-17A played an important role in the expression level of SynNotch.
Figure2. The SynNotch system stabilizing FOXP3 in Treg under inflammatory conditions
Reference:
1.Roybal KT, Williams JZ, et al. Engineering T Cells with Customized Therapeutic Response Programs Using Synthetic Notch Receptors. Cell 2016. doi: 10.1016/j.cell.2016.09.011.
2.Klebanoff CA, Restifo NP. Customizing Functionality and Payload Delivery for Receptor-Engineered T Cells. Cell 2016. doi: 10.1016/j.cell.2016.09.033.
3.Ellebrecht CT, Bhoj VG, et al. Reengineering chimeric antigen receptor T cells for targeted therapy of autoimmune disease. Science 2016. doi: 10.1126/science.aaf6756.
4.Fransson M, Piras E, et al. CAR/FoxP3-engineered T regulatory cells target the CNS and suppress EAE upon intranasal delivery. J Neuroinflammation. 2012. doi: 10.1186/1742-2094-9-112.
5.MacDonald KG, Hoeppli RE, et al. Alloantigen-specific regulatory T cells generated with a chimeric antigen receptor. J Clin Invest. 2016. doi: 10.1172/JCI82771. Epub 2016 Mar 21.
6.Roybal KT, Rupp LJ. et al. Precision Tumor Recognition by T Cells With Combinatorial Antigen-Sensing Circuits. Cell. 2016. doi: 10.1016/j.cell.2016.01.011.
7.Kononenko AV, Lee NC. et al. Generation of a conditionally self-eliminating HAC gene delivery vector through incorporation of a tTAVP64 expression cassette. Nucleic Acids Res. 2015. doi: 10.1093/nar/gkv124.
8.Müller K, Zurbriggen MD, Weber W. An optogenetic upgrade for the Tet-OFF system. Biotechnol Bioeng. 2015. doi: 10.1002/bit.25562.
9.Khalil DN, Smith EL, et al. The future of cancer treatment: immunomodulation, CARs and combination immunotherapy. Nat Rev Clin Oncol. 2016 May. doi: 10.1038/nrclinonc.2016.25.
10.Chen Z, Barbi J, et al. The ubiquitin ligase Stub1 negatively modulates regulatory T cell suppressive activity by promoting degradation of the transcription factor Foxp3. Immunity. 2013. doi: 10.1016/j.immuni.2013.08.006.
11.Van Loosdregt J, Fleskens V, et al. Stabilization of the transcription factor Foxp3 by the deubiquitinase USP7 increases Treg-cell-suppressive capacity. Immunity. 2013. doi: 10.1016/j.immuni.2013.05.018.
12.Wang L, Kumar S, et al. Ubiquitin-specific Protease-7 Inhibition Impairs Tip60-dependent Foxp3+ T-regulatory Cell Function and Promotes Antitumor Immunity. EBioMedicine. 2016. doi: 10.1016/j.ebiom.2016.10.018.
13.Chen X, Oppenheim JJ. Th17 cells and Tregs: unlikely allies. J Leukoc Biol. 2014 May;95(5):723-731. Epub 2014 Feb 21
14. Ren J, Li B. The Functional Stability of FOXP3 and RORγt in Treg and Th17 and Their Therapeutic Applications. Adv Protein Chem Struct Biol.2017;107:155-189. doi: 10.1016/ bs.apcsb.2016.10.002. Epub 2016 Dec 15.
15. Chen X, Oppenheim JJ. Th17 cells and Tregs: unlikely allies. J Leukoc Biol. 2014 May;95(5):723-731. Epub 2014 Feb 21.
16.Brudno JN, Kochenderfer JN. Chimeric antigen receptor T-cell therapies for lymphoma. Nat Rev Clin Oncol. 2017 Aug 31. doi: 10.1038/nrclinonc.2017.128.
17.Miossec P, Kolls JK. Targeting IL-17 and TH17 cells in chronic inflammation. Nat Rev Drug Discov. 2012 Oct;11(10):763-76. doi: 10.1038/nrd3794.
18.Mills KH. TLR-dependent T cell activation in autoimmunity. Nat Rev Immunol. 2011 Nov 18;11(12):807-22. doi: 10.1038/nri3095.
19.Burzyn D, Benoist C, Mathis D. Regulatory T cells in nonlymphoid tissues. Nat Immunol. 2013 Oct;14(10):1007-13. doi: 10.1038/ni.2683. Epub 2013 Sep 18.
20.Sakaguchi S, Yamaguchi T, Nomura T, Ono M. Regulatory T cells and immune tolerance. Cell. 2008 May 30;133(5):775-87. doi: 10.1016/j.cell.2008.05.009.
To test SynNotch’s stabilization function on FOXP3 in Treg cells under inflammatory conditions, inflammatory factor IL-6 was added into the culture medium to simulate the microenvironment in RA patients, then western blot and quantitative real-time PCR were performed. Without IL-17A, the expression of FOXP3 was significantly reduced compared to normal one due to the inactivation of SynNotch. However, with the addition of IL-17A, the FOXP3 level was greatly uplifted (Figure 2), indicating that the SynNotch system stabilized FOXP3 in Treg cells with the presence of IL-6.
To explore the effect of IL-17A concentration on the function of SynNotch with the presence of IL-6, various concentrations of IL-17A were given and the expression of USP7 and FOXP3 was tested. With a higher concentration of IL-17A, a higher expression of USP7 and FOXP3 was detected, indicating that the concentration of IL-17A played an important role in the expression level of SynNotch.
