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Stephens EA, Ludwicki MB, Meksiriporn B, Li M, Ye T, Monticello C, Forsythe KJ, Kummer L, Zhou P, Plückthun A, DeLisa MP. Engineering Single Pan-Specific Ubiquibodies for Targeted Degradation of All Forms of Endogenous ERK Protein Kinase. ACS Synth Biol 2021; 10:2396-2408. [PMID: 34399052 DOI: 10.1021/acssynbio.1c00357] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Ubiquibodies (uAbs) are a customizable proteome editing technology that utilizes E3 ubiquitin ligases genetically fused to synthetic binding proteins to steer otherwise stable proteins of interest (POIs) to the 26S proteasome for degradation. The ability of engineered uAbs to accelerate the turnover of exogenous or endogenous POIs in a post-translational manner offers a simple yet robust tool for dissecting diverse functional properties of cellular proteins as well as for expanding the druggable proteome to include tumorigenic protein families that have yet-to-be successfully drugged by conventional inhibitors. Here, we describe the engineering of uAbs composed of human carboxyl-terminus of Hsc70-interacting protein (CHIP), a highly modular human E3 ubiquitin ligase, tethered to differently designed ankyrin repeat proteins (DARPins) that bind to nonphosphorylated (inactive) and/or doubly phosphorylated (active) forms of extracellular signal-regulated kinase 1 and 2 (ERK1/2). Two of the resulting uAbs were found to be global ERK degraders, pan-specifically capturing all endogenous ERK1/2 protein forms and redirecting them to the proteasome for degradation in different cell lines, including MCF7 breast cancer cells. Taken together, these results demonstrate how the substrate specificity of an E3 ubiquitin ligase can be reprogrammed to generate designer uAbs against difficult-to-drug targets, enabling a modular platform for remodeling the mammalian proteome.
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Affiliation(s)
- Erin A Stephens
- Biochemistry, Molecular and Cell Biology, Cornell University, Ithaca, New York 14853, United States
| | - Morgan B Ludwicki
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Bunyarit Meksiriporn
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Mingji Li
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Tianzheng Ye
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Connor Monticello
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Katherine J Forsythe
- College of Arts and Sciences, Cornell University, Ithaca, New York 14853, United States
| | - Lutz Kummer
- Department of Biochemistry, University of Zürich, 8057 Zürich, Switzerland
| | - Pengbo Zhou
- Department of Pathology and Laboratory Medicine, The Joan and Stanford I. Weill Medical College of Cornell University, New York, New York 10065, United States
| | - Andreas Plückthun
- Department of Biochemistry, University of Zürich, 8057 Zürich, Switzerland
| | - Matthew P DeLisa
- Biochemistry, Molecular and Cell Biology, Cornell University, Ithaca, New York 14853, United States
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York 14853, United States
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2
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Chen RP, Gaynor AS, Chen W. Synthetic biology approaches for targeted protein degradation. Biotechnol Adv 2019; 37:107446. [DOI: 10.1016/j.biotechadv.2019.107446] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 09/03/2019] [Accepted: 09/06/2019] [Indexed: 12/12/2022]
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3
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Lopez‐Barbosa N, Ludwicki MB, DeLisa MP. Proteome editing using engineered proteins that hijack cellular quality control machinery. AIChE J 2019. [DOI: 10.1002/aic.16854] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Natalia Lopez‐Barbosa
- Robert F. Smith School of Chemical and Biomolecular Engineering Cornell University Ithaca New York
| | - Morgan B. Ludwicki
- Robert F. Smith School of Chemical and Biomolecular Engineering Cornell University Ithaca New York
| | - Matthew P. DeLisa
- Robert F. Smith School of Chemical and Biomolecular Engineering Cornell University Ithaca New York
- Nancy E. and Peter C. Meinig School of Biomedical Engineering Cornell University Ithaca New York
- Biochemistry, Molecular and Cell Biology Cornell University Ithaca New York
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4
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Zhu HQ, Gao FH. Regulatory Molecules and Corresponding Processes of BCR-ABL Protein Degradation. J Cancer 2019; 10:2488-2500. [PMID: 31258755 PMCID: PMC6584333 DOI: 10.7150/jca.29528] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 05/02/2019] [Indexed: 12/24/2022] Open
Abstract
The BCR-ABL fusion protein with strong tyrosine kinase activity is one of the molecular biological bases of leukemia. Imatinib (Gleevec), a specific targeted drug for the treatment of chronic myeloid leukemia (CML), was developed for inhibiting the kinase activity of the BCR-ABL fusion protein. Despite the positive clinical efficacy of imatinib, the proportion of imatinib resistance has gradually increased. The main reason for the resistance is a decrease in sensitivity to imatinib caused by mutation or amplification of the BCR-ABL gene. In response to this phenomenon, the new generation of tyrosine kinase inhibitors (TKIs) targeting the BCR-ABL fusion protein was developed to solve the problem. However this strategy only selectively inhibits the tyrosine kinase activity of the BCR-ABL protein without eliminating the BCR-ABL protein, it does not fundamentally cure the BCR-ABL-positive leukemia patients. With the accumulation of the knowledge of cellular molecular biology, it has become possible to specifically eliminate certain proteins by cellular proteases in a specific way. Therefore, the therapeutic strategy to induce the degradation of the BCR-ABL fusion protein is superior to the strategy of inhibiting its activity. The protein degradation strategy is also a solution to the TKI resistance caused by different BCR-ABL gene point mutations. In order to provide possible exploration directions and clues for eliminating the BCR-ABL fusion protein in tumor cells, we summarize the significant molecules involved in the degradation pathway of the BCR-ABL protein, as well as the reported potent compounds that can target the BCR-ABL protein for degradation.
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Affiliation(s)
- Han-Qing Zhu
- Department of Oncology, Shanghai 9th People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
| | - Feng-Hou Gao
- Department of Oncology, Shanghai 9th People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
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5
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Ludwicki MB, Li J, Stephens EA, Roberts RW, Koide S, Hammond PT, DeLisa MP. Broad-Spectrum Proteome Editing with an Engineered Bacterial Ubiquitin Ligase Mimic. ACS CENTRAL SCIENCE 2019; 5:852-866. [PMID: 31139721 PMCID: PMC6535771 DOI: 10.1021/acscentsci.9b00127] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Indexed: 05/03/2023]
Abstract
Manipulation of the ubiquitin-proteasome pathway to achieve targeted silencing of cellular proteins has emerged as a reliable and customizable strategy for remodeling the mammalian proteome. One such approach involves engineering bifunctional proteins called ubiquibodies that are comprised of a synthetic binding protein fused to an E3 ubiquitin ligase, thus enabling post-translational ubiquitination and degradation of a target protein independent of its function. Here, we have designed a panel of new ubiquibodies based on E3 ubiquitin ligase mimics from bacterial pathogens that are capable of effectively interfacing with the mammalian proteasomal degradation machinery for selective removal of proteins of interest. One of these, the Shigella flexneri effector protein IpaH9.8 fused to a fibronectin type III (FN3) monobody that specifically recognizes green fluorescent protein (GFP), was observed to potently eliminate GFP and its spectral derivatives as well as 15 different FP-tagged mammalian proteins that varied in size (27-179 kDa) and subcellular localization (cytoplasm, nucleus, membrane-associated, and transmembrane). To demonstrate therapeutically relevant delivery of ubiquibodies, we leveraged a bioinspired molecular assembly method whereby synthetic mRNA encoding the GFP-specific ubiquibody was coassembled with poly A binding proteins and packaged into nanosized complexes using biocompatible, structurally defined polypolypeptides bearing cationic amine side groups. The resulting nanoplexes delivered ubiquibody mRNA in a manner that caused efficient target depletion in cultured mammalian cells stably expressing GFP as well as in transgenic mice expressing GFP ubiquitously. Overall, our results suggest that IpaH9.8-based ubiquibodies are a highly modular proteome editing technology with the potential for pharmacologically modulating disease-causing proteins.
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Affiliation(s)
- Morgan B. Ludwicki
- Robert F. Smith
School of Chemical and Biomolecular Engineering, Cornell University, 120 Olin Hall, Ithaca, New
York 14853, United
States
| | - Jiahe Li
- Department of Chemical Engineering and Koch Institute for
Integrative Cancer Research, Massachusetts
Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Erin A. Stephens
- Biochemistry, Molecular and Cell Biology, Cornell University, Ithaca, New York 14853, United States
| | - Richard W. Roberts
- Department
of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - Shohei Koide
- Perlmutter Cancer Center, New York University
Langone Medical Center, New York, New York 10016, United States
- Department of Biochemistry and Molecular
Pharmacology, New York University School
of Medicine, New York, New York 10016, United States
| | - Paula T. Hammond
- Department of Chemical Engineering and Koch Institute for
Integrative Cancer Research, Massachusetts
Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Matthew P. DeLisa
- Robert F. Smith
School of Chemical and Biomolecular Engineering, Cornell University, 120 Olin Hall, Ithaca, New
York 14853, United
States
- Biochemistry, Molecular and Cell Biology, Cornell University, Ithaca, New York 14853, United States
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Cheng J, Guo J, North BJ, Tao K, Zhou P, Wei W. The emerging role for Cullin 4 family of E3 ligases in tumorigenesis. Biochim Biophys Acta Rev Cancer 2018; 1871:138-159. [PMID: 30602127 DOI: 10.1016/j.bbcan.2018.11.007] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Revised: 11/28/2018] [Accepted: 11/29/2018] [Indexed: 02/06/2023]
Abstract
As a member of the Cullin-RING ligase family, Cullin-RING ligase 4 (CRL4) has drawn much attention due to its broad regulatory roles under physiological and pathological conditions, especially in neoplastic events. Based on evidence from knockout and transgenic mouse models, human clinical data, and biochemical interactions, we summarize the distinct roles of the CRL4 E3 ligase complexes in tumorigenesis, which appears to be tissue- and context-dependent. Notably, targeting CRL4 has recently emerged as a noval anti-cancer strategy, including thalidomide and its derivatives that bind to the substrate recognition receptor cereblon (CRBN), and anticancer sulfonamides that target DCAF15 to suppress the neoplastic proliferation of multiple myeloma and colorectal cancers, respectively. To this end, PROTACs have been developed as a group of engineered bi-functional chemical glues that induce the ubiquitination-mediated degradation of substrates via recruiting E3 ligases, such as CRL4 (CRBN) and CRL2 (pVHL). We summarize the recent major advances in the CRL4 research field towards understanding its involvement in tumorigenesis and further discuss its clinical implications. The anti-tumor effects using the PROTAC approach to target the degradation of undruggable targets are also highlighted.
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Affiliation(s)
- Ji Cheng
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China; Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Jianping Guo
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Brian J North
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Kaixiong Tao
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Pengbo Zhou
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, 1300 York Ave., New York, NY 10065, USA.
| | - Wenyi Wei
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA.
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The chimeric ubiquitin ligase SH2-U-box inhibits the growth of imatinib-sensitive and resistant CML by targeting the native and T315I-mutant BCR-ABL. Sci Rep 2016; 6:28352. [PMID: 27329306 PMCID: PMC4916441 DOI: 10.1038/srep28352] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 06/02/2016] [Indexed: 01/01/2023] Open
Abstract
Chronic myeloid leukemia (CML) is characterized by constitutively active fusion protein tyrosine kinase BCR-ABL. Although the tyrosine kinase inhibitor (TKI) against BCR-ABL, imatinib, is the first-line therapy for CML, acquired resistance almost inevitably emerges. The underlying mechanism are point mutations within the BCR-ABL gene, among which T315I is notorious because it resists to almost all currently available inhibitors. Here we took use of a previously generated chimeric ubiquitin ligase, SH2-U-box, in which SH2 from the adaptor protein Grb2 acts as a binding domain for activated BCR-ABL, while U-box from CHIP functions as an E3 ubiquitin ligase domain, so as to target the ubiquitination and degradation of both native and T315I-mutant BCR-ABL. As such, SH2-U-box significantly inhibited proliferation and induced apoptosis in CML cells harboring either the wild-type or T315I-mutant BCR-ABL (K562 or K562R), with BCR-ABL-dependent signaling pathways being repressed. Moreover, SH2-U-box worked in concert with imatinib in K562 cells. Importantly, SH2-U-box-carrying lentivirus could markedly suppress the growth of K562-xenografts in nude mice or K562R-xenografts in SCID mice, as well as that of primary CML cells. Collectively, by degrading the native and T315I-mutant BCR-ABL, the chimeric ubiquitin ligase SH2-U-box may serve as a potential therapy for both imatinib-sensitive and resistant CML.
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Zhong D, Ru Y, Wang Q, Zhang J, Zhang J, Wei J, Wu J, Yao L, Li X, Li X. Chimeric ubiquitin ligases inhibit non-small cell lung cancer via negative modulation of EGFR signaling. Cancer Lett 2015; 359:57-64. [DOI: 10.1016/j.canlet.2014.12.043] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Revised: 12/10/2014] [Accepted: 12/18/2014] [Indexed: 01/15/2023]
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9
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Yang C, Boyson CA, Di Liberto M, Huang X, Hannah J, Dorn DC, Moore MAS, Chen-Kiang S, Zhou P. CDK4/6 Inhibitor PD 0332991 Sensitizes Acute Myeloid Leukemia to Cytarabine-Mediated Cytotoxicity. Cancer Res 2015; 75:1838-45. [PMID: 25744718 DOI: 10.1158/0008-5472.can-14-2486] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 01/13/2015] [Indexed: 12/17/2022]
Abstract
Cyclin-dependent kinase (CDK)4 and CDK6 are frequently overexpressed or hyperactivated in human cancers. Targeting CDK4/CDK6 in combination with cytotoxic killing therefore represents a rational approach to cancer therapy. By selective inhibition of CDK4/CDK6 with PD 0332991, which leads to early G1 arrest and synchronous S-phase entry upon release of the G1 block, we have developed a novel strategy to prime acute myeloid leukemia (AML) cells for cytotoxic killing by cytarabine (Ara-C). This sensitization is achieved in part through enrichment of S-phase cells, which maximizes the AML populations for Ara-C incorporation into replicating DNA to elicit DNA damage. Moreover, PD 0332991 triggered apoptosis of AML cells through inhibition of the homeobox (HOX)A9 oncogene expression, reducing the transcription of its target PIM1. Reduced PIM1 synthesis attenuates PIM1-mediated phosphorylation of the proapoptotic BAD and activates BAD-dependent apoptosis. In vivo, timely inhibition of CDK4/CDK6 by PD 0332991 and release profoundly suppresses tumor growth in response to reduced doses of Ara-C in a xenograft AML model. Collectively, these data suggest selective and reversible inhibition of CDK4/CDK6 as an effective means to enhance Ara-C killing of AML cells at reduced doses, which has implications for the treatment of elderly AML patients who are unable to tolerate high-dose Ara-C therapy.
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MESH Headings
- Animals
- Antineoplastic Agents/pharmacology
- Apoptosis/drug effects
- Apoptosis/genetics
- Cell Line
- Cyclin-Dependent Kinase 4/antagonists & inhibitors
- Cyclin-Dependent Kinase 4/genetics
- Cyclin-Dependent Kinase 4/metabolism
- Cyclin-Dependent Kinase 6/antagonists & inhibitors
- Cyclin-Dependent Kinase 6/genetics
- Cyclin-Dependent Kinase 6/metabolism
- Cytarabine/pharmacology
- DNA Damage/drug effects
- DNA Replication/drug effects
- HEK293 Cells
- HL-60 Cells
- Humans
- Leukemia, Myeloid, Acute/drug therapy
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/metabolism
- Mice, Inbred NOD
- Mice, SCID
- Phosphorylation/drug effects
- Piperazines/pharmacology
- Protein Kinase Inhibitors/pharmacology
- Proto-Oncogene Proteins c-pim-1/genetics
- Proto-Oncogene Proteins c-pim-1/metabolism
- Pyridines/pharmacology
- S Phase/drug effects
- S Phase/genetics
- Transcription, Genetic/drug effects
- Tumor Cells, Cultured
- Xenograft Model Antitumor Assays
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Affiliation(s)
- Chenyi Yang
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
| | - Cynthia A Boyson
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Maurizio Di Liberto
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
| | - Xiangao Huang
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
| | - Jeffrey Hannah
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
| | - David C Dorn
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Malcolm A S Moore
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Selina Chen-Kiang
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York.
| | - Pengbo Zhou
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York.
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Dantuma NP, Bott LC. The ubiquitin-proteasome system in neurodegenerative diseases: precipitating factor, yet part of the solution. Front Mol Neurosci 2014; 7:70. [PMID: 25132814 PMCID: PMC4117186 DOI: 10.3389/fnmol.2014.00070] [Citation(s) in RCA: 213] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2014] [Accepted: 07/09/2014] [Indexed: 01/17/2023] Open
Abstract
The ubiquitin-proteasome system (UPS) has been implicated in neurodegenerative diseases based on the presence of deposits consisting of ubiquitylated proteins in affected neurons. It has been postulated that aggregation-prone proteins associated with these disorders, such as α-synuclein, β-amyloid peptide, and polyglutamine proteins, compromise UPS function, and delay the degradation of other proteasome substrates. Many of these substrates play important regulatory roles in signaling, cell cycle progression, or apoptosis, and their inadvertent stabilization due to an overloaded and improperly functioning UPS may thus be responsible for cellular demise in neurodegeneration. Over the past decade, numerous studies have addressed the UPS dysfunction hypothesis using various model systems and techniques that differ in their readout and sensitivity. While an inhibitory effect of some disease proteins on the UPS has been demonstrated, increasing evidence attests that the UPS remains operative in many disease models, which opens new possibilities for treatment. In this review, we will discuss the paradigm shift that repositioned the UPS from being a prime suspect in the pathophysiology of neurodegeneration to an attractive therapeutic target that can be harnessed to accelerate the clearance of disease-linked proteins.
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Affiliation(s)
- Nico P Dantuma
- Department of Cell and Molecular Biology, Karolinska Institutet Stockholm, Sweden
| | - Laura C Bott
- Department of Cell and Molecular Biology, Karolinska Institutet Stockholm, Sweden ; Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health Bethesda, MD, USA
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Wang Q, Ru Y, Zhong D, Zhang J, Yao L, Li X. Engineered ubiquitin ligase PTB-U-box targets insulin/insulin-like growth factor receptor for degradation and coordinately inhibits cancer malignancy. Oncotarget 2014; 5:4945-58. [PMID: 24970814 PMCID: PMC4148113 DOI: 10.18632/oncotarget.2066] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Accepted: 06/05/2014] [Indexed: 12/27/2022] Open
Abstract
The type 1 insulin-like growth factor receptor (IGF-1R) is a promising target for cancer therapy with antibodies and small molecule tyrosine kinase inhibitors (TKIs) which have been actively tested clinically. Evidences have demonstrated that insulin receptor (IR), which is implicated in tumorigenesis, conveys resistance to IGF-1R targeted therapy. This provided the compelling rationale for co-targeting IGF-1R and IR. Herein we have developed an approach to simultaneously down-regulate IGF-1R and IR in protein levels. By generating and screening several engineered ubiquitin ligases, we have identified that, PTB-U-box, which is composed of an IGF-1R/IR-binding domain and a functional E3 ubiquitin ligase domain, binds activated IGF-1R/IR and targets their ubiquitination and degradation. When ectopically expressed in HepG2 and HeLa cells, PTB-U-box inhibits cell proliferation and invasion, increases chemo-sensitivity, as well as interrupts glucose metabolism. Finally, intratumoral injection of adenovirus carrying PTB-U-box dramatically retards the growth of HepG2 xenograft. Therefore, well-designed engineered ubiquitin ligase represents an effective therapeutic strategy for the treatment of the cancers with co-expressed IGF-1R/IR.
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Affiliation(s)
- Qinhao Wang
- State Key Laboratory of Cancer Biology, Departments of Biochemistry and Molecular Biology, the Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Yi Ru
- State Key Laboratory of Cancer Biology, Departments of Biochemistry and Molecular Biology, the Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Daixing Zhong
- Department of Thoracic Surgery, Tangdu Hospital, the Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Jing Zhang
- Experiment Teaching Center, the Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Libo Yao
- State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, the Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Xia Li
- State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, the Fourth Military Medical University, Xi’an, Shaanxi, China
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Anania VG, Pham VC, Huang X, Masselot A, Lill JR, Kirkpatrick DS. Peptide level immunoaffinity enrichment enhances ubiquitination site identification on individual proteins. Mol Cell Proteomics 2013; 13:145-56. [PMID: 24142993 PMCID: PMC3879610 DOI: 10.1074/mcp.m113.031062] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Ubiquitination is a process that involves the covalent attachment of the 76-residue ubiquitin protein through its C-terminal di-glycine (GG) to lysine (K) residues on substrate proteins. This post-translational modification elicits a wide range of functional consequences including targeting proteins for proteasomal degradation, altering subcellular trafficking events, and facilitating protein-protein interactions. A number of methods exist for identifying the sites of ubiquitination on proteins of interest, including site-directed mutagenesis and affinity-purification mass spectrometry (AP-MS). Recent publications have also highlighted the use of peptide-level immunoaffinity enrichment of K-GG modified peptides from whole cell lysates for global characterization of ubiquitination sites. Here we investigated the utility of this technique for focused mapping of ubiquitination sites on individual proteins. For a series of membrane-associated and cytoplasmic substrates including erbB-2 (HER2), Dishevelled-2 (DVL2), and T cell receptor α (TCRα), we observed that K-GG peptide immunoaffinity enrichment consistently yielded additional ubiquitination sites beyond those identified in protein level AP-MS experiments. To assess this quantitatively, SILAC-labeled lysates were prepared and used to compare the abundances of individual K-GG peptides from samples prepared in parallel. Consistently, K-GG peptide immunoaffinity enrichment yielded greater than fourfold higher levels of modified peptides than AP-MS approaches. Using this approach, we went on to characterize inducible ubiquitination on multiple members of the T-cell receptor complex that are functionally affected by endoplasmic reticulum (ER) stress. Together, these data demonstrate the utility of immunoaffinity peptide enrichment for single protein ubiquitination site analysis and provide insights into the ubiquitination of HER2, DVL2, and proteins in the T-cell receptor complex.
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