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Kim MS, Bhargava HK, Shavey GE, Lim WA, El-Samad H, Ng AH. Degron-Based bioPROTACs for Controlling Signaling in CAR T Cells. ACS Synth Biol 2024; 13:2313-2327. [PMID: 38991546 DOI: 10.1021/acssynbio.4c00109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2024]
Abstract
Chimeric antigen receptor (CAR) T cells have made a tremendous impact in the clinic, but potent signaling through the CAR can be detrimental to treatment safety and efficacy. The use of protein degradation to control CAR signaling can address these issues in preclinical models. Existing strategies for regulating CAR stability rely on small molecules to induce systemic degradation. In contrast to small molecule regulation, genetic circuits offer a more precise method to control CAR signaling in an autonomous cell-by-cell fashion. Here, we describe a programmable protein degradation tool that adopts the framework of bioPROTACs, heterobifunctional proteins that are composed of a target recognition domain fused to a domain that recruits the endogenous ubiquitin proteasome system. We develop novel bioPROTACs that utilize a compact four-residue degron and demonstrate degradation of cytosolic and membrane protein targets using either a nanobody or synthetic leucine zipper as a protein binder. Our bioPROTACs exhibit potent degradation of CARs and can inhibit CAR signaling in primary human T cells. We demonstrate the utility of our bioPROTACs by constructing a genetic circuit to degrade the tyrosine kinase ZAP70 in response to recognition of a specific membrane-bound antigen. This circuit can disrupt CAR T cell signaling only in the presence of a specific cell population. These results suggest that bioPROTACs are powerful tools for expanding the CAR T cell engineering toolbox.
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Affiliation(s)
- Matthew S Kim
- Tetrad Graduate Program, University of California San Francisco, San Francisco, California 94158, United States
- Cell Design Institute, University of California San Francisco, San Francisco, California 94158, United States
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California 94158, United States
| | - Hersh K Bhargava
- Cell Design Institute, University of California San Francisco, San Francisco, California 94158, United States
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California 94158, United States
- Biophysics Graduate Program, University of California San Francisco, San Francisco, California 94158, United States
| | - Gavin E Shavey
- Cell Design Institute, University of California San Francisco, San Francisco, California 94158, United States
| | - Wendell A Lim
- Cell Design Institute, University of California San Francisco, San Francisco, California 94158, United States
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California 94158, United States
| | - Hana El-Samad
- Cell Design Institute, University of California San Francisco, San Francisco, California 94158, United States
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California 94158, United States
- Chan-Zuckerberg Biohub, San Francisco, California 94158, United States
- Altos Labs Inc., Redwood City, California, 94065, United States
| | - Andrew H Ng
- Cell Design Institute, University of California San Francisco, San Francisco, California 94158, United States
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California 94158, United States
- Department of Molecular Biology, Genentech Inc., South San Francisco, California 94080, United States
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Kim MS, Bhargava HK, Shavey GE, Lim WA, El-Samad H, Ng AH. Degron-based bioPROTACs for controlling signaling in CAR T cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.16.580396. [PMID: 38405763 PMCID: PMC10888892 DOI: 10.1101/2024.02.16.580396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Chimeric antigen receptor (CAR) T cells have made a tremendous impact in the clinic, but potent signaling through the CAR can be detrimental to treatment safety and efficacy. The use of protein degradation to control CAR signaling can address these issues in pre-clinical models. Existing strategies for regulating CAR stability rely on small molecules to induce systemic degradation. In contrast to small molecule regulation, genetic circuits offer a more precise method to control CAR signaling in an autonomous, cell-by-cell fashion. Here, we describe a programmable protein degradation tool that adopts the framework of bioPROTACs, heterobifunctional proteins that are composed of a target recognition domain fused to a domain that recruits the endogenous ubiquitin proteasome system. We develop novel bioPROTACs that utilize a compact four residue degron and demonstrate degradation of cytosolic and membrane protein targets using either a nanobody or synthetic leucine zipper as a protein binder. Our bioPROTACs exhibit potent degradation of CARs and can inhibit CAR signaling in primary human T cells. We demonstrate the utility of our bioPROTACs by constructing a genetic circuit to degrade the tyrosine kinase ZAP70 in response to recognition of a specific membrane-bound antigen. This circuit is able to disrupt CAR T cell signaling only in the presence of a specific cell population. These results suggest that bioPROTACs are a powerful tool for expanding the cell engineering toolbox for CAR T cells.
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Affiliation(s)
- Matthew S Kim
- Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA; Cell Design Institute, University of California, San Francisco, San Francisco, CA
| | - Hersh K Bhargava
- Biophysics Graduate Program, University of California, San Francisco, San Francisco, CA; Cell Design Institute, University of California, San Francisco, San Francisco, CA; Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA
| | - Gavin E Shavey
- Current: Arsenal Biociences, Inc., South San Francisco, CA; Cell Design Institute, University of California, San Francisco, San Francisco, CA
| | - Wendell A Lim
- Cell Design Institute, University of California, San Francisco, San Francisco, CA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA
| | - Hana El-Samad
- Current: Altos Labs, Redwood City, CA; Cell Design Institute, University of California, San Francisco, San Francisco, CA; Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA; Chan-Zuckerberg Biohub, San Francisco, CA; Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA
| | - Andrew H Ng
- Current: Department of Molecular Biology, Genentech Inc., South San Francisco, CA, USA; Cell Design Institute, University of California, San Francisco, San Francisco, CA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA
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Recent Advances in the Applications of Small Molecules in the Treatment of Multiple Myeloma. Int J Mol Sci 2023; 24:ijms24032645. [PMID: 36768967 PMCID: PMC9917049 DOI: 10.3390/ijms24032645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 01/15/2023] [Accepted: 01/24/2023] [Indexed: 02/01/2023] Open
Abstract
Therapy for multiple myeloma (MM), a hematologic neoplasm of plasma cells, has undergone remarkable changes over the past 25 years. Small molecules (molecular weight of less than one kDa), together with newer immunotherapies that include monoclonal antibodies, antibody-drug conjugates, and most recently, chimeric antigen receptor (CAR) T-cells, have combined to double the disease's five-year survival rate to over 50% during the past few decades. Despite these advances, the disease is still considered incurable, and its treatment continues to pose substantial challenges, since therapeutic refractoriness and patient relapse are exceedingly common. This review focuses on the current pipeline, along with the contemporary roles and future prospects for small molecules in MM therapy. While small molecules offer prospective benefits in terms of oral bioavailability, cellular penetration, simplicity of preparation, and improved cost-benefit considerations, they also pose problems of toxicity due to off-target effects. Highlighted in the discussion are recent developments in the applications of alkylating agents, immunomodulators, proteasome inhibitors, apoptosis inducers, kinesin spindle protein inhibitors, blockers of nuclear transport, and drugs that affect various kinases involved in intracellular signaling pathways. Molecular and cellular targets are described for each class of agents in relation to their roles as drivers of MM.
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Houston K, Melvin AT, Woss GS, Fayer EL, Waters ML, Allbritton NL. Development of β-Hairpin Peptides for the Measurement of SCF-Family E3 Ligase Activity in Vitro via Ornithine Ubiquitination. ACS OMEGA 2017; 2:1198-1206. [PMID: 28393136 PMCID: PMC5377275 DOI: 10.1021/acsomega.7b00109] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 03/15/2017] [Indexed: 06/07/2023]
Abstract
Regulation of the ubiquitin-proteasome system (UPS) to treat select types of cancer has become a popular area of drug discovery research. The FDA approval of proteasome inhibitors Bortezomib and Carfilzomib in the treatment of multiple myeloma has led to an increased need for chemical reporters capable of detecting and quantifying protein ubiquitination and the activity of members of the UPS including E3 ubiquitin ligases and the proteasome in the tumor cells of the patients. One limitation of peptide-based reporters is their rapid degradation in the cellular environment by cytosolic peptidases. Conversely, β-hairpin "protectides" exhibit a pronounced secondary structure that significantly increases their lifetime under cellular conditions. The goal of this work was to develop a family of novel, ornithine-rich protectides that could act as primary degrons serving as substrates for in vitro ubiquitination. The fluorescent peptide-based reporters were demonstrated to be highly resistant to degradation in multiple myeloma cell lysates. The most stable β-hairpin primary degron, containing a single ornithine residue at the N-terminus, OWRWR [Ac-OWVRVpGO(FAM)WIRQ-NH2], demonstrated rapid ubiquitination kinetics and a 20-fold increase in stability when compared with an unstructured primary degron. A screen of E1 and E3 enzyme inhibitors in cell lysates showed that ubiquitination of OWRWR was significantly impaired by inhibitors of the SCF family of E3 ligases. Furthermore, this is the first report demonstrating the use of an ornithine residue on a primary degron as a ubiquitination site. This study serves as a strong foundation for the development of stable, fluorescent, peptide-based reporters capable of quantifying protein ubiquitination and the enzymatic activity of members of the UPS.
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Affiliation(s)
- Kaiulani
M. Houston
- Department
of Chemistry, University of
North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Adam T. Melvin
- Cain
Department of Chemical Engineering, Louisiana
State University, Baton
Rouge, Louisiana 70803, United States
| | - Gregery S. Woss
- Department
of Chemistry, University of
North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Effrat L. Fayer
- Department
of Chemistry, University of
North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Marcey L. Waters
- Department
of Chemistry, University of
North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Nancy L. Allbritton
- Department
of Chemistry, University of
North Carolina, Chapel Hill, North Carolina 27599, United States
- Joint Department of
Biomedical Engineering, University of North
Carolina, Chapel Hill, North Carolina 27599, United States
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Hwang SJ, Park HG, Park Y, Lee HJ. An α-quaternary chiral latam derivative, YH-304 as a novel broad-spectrum anticancer agent. Int J Oncol 2016; 49:2480-2486. [PMID: 27748805 DOI: 10.3892/ijo.2016.3726] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 09/30/2016] [Indexed: 11/06/2022] Open
Abstract
Previously, we reported that α-quaternary chiral lactam derivatives have broad spectrum anticancer activity. However, the underlying molecular mechanisms and its relevance are largely unknown. In the present study, we report progress on α-quaternary chiral lactam analogues that address this, focusing on the novel analogue YH-304 as a candidate to broadly target human cancer cells. The effect of YH-304 on cell transformation was assessed by clonogenic assay in non-small cell lung cancer cells (NSCLCs) A549 and 226B. Proapoptotic activity of YH-304 was determined by TUNEL assay and cleaved PARP, cleaved caspase-9, and Bax as markers for apoptosis. The p53-dependency and therapeutic spectrum of YH-304 was assessed by western blot analysis, real-time PCR, and cell viability assays in cells expressing endogenous wild or mutant p53. The effect of YH-304 on angiogenesis in vivo was examined by bFGF-mediated angiogenesis assay in zebrafish. Finally, the effect of YH-304 on AKT and ERK activation (phosphorylation) as a putative mechanism underlying the effect of YH-304 on bFGF-mediated angiogenesis was assessed using western blotting. We found that YH-304 significantly decreases the colony-forming activities of both A549 and 226B cells, inducing cellular apoptosis. Unlike nutlin-3 (p53 pathway activator), YH-304 did not affect the expression levels of p53 and its target gene such as p21 and thus showed p53-independent anticancer activity with broad spectrum. In addition, YH-304 inhibited bFGF-induced angiogenesis in vivo through mediating AKT and ERK signaling pathway, which plays an important role in bFGF activation and angiogenesis. Taken together, our data indicate that YH-304 may represent a novel therapeutic option for the treatment of cancer in a p53-independent manner.
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Affiliation(s)
- Su Jung Hwang
- College of Pharmacy and Inje Institute of Pharmaceutical Sciences and Research, Inje University, Gimhae, Gyeongnam 621-749, Republic of Korea
| | - Hyeung-Geun Park
- Research Institute of Pharmaceutical Science and College of Pharmacy, Seoul National University, Seoul 151-742, Republic of Korea
| | - Yohan Park
- College of Pharmacy and Inje Institute of Pharmaceutical Sciences and Research, Inje University, Gimhae, Gyeongnam 621-749, Republic of Korea
| | - Hyo-Jong Lee
- College of Pharmacy and Inje Institute of Pharmaceutical Sciences and Research, Inje University, Gimhae, Gyeongnam 621-749, Republic of Korea
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