101
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Li W, Garcia-Rivera EM, Mitchell DC, Chick JM, Maetani M, Knapp JM, Matthews GM, Shirasaki R, de Matos Simoes R, Viswanathan V, Pulice JL, Rees MG, Roth JA, Gygi SP, Mitsiades CS, Kadoch C, Schreiber SL, Ostrem JML. Highly specific intracellular ubiquitination of a small molecule. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.26.577493. [PMID: 38328167 PMCID: PMC10849632 DOI: 10.1101/2024.01.26.577493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Ubiquitin is a small, highly conserved protein that acts as a posttranslational modification in eukaryotes. Ubiquitination of proteins frequently serves as a degradation signal, marking them for disposal by the proteasome. Here, we report a novel small molecule from a diversity-oriented synthesis library, BRD1732, that is directly ubiquitinated in cells, resulting in dramatic accumulation of inactive ubiquitin monomers and polyubiquitin chains causing broad inhibition of the ubiquitin-proteasome system. Ubiquitination of BRD1732 and its associated cytotoxicity are stereospecific and dependent upon two homologous E3 ubiquitin ligases, RNF19A and RNF19B. Our finding opens the possibility for indirect ubiquitination of a target through a ubiquitinated bifunctional small molecule, and more broadly raises the potential for posttranslational modification in trans .
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102
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Al-Ghabkari A, Huang B, Park M. Aberrant MET Receptor Tyrosine Kinase Signaling in Glioblastoma: Targeted Therapy and Future Directions. Cells 2024; 13:218. [PMID: 38334610 PMCID: PMC10854665 DOI: 10.3390/cells13030218] [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] [Received: 11/08/2023] [Revised: 11/27/2023] [Accepted: 01/12/2024] [Indexed: 02/10/2024] Open
Abstract
Brain tumors represent a heterogeneous group of neoplasms characterized by a high degree of aggressiveness and a poor prognosis. Despite recent therapeutic advances, the treatment of brain tumors, including glioblastoma (GBM), an aggressive primary brain tumor associated with poor prognosis and resistance to therapy, remains a significant challenge. Receptor tyrosine kinases (RTKs) are critical during development and in adulthood. Dysregulation of RTKs through activating mutations and gene amplification contributes to many human cancers and provides attractive therapeutic targets for treatment. Under physiological conditions, the Met RTK, the hepatocyte growth factor/scatter factor (HGF/SF) receptor, promotes fundamental signaling cascades that modulate epithelial-to-mesenchymal transition (EMT) involved in tissue repair and embryogenesis. In cancer, increased Met activity promotes tumor growth and metastasis by providing signals for proliferation, survival, and migration/invasion. Recent clinical genomic studies have unveiled multiple mechanisms by which MET is genetically altered in GBM, including focal amplification, chromosomal rearrangements generating gene fusions, and a splicing variant mutation (exon 14 skipping, METex14del). Notably, MET overexpression contributes to chemotherapy resistance in GBM by promoting the survival of cancer stem-like cells. This is linked to distinctive Met-induced pathways, such as the upregulation of DNA repair mechanisms, which can protect tumor cells from the cytotoxic effects of chemotherapy. The development of MET-targeted therapies represents a major step forward in the treatment of brain tumours. Preclinical studies have shown that MET-targeted therapies (monoclonal antibodies or small molecule inhibitors) can suppress growth and invasion, enhancing the efficacy of conventional therapies. Early-phase clinical trials have demonstrated promising results with MET-targeted therapies in improving overall survival for patients with recurrent GBM. However, challenges remain, including the need for patient stratification, the optimization of treatment regimens, and the identification of mechanisms of resistance. This review aims to highlight the current understanding of mechanisms underlying MET dysregulation in GBM. In addition, it will focus on the ongoing preclinical and clinical assessment of therapies targeting MET dysregulation in GBM.
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Affiliation(s)
- Abdulhameed Al-Ghabkari
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, QC H3A 1A3, Canada; (A.A.-G.); (B.H.)
| | - Bruce Huang
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, QC H3A 1A3, Canada; (A.A.-G.); (B.H.)
- Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Morag Park
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, QC H3A 1A3, Canada; (A.A.-G.); (B.H.)
- Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada
- Department of Oncology, McGill University, Montreal, QC H4A 3T2, Canada
- Department of Medicine, McGill University, Montreal, QC H4A 3J1, Canada
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103
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Oleinikovas V, Gainza P, Ryckmans T, Fasching B, Thomä NH. From Thalidomide to Rational Molecular Glue Design for Targeted Protein Degradation. Annu Rev Pharmacol Toxicol 2024; 64:291-312. [PMID: 37585660 DOI: 10.1146/annurev-pharmtox-022123-104147] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/18/2023]
Abstract
Thalidomide and its derivatives are powerful cancer therapeutics that are among the best-understood molecular glue degraders (MGDs). These drugs selectively reprogram the E3 ubiquitin ligase cereblon (CRBN) to commit target proteins for degradation by the ubiquitin-proteasome system. MGDs create novel recognition interfaces on the surface of the E3 ligase that engage in induced protein-protein interactions with neosubstrates. Molecular insight into their mechanism of action opens exciting opportunities to engage a plethora of targets through a specific recognition motif, the G-loop. Our analysis shows that current CRBN-based MGDs can in principle recognize over 2,500 proteins in the human proteome that contain a G-loop. We review recent advances in tuning the specificity between CRBN and its MGD-induced neosubstrates and deduce a set of simple rules that govern these interactions. We conclude that rational MGD design efforts will enable selective degradation of many more proteins, expanding this therapeutic modality to more disease areas.
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Affiliation(s)
| | | | | | | | - Nicolas H Thomä
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland;
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104
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Cockram PE, Walters BT, Lictao A, Shanahan F, Wertz IE, Foster SA, Rudolph J. Allosteric Inhibitors of the SARS-COV-2 Papain-like Protease Domain Induce Proteasomal Degradation of Its Parent Protein NSP3. ACS Chem Biol 2024; 19:22-36. [PMID: 38150587 DOI: 10.1021/acschembio.3c00312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2023]
Abstract
The papain-like protease of SARS-COV-2 is essential for viral replication and pathogenesis. Its location within a much larger multifunctional protein, NSP3, makes it an ideal candidate for a targeted degradation approach capable of eliminating multiple functions with a single-molecule treatment. In this work, we have developed a HiBiT-based cellular model to study NSP3 degradation and used this platform for the discovery of monovalent NSP3 degraders. We present previously unreported degradation activity of published papain-like protease inhibitors. Follow-up exploration of structure-activity relationships and mechanism-of-action studies points to the recruitment of the ubiquitin-proteasome machinery that is solely driven by site occupancy, regardless of molecular features of the ligand. Supported by HDX data, we hypothesize that binding-induced structural changes in NSP3 trigger the recruitment of an E3 ligase and lead to proteasomal degradation.
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Affiliation(s)
- Peter E Cockram
- Discovery Chemistry, Genentech, South San Francisco, California 94080, United States
- Discovery Oncology, Genentech, South San Francisco, California 94080, United States
| | - Benjamin T Walters
- Biochemical and Cellular Pharmacology, Genentech, South San Francisco, California 94080, United States
| | - Aaron Lictao
- Biochemical and Cellular Pharmacology, Genentech, South San Francisco, California 94080, United States
| | - Frances Shanahan
- Discovery Oncology, Genentech, South San Francisco, California 94080, United States
| | - Ingrid E Wertz
- Discovery Oncology, Genentech, South San Francisco, California 94080, United States
| | - Scott A Foster
- Discovery Oncology, Genentech, South San Francisco, California 94080, United States
| | - Joachim Rudolph
- Discovery Chemistry, Genentech, South San Francisco, California 94080, United States
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105
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Nishiguchi G, Mascibroda LG, Young SM, Caine EA, Abdelhamed S, Kooijman JJ, Miller DJ, Das S, McGowan K, Mayasundari A, Shi Z, Barajas JM, Hiltenbrand R, Aggarwal A, Chang Y, Mishra V, Narina S, Thomas M, Loughran AJ, Kalathur R, Yu K, Zhou S, Wang X, High AA, Peng J, Pruett-Miller SM, Daniels DL, Urh M, Shelat AA, Mullighan CG, Riching KM, Zaman GJR, Fischer M, Klco JM, Rankovic Z. Selective CK1α degraders exert antiproliferative activity against a broad range of human cancer cell lines. Nat Commun 2024; 15:482. [PMID: 38228616 PMCID: PMC10791743 DOI: 10.1038/s41467-024-44698-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 12/21/2023] [Indexed: 01/18/2024] Open
Abstract
Molecular-glue degraders are small molecules that induce a specific interaction between an E3 ligase and a target protein, resulting in the target proteolysis. The discovery of molecular glue degraders currently relies mostly on screening approaches. Here, we describe screening of a library of cereblon (CRBN) ligands against a panel of patient-derived cancer cell lines, leading to the discovery of SJ7095, a potent degrader of CK1α, IKZF1 and IKZF3 proteins. Through a structure-informed exploration of structure activity relationship (SAR) around this small molecule we develop SJ3149, a selective and potent degrader of CK1α protein in vitro and in vivo. The structure of SJ3149 co-crystalized in complex with CK1α + CRBN + DDB1 provides a rationale for the improved degradation properties of this compound. In a panel of 115 cancer cell lines SJ3149 displays a broad antiproliferative activity profile, which shows statistically significant correlation with MDM2 inhibitor Nutlin-3a. These findings suggest potential utility of selective CK1α degraders for treatment of hematological cancers and solid tumors.
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Affiliation(s)
- Gisele Nishiguchi
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Lauren G Mascibroda
- Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Sarah M Young
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Elizabeth A Caine
- Promega Corporation, 5430 East Cheryl Drive, Madison, WI, 53711, USA
| | - Sherif Abdelhamed
- Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | | | - Darcie J Miller
- Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Sourav Das
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Kevin McGowan
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Anand Mayasundari
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Zhe Shi
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Juan M Barajas
- Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Ryan Hiltenbrand
- Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Anup Aggarwal
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Yunchao Chang
- Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Vibhor Mishra
- Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Shilpa Narina
- Center for Advanced Genome Engineering, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Melvin Thomas
- Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Allister J Loughran
- Center for Advanced Genome Engineering, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Ravi Kalathur
- Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Kaiwen Yu
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Suiping Zhou
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Xusheng Wang
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Anthony A High
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Junmin Peng
- Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Shondra M Pruett-Miller
- Center for Advanced Genome Engineering, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Memphis, TN, 38105, USA
| | - Danette L Daniels
- Promega Corporation, 5430 East Cheryl Drive, Madison, WI, 53711, USA
| | - Marjeta Urh
- Promega Corporation, 5430 East Cheryl Drive, Madison, WI, 53711, USA
| | - Anang A Shelat
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Charles G Mullighan
- Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Kristin M Riching
- Promega Corporation, 5430 East Cheryl Drive, Madison, WI, 53711, USA
| | - Guido J R Zaman
- Oncolines B.V., Kloosterstraat 9, 5349 AB, Oss, The Netherlands
| | - Marcus Fischer
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA.
| | - Jeffery M Klco
- Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA.
| | - Zoran Rankovic
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA.
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106
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Guo M, Li Z, Gu M, Gu J, You Q, Wang L. Targeting phosphatases: From molecule design to clinical trials. Eur J Med Chem 2024; 264:116031. [PMID: 38101039 DOI: 10.1016/j.ejmech.2023.116031] [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] [Received: 10/23/2023] [Revised: 12/03/2023] [Accepted: 12/04/2023] [Indexed: 12/17/2023]
Abstract
Phosphatase is a kind of enzyme that can dephosphorylate target proteins, which can be divided into serine/threonine phosphatase and tyrosine phosphatase according to its mode of action. Current evidence showed multiple phosphatases were highly correlated with diseases including various cancers, demonstrating them as potential targets. However, currently, targeting phosphatases with small molecules faces many challenges, resulting in no drug approved. In this case, phosphatases are even regarded as "undruggable" targets for a long time. Recently, a variety of strategies have been adopted in the design of small molecule inhibitors targeting phosphatases, leading many of them to enter into the clinical trials. In this review, we classified these inhibitors into 4 types, including (1) molecular glues, (2) small molecules targeting catalytic sites, (3) allosteric inhibition, and (4) bifunctional molecules (proteolysis targeting chimeras, PROTACs). These molecules with diverse strategies prove the feasibility of phosphatases as drug targets. In addition, the combination therapy of phosphatase inhibitors with other drugs has also entered clinical trials, which suggests a broad prospect. Thus, targeting phosphatases with small molecules by different strategies is emerging as a promising way in the modulation of pathogenetic phosphorylation.
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Affiliation(s)
- Mochen Guo
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Zekun Li
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Mingxiao Gu
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Junrui Gu
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Qidong You
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China.
| | - Lei Wang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China.
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107
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Neri P, Barwick BG, Jung D, Patton JC, Maity R, Tagoug I, Stein CK, Tilmont R, Leblay N, Ahn S, Lee H, Welsh SJ, Riggs DL, Stong N, Flynt E, Thakurta A, Keats JJ, Lonial S, Bergsagel PL, Boise LH, Bahlis NJ. ETV4-Dependent Transcriptional Plasticity Maintains MYC Expression and Results in IMiD Resistance in Multiple Myeloma. Blood Cancer Discov 2024; 5:56-73. [PMID: 37934799 PMCID: PMC10772538 DOI: 10.1158/2643-3230.bcd-23-0061] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 10/01/2023] [Accepted: 11/03/2023] [Indexed: 11/09/2023] Open
Abstract
Immunomodulatory drugs (IMiD) are a backbone therapy for multiple myeloma (MM). Despite their efficacy, most patients develop resistance, and the mechanisms are not fully defined. Here, we show that IMiD responses are directed by IMiD-dependent degradation of IKZF1 and IKZF3 that bind to enhancers necessary to sustain the expression of MYC and other myeloma oncogenes. IMiD treatment universally depleted chromatin-bound IKZF1, but eviction of P300 and BRD4 coactivators only occurred in IMiD-sensitive cells. IKZF1-bound enhancers overlapped other transcription factor binding motifs, including ETV4. Chromatin immunoprecipitation sequencing showed that ETV4 bound to the same enhancers as IKZF1, and ETV4 CRISPR/Cas9-mediated ablation resulted in sensitization of IMiD-resistant MM. ETV4 expression is associated with IMiD resistance in cell lines, poor prognosis in patients, and is upregulated at relapse. These data indicate that ETV4 alleviates IKZF1 and IKZF3 dependency in MM by maintaining oncogenic enhancer activity and identify transcriptional plasticity as a previously unrecognized mechanism of IMiD resistance. SIGNIFICANCE We show that IKZF1-bound enhancers are critical for IMiD efficacy and that the factor ETV4 can bind the same enhancers and substitute for IKZF1 and mediate IMiD resistance by maintaining MYC and other oncogenes. These data implicate transcription factor redundancy as a previously unrecognized mode of IMiD resistance in MM. See related article by Welsh, Barwick, et al., p. 34. See related commentary by Yun and Cleveland, p. 5. This article is featured in Selected Articles from This Issue, p. 4.
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Affiliation(s)
- Paola Neri
- Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Canada
| | - Benjamin G. Barwick
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University, Atlanta, Georgia
| | - David Jung
- Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Canada
| | - Jonathan C. Patton
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University, Atlanta, Georgia
| | - Ranjan Maity
- Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Canada
| | - Ines Tagoug
- Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Canada
| | - Caleb K. Stein
- Division of Hematology and Oncology, Mayo Clinic, Scottsdale, Arizona
| | - Remi Tilmont
- Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Canada
| | - Noemie Leblay
- Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Canada
| | - Sungwoo Ahn
- Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Canada
| | - Holly Lee
- Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Canada
| | - Seth J. Welsh
- Division of Hematology and Oncology, Mayo Clinic, Scottsdale, Arizona
| | - Daniel L. Riggs
- Division of Hematology and Oncology, Mayo Clinic, Scottsdale, Arizona
| | - Nicholas Stong
- Translational Medicine, Bristol Myers Squibb, Summit, New Jersey
| | - Erin Flynt
- Predictive Sciences, Bristol Myers Squibb, Summit, New Jersey
| | - Anjan Thakurta
- Oxford Centre for Translational Myeloma Research, University of Oxford, Oxford, United Kingdom
| | | | - Sagar Lonial
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University, Atlanta, Georgia
| | - P. Leif Bergsagel
- Division of Hematology and Oncology, Mayo Clinic, Scottsdale, Arizona
| | - Lawrence H. Boise
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University, Atlanta, Georgia
| | - Nizar J. Bahlis
- Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Canada
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108
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Welsh SJ, Barwick BG, Meermeier EW, Riggs DL, Shi CX, Zhu YX, Sharik ME, Du MT, Abrego Rocha LD, Garbitt VM, Stein CK, Petit JL, Meurice N, Tafoya Alvarado Y, Fonseca R, Todd KT, Brown S, Hammond ZJ, Cuc NH, Wittenberg C, Herzog C, Roschke AV, Demchenko YN, Chen WDD, Li P, Liao W, Leonard WJ, Lonial S, Bahlis NJ, Neri P, Boise LH, Chesi M, Bergsagel PL. Transcriptional Heterogeneity Overcomes Super-Enhancer Disrupting Drug Combinations in Multiple Myeloma. Blood Cancer Discov 2024; 5:34-55. [PMID: 37767768 PMCID: PMC10772542 DOI: 10.1158/2643-3230.bcd-23-0062] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 09/05/2023] [Accepted: 09/27/2023] [Indexed: 09/29/2023] Open
Abstract
Multiple myeloma (MM) is a malignancy that is often driven by MYC and that is sustained by IRF4, which are upregulated by super-enhancers. IKZF1 and IKZF3 bind to super-enhancers and can be degraded using immunomodulatory imide drugs (IMiD). Successful IMiD responses downregulate MYC and IRF4; however, this fails in IMiD-resistant cells. MYC and IRF4 downregulation can also be achieved in IMiD-resistant tumors using inhibitors of BET and EP300 transcriptional coactivator proteins; however, in vivo these drugs have a narrow therapeutic window. By combining IMiDs with EP300 inhibition, we demonstrate greater downregulation of MYC and IRF4, synergistic killing of myeloma in vitro and in vivo, and an increased therapeutic window. Interestingly, this potent combination failed where MYC and IRF4 expression was maintained by high levels of the AP-1 factor BATF. Our results identify an effective drug combination and a previously unrecognized mechanism of IMiD resistance. SIGNIFICANCE These results highlight the dependence of MM on IKZF1-bound super-enhancers, which can be effectively targeted by a potent therapeutic combination pairing IMiD-mediated degradation of IKZF1 and IKZF3 with EP300 inhibition. They also identify AP-1 factors as an unrecognized mechanism of IMiD resistance in MM. See related article by Neri, Barwick, et al., p. 56. See related commentary by Yun and Cleveland, p. 5. This article is featured in Selected Articles from This Issue, p. 4.
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Affiliation(s)
- Seth J. Welsh
- Department of Medicine, Division of Hematology/Oncology, Mayo Clinic, Scottsdale, Arizona
| | - Benjamin G. Barwick
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University School of Medicine, Atlanta, Georgia
| | - Erin W. Meermeier
- Department of Medicine, Division of Hematology/Oncology, Mayo Clinic, Scottsdale, Arizona
| | - Daniel L. Riggs
- Department of Medicine, Division of Hematology/Oncology, Mayo Clinic, Scottsdale, Arizona
| | - Chang-Xin Shi
- Department of Medicine, Division of Hematology/Oncology, Mayo Clinic, Scottsdale, Arizona
| | - Yuan Xiao Zhu
- Department of Medicine, Division of Hematology/Oncology, Mayo Clinic, Scottsdale, Arizona
| | - Meaghen E. Sharik
- Department of Medicine, Division of Hematology/Oncology, Mayo Clinic, Scottsdale, Arizona
| | - Megan T. Du
- Department of Medicine, Division of Hematology/Oncology, Mayo Clinic, Scottsdale, Arizona
| | - Leslie D. Abrego Rocha
- Department of Medicine, Division of Hematology/Oncology, Mayo Clinic, Scottsdale, Arizona
| | - Victoria M. Garbitt
- Department of Medicine, Division of Hematology/Oncology, Mayo Clinic, Scottsdale, Arizona
| | - Caleb K. Stein
- Department of Medicine, Division of Hematology/Oncology, Mayo Clinic, Scottsdale, Arizona
| | - Joachim L. Petit
- Department of Medicine, Division of Hematology/Oncology, Mayo Clinic, Scottsdale, Arizona
| | - Nathalie Meurice
- Department of Medicine, Division of Hematology/Oncology, Mayo Clinic, Scottsdale, Arizona
| | - Yuliza Tafoya Alvarado
- Department of Medicine, Division of Hematology/Oncology, Mayo Clinic, Scottsdale, Arizona
| | - Rodrigo Fonseca
- Department of Medicine, Division of Hematology/Oncology, Mayo Clinic, Scottsdale, Arizona
| | - Kennedi T. Todd
- Department of Medicine, Division of Hematology/Oncology, Mayo Clinic, Scottsdale, Arizona
| | - Sochilt Brown
- Department of Medicine, Division of Hematology/Oncology, Mayo Clinic, Scottsdale, Arizona
| | - Zachery J. Hammond
- Department of Medicine, Division of Hematology/Oncology, Mayo Clinic, Scottsdale, Arizona
| | - Nicklus H. Cuc
- Department of Medicine, Division of Hematology/Oncology, Mayo Clinic, Scottsdale, Arizona
| | - Courtney Wittenberg
- Department of Medicine, Division of Hematology/Oncology, Mayo Clinic, Scottsdale, Arizona
| | - Camille Herzog
- Department of Medicine, Division of Hematology/Oncology, Mayo Clinic, Scottsdale, Arizona
| | - Anna V. Roschke
- Genetics Branch, Center for Cancer Research, NCI, Bethesda, Maryland
| | | | - Wei-dong D. Chen
- Genetics Branch, Center for Cancer Research, NCI, Bethesda, Maryland
| | - Peng Li
- Laboratory of Molecular Immunology and the Immunology Center, National Heart, Lung and Blood Institute, NIH, Bethesda, Maryland
| | - Wei Liao
- Laboratory of Molecular Immunology and the Immunology Center, National Heart, Lung and Blood Institute, NIH, Bethesda, Maryland
| | - Warren J. Leonard
- Laboratory of Molecular Immunology and the Immunology Center, National Heart, Lung and Blood Institute, NIH, Bethesda, Maryland
| | - Sagar Lonial
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University School of Medicine, Atlanta, Georgia
| | - Nizar J. Bahlis
- Department of Medical Oncology and Hematology, Tom Baker Cancer Center, Calgary, Canada
- Charbonneau Cancer Research Institute, University of Calgary, Calgary, Canada
| | - Paola Neri
- Department of Medical Oncology and Hematology, Tom Baker Cancer Center, Calgary, Canada
- Charbonneau Cancer Research Institute, University of Calgary, Calgary, Canada
| | - Lawrence H. Boise
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University School of Medicine, Atlanta, Georgia
| | - Marta Chesi
- Department of Medicine, Division of Hematology/Oncology, Mayo Clinic, Scottsdale, Arizona
| | - P. Leif Bergsagel
- Department of Medicine, Division of Hematology/Oncology, Mayo Clinic, Scottsdale, Arizona
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Yun S, Cleveland JL. Transcriptional Plasticity Drives IMiD and p300 Inhibitor Resistance in Multiple Myeloma. Blood Cancer Discov 2024; 5:5-7. [PMID: 38085608 PMCID: PMC10772544 DOI: 10.1158/2643-3230.bcd-23-0223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2024] Open
Abstract
SUMMARY In this issue of Blood Cancer Discovery, Neri, Barwick, and colleagues and Welsh, Barwick, and colleagues performed RNA sequencing, chromatin immunoprecipitation sequencing, assay for transposase-accessible chromatin using sequencing, and genetic studies to characterize the underlying mechanisms of immunomodulatory drug (IMiD) resistance in multiple myeloma. They demonstrated that IMiD resistance is driven by sustained expression of MYC and IRF4 via transcriptional plasticity that involves induction of ETV4 and BATF proteins, the binding of these proteins to their super-enhancers, and the recruitment of BRD4 and p300. Finally, these studies suggest IMiD and p300 inhibitor combination as a promising therapeutic strategy in multiple myeloma. See related article by Neri, Barwick, et al., p. 56 (9). See related article by Welsh, Barwick, et al., p. 34 (10).
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Affiliation(s)
- Seongseok Yun
- Department of Malignant Hematology, Moffitt Cancer Center & Research Institute, Tampa, Florida
| | - John L. Cleveland
- Department of Tumor Microenvironment & Metastasis, Moffitt Cancer Center & Research Institute, Tampa, Florida
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Jiang W, Jiang Y, Luo Y, Qiao W, Yang T. Facilitating the development of molecular glues: Opportunities from serendipity and rational design. Eur J Med Chem 2024; 263:115950. [PMID: 37984298 DOI: 10.1016/j.ejmech.2023.115950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 11/09/2023] [Accepted: 11/09/2023] [Indexed: 11/22/2023]
Abstract
Molecular glues can specifically induce interactions between two or more proteins to modulate biological functions and have been proven to be a powerful therapeutic modality in drug discovery. It plays a variety of vital roles in several biological processes, such as complex stabilization, interactome modulation and transporter inhibition, thus enabling challenging therapeutic targets to be druggable. Most known molecular glues were identified serendipitously, such as IMiDs, auxin, and rapamycin. In recent years, more rational strategies were explored with the development of chemical biology and a deep understanding of the interaction between molecular glues and proteins, which led to the rational discovery of several molecular glues. Thus, in this review, we aim to highlight the discovery strategies of molecular glues from three aspects: serendipitous discovery, screening methods and rational design principles. We expect that this review will provide a reasonable reference and insights for the discovery of molecular glues.
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Affiliation(s)
- Weiqing Jiang
- Laboratory of Human Diseases and Immunotherapies, and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China; Institute of Immunology and Inflammation, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Yunhan Jiang
- Laboratory of Human Diseases and Immunotherapies, and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China; Institute of Immunology and Inflammation, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, China; Cardiovascular Surgery Research Laboratory, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Youfu Luo
- Laboratory of Human Diseases and Immunotherapies, and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China.
| | - Wenliang Qiao
- Lung Cancer Center, Laboratory of Lung Cancer, West China Hospital, Sichuan University, Chengdu, 610041, China.
| | - Tao Yang
- Laboratory of Human Diseases and Immunotherapies, and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China; Institute of Immunology and Inflammation, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, China.
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111
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Liu BH, Liu M, Radhakrishnan S, Jaladanki CK, Gao C, Tang JP, Kumari K, Go ML, Vu KAL, Seo HS, Song K, Tian X, Feng L, Tan JL, Bassal MA, Arthanari H, Qi J, Dhe-Paganon S, Fan H, Tenen DG, Chai L. Targeting transcription factors through an IMiD independent zinc finger domain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.03.574032. [PMID: 38260640 PMCID: PMC10802279 DOI: 10.1101/2024.01.03.574032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Immunomodulatory imide drugs (IMiDs) degrade specific C2H2 zinc finger degrons in transcription factors, making them effective against certain cancers. SALL4, a cancer driver, contains seven C2H2 zinc fingers in four clusters, including an IMiD degron in zinc finger cluster two (ZFC2). Surprisingly, IMiDs do not inhibit growth of SALL4 expressing cancer cells. To overcome this limit, we focused on a non-IMiD degron, SALL4 zinc finger cluster four (ZFC4). By combining AlphaFold and the ZFC4-DNA crystal structure, we identified a potential ZFC4 drug pocket. Utilizing an in silico docking algorithm and cell viability assays, we screened chemical libraries and discovered SH6, which selectively targets SALL4-expressing cancer cells. Mechanistic studies revealed that SH6 degrades SALL4 protein through the CUL4A/CRBN pathway, while deletion of ZFC4 abolished this activity. Moreover, SH6 led to significant 62% tumor growth inhibition of SALL4+ xenografts in vivo and demonstrated good bioavailability in pharmacokinetic studies. In summary, these studies represent a new approach for IMiD independent drug discovery targeting C2H2 transcription factors in cancer.
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Yoon H, Rutter JC, Li YD, Ebert BL. Induced protein degradation for therapeutics: past, present, and future. J Clin Invest 2024; 134:e175265. [PMID: 38165043 PMCID: PMC10760958 DOI: 10.1172/jci175265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024] Open
Abstract
The concept of induced protein degradation by small molecules has emerged as a promising therapeutic strategy that is particularly effective in targeting proteins previously considered "undruggable." Thalidomide analogs, employed in the treatment of multiple myeloma, stand as prime examples. These compounds serve as molecular glues, redirecting the CRBN E3 ubiquitin ligase to degrade myeloma-dependency factors, IKZF1 and IKZF3. The clinical success of thalidomide analogs demonstrates the therapeutic potential of induced protein degradation. Beyond molecular glue degraders, several additional modalities to trigger protein degradation have been developed and are currently under clinical evaluation. These include heterobifunctional degraders, polymerization-induced degradation, ligand-dependent degradation of nuclear hormone receptors, disruption of protein interactions, and various other strategies. In this Review, we will provide a concise overview of various degradation modalities, their clinical applications, and potential future directions in the field of protein degradation.
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Affiliation(s)
- Hojong Yoon
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Justine C. Rutter
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Yen-Der Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Benjamin L. Ebert
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Howard Hughes Medical Institute, Boston, Massachusetts, USA
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Basu B, Kal S, Karmakar S, Basu M, Ghosh MK. E3 ubiquitin ligases in lung cancer: Emerging insights and therapeutic opportunities. Life Sci 2024; 336:122333. [PMID: 38061537 DOI: 10.1016/j.lfs.2023.122333] [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] [Received: 10/11/2023] [Revised: 11/29/2023] [Accepted: 12/04/2023] [Indexed: 12/18/2023]
Abstract
Aim In this review, we have attempted to provide the readers with an updated account of the role of a family of proteins known as E3 ligases in different aspects of lung cancer progression, along with insights into the deregulation of expression of these proteins during lung cancer. A detailed account of the therapeutic strategies involving E3 ligases that have been developed or currently under development has also been provided in this review. MATERIALS AND METHODS: The review article employs extensive literature search, along with differential gene expression analysis of lung cancer associated E3 ligases using the DESeq2 package in R, and the Gene Expression Profiling Interactive Analysis (GEPIA) database (http://gepia.cancer-pku.cn/). Protein expression analysis of CPTAC lung cancer samples was carried out using the UALCAN webtool (https://ualcan.path.uab.edu/index.html). Assessment of patient overall survival (OS) in response to high and low expression of selected E3 ligases was performed using the online Kaplan-Meier plotter (https://kmplot.com/analysis/index.php?p=background). KEY FINDINGS: SIGNIFICANCE: The review provides an in-depth understanding of the role of E3 ligases in lung cancer progression and an up-to-date account of the different therapeutic strategies targeting oncogenic E3 ligases for improved lung cancer management.
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Affiliation(s)
- Bhaskar Basu
- Cancer Biology and Inflammatory Disorder Division, Council of Scientific and Industrial Research-Indian Institute of Chemical Biology (CSIR-IICB), TRUE Campus, CN-6, Sector-V, Salt Lake, Kolkata- 700091 & 4, Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Satadeepa Kal
- Cancer Biology and Inflammatory Disorder Division, Council of Scientific and Industrial Research-Indian Institute of Chemical Biology (CSIR-IICB), TRUE Campus, CN-6, Sector-V, Salt Lake, Kolkata- 700091 & 4, Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Subhajit Karmakar
- Cancer Biology and Inflammatory Disorder Division, Council of Scientific and Industrial Research-Indian Institute of Chemical Biology (CSIR-IICB), TRUE Campus, CN-6, Sector-V, Salt Lake, Kolkata- 700091 & 4, Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Malini Basu
- Department of Microbiology, Dhruba Chand Halder College, Dakshin Barasat, South 24 Parganas, PIN -743372, India
| | - Mrinal K Ghosh
- Cancer Biology and Inflammatory Disorder Division, Council of Scientific and Industrial Research-Indian Institute of Chemical Biology (CSIR-IICB), TRUE Campus, CN-6, Sector-V, Salt Lake, Kolkata- 700091 & 4, Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India.
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114
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Hasan A, Khan NA, Uddin S, Khan AQ, Steinhoff M. Deregulated transcription factors in the emerging cancer hallmarks. Semin Cancer Biol 2024; 98:31-50. [PMID: 38123029 DOI: 10.1016/j.semcancer.2023.12.001] [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] [Received: 09/28/2023] [Revised: 11/25/2023] [Accepted: 12/14/2023] [Indexed: 12/23/2023]
Abstract
Cancer progression is a multifaceted process that entails several stages and demands the persistent expression or activation of transcription factors (TFs) to facilitate growth and survival. TFs are a cluster of proteins with DNA-binding domains that attach to promoter or enhancer DNA strands to start the transcription of genes by collaborating with RNA polymerase and other supporting proteins. They are generally acknowledged as the major regulatory molecules that coordinate biological homeostasis and the appropriate functioning of cellular components, subsequently contributing to human physiology. TFs proteins are crucial for controlling transcription during the embryonic stage and development, and the stability of different cell types depends on how they function in different cell types. The development and progression of cancer cells and tumors might be triggered by any anomaly in transcription factor function. It has long been acknowledged that cancer development is accompanied by the dysregulated activity of TF alterations which might result in faulty gene expression. Recent studies have suggested that dysregulated transcription factors play a major role in developing various human malignancies by altering and rewiring metabolic processes, modifying the immune response, and triggering oncogenic signaling cascades. This review emphasizes the interplay between TFs involved in metabolic and epigenetic reprogramming, evading immune attacks, cellular senescence, and the maintenance of cancer stemness in cancerous cells. The insights presented herein will facilitate the development of innovative therapeutic modalities to tackle the dysregulated transcription factors underlying cancer.
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Affiliation(s)
- Adria Hasan
- Molecular Cell Biology Laboratory, Integral Information and Research Centre-4 (IIRC-4), Integral University, Lucknow 226026, India; Department of Bioengineering, Faculty of Engineering, Integral University, Lucknow 226026, India
| | - Naushad Ahmad Khan
- Department of Surgery, Trauma and Vascular Surgery Clinical Research, Hamad General Hospital, Doha 3050, Qatar
| | - Shahab Uddin
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha 3050, Qatar; Department of Biosciences, Integral University, Lucknow 226026, India; Animal Research Center, Qatar University, Doha, Qatar; Dermatology Institute, Academic Health System, Hamad Medical Corporation, Doha 3050, Qatar
| | - Abdul Q Khan
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha 3050, Qatar.
| | - Martin Steinhoff
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha 3050, Qatar; Animal Research Center, Qatar University, Doha, Qatar; Department of Dermatology and Venereology, Rumailah Hospital, Hamad Medical Corporation, Doha 3050, Qatar; Department of Medicine, Weill Cornell Medicine Qatar, Qatar Foundation-Education City, Doha 24144, Qatar; Department of Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA; College of Medicine, Qatar University, Doha 2713, Qatar
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115
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Liu Z, Jiang S, Hao B, Xie S, Liu Y, Huang Y, Xu H, Luo C, Huang M, Tan M, Xu JY. A proteomic landscape of pharmacologic perturbations for functional relevance. J Pharm Anal 2024; 14:128-139. [PMID: 38352953 PMCID: PMC10859532 DOI: 10.1016/j.jpha.2023.08.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Revised: 08/11/2023] [Accepted: 08/29/2023] [Indexed: 02/16/2024] Open
Abstract
Pharmacological perturbation studies based on protein-level signatures are fundamental for drug discovery. In the present study, we used a mass spectrometry (MS)-based proteomic platform to profile the whole proteome of the breast cancer MCF7 cell line under stress induced by 78 bioactive compounds. The integrated analysis of perturbed signal abundance revealed the connectivity between phenotypic behaviors and molecular features in cancer cells. Our data showed functional relevance in exploring the novel pharmacological activity of phenolic xanthohumol, as well as the noncanonical targets of clinically approved tamoxifen, lovastatin, and their derivatives. Furthermore, the rational design of synergistic inhibition using a combination of histone methyltransferase and topoisomerase was identified based on their complementary drug fingerprints. This study provides rich resources for the proteomic landscape of drug responses for precision therapeutic medicine.
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Affiliation(s)
- Zhiwei Liu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Shangwen Jiang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Bingbing Hao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Shuyu Xie
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Yingluo Liu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Yuqi Huang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Heng Xu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Cheng Luo
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Min Huang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Minjia Tan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, 210023, China
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan, Guangdong, 528400, China
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, 210023, China
| | - Jun-Yu Xu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, 210023, China
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan, Guangdong, 528400, China
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116
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Aquilanti E, Goldoni S, Baker A, Kotynkova K, Andersen S, Bozinov V, Gao GF, Cherniack AD, Lange M, Lesche R, Kopitz C, Lienau P, Lewis TA, Garrido M, Gradl S, Seidel H, Tseng YY, Ligon KL, Wen PY, Meyerson M, Greulich H. Velcrin molecular glues induce apoptosis in glioblastomas with high PDE3A and SLFN12 expression. Neurooncol Adv 2024; 6:vdae115. [PMID: 39166256 PMCID: PMC11333922 DOI: 10.1093/noajnl/vdae115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/22/2024] Open
Abstract
Background Velcrins are molecular glues that kill cells by inducing the formation of a protein complex between the RNase SLFN12 and the phosphodiesterase PDE3A. Formation of the complex activates SLFN12, which cleaves tRNALeu(TAA) and induces apoptosis. Velcrins such as the clinical investigational compound, BAY 2666605, were found to have activity across multiple solid tumor cell lines from the cancer cell line encyclopedia, including glioblastoma cell lines. We therefore aim to characterize velcrins as novel therapeutic agents in glioblastoma. Materials and Methods PDE3A and SLFN12 expression levels were measured in glioblastoma cell lines, the Cancer Genome Atlas (TCGA) tumor samples, and tumor neurospheres. Velcrin-treated cells were assayed for viability, induction of apoptosis, cell cycle phases, and global changes in translation. Transcriptional profiling of the cells was obtained. Xenograft-harboring mice treated with velcrins were also monitored for survival. Results We identified several velcrin-sensitive glioblastoma cell lines and 4 velcrin-sensitive glioblastoma patient-derived models. We determined that BAY 2666605 crosses the blood-brain barrier and elicits full tumor regression in an orthotopic xenograft model of GB1 cells. We also determined that the velcrins BAY 2666605 and BRD3800 induce tumor regression in subcutaneous glioblastoma PDX models. Conclusions Velcrins have antitumor activity in preclinical models of glioblastoma, warranting further investigation as potential therapeutic agents.
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Affiliation(s)
- Elisa Aquilanti
- Cancer Program, Broad Institute, Cambridge, Massachusetts, USA
- Division of Neuro-Oncology, Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts, USA
| | - Silvia Goldoni
- Bayer Pharmaceuticals, Research and Early Development Oncology, Cambridge, Massachusetts, USA
| | - Andrew Baker
- Department of Pediatric Oncology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | | | - Sawyer Andersen
- Cancer Program, Broad Institute, Cambridge, Massachusetts, USA
| | - Vincent Bozinov
- Cancer Program, Broad Institute, Cambridge, Massachusetts, USA
| | - Galen F Gao
- School of Medicine, University of Texas Southwestern, Dallas, Texas, USA
| | - Andrew D Cherniack
- Cancer Program, Broad Institute, Cambridge, Massachusetts, USA
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts, USA
| | - Martin Lange
- Nuvisan ICB GmbH, Therapeutic Research, Berlin, Germany
- Research and Development, Pharmaceuticals, Bayer AG, Berlin, Germany
| | - Ralf Lesche
- Nuvisan ICB GmbH, Therapeutic Research, Berlin, Germany
- Research and Development, Pharmaceuticals, Bayer AG, Berlin, Germany
| | - Charlotte Kopitz
- Nuvisan ICB GmbH, Therapeutic Research, Berlin, Germany
- Research and Development, Pharmaceuticals, Bayer AG, Berlin, Germany
| | - Philip Lienau
- Research and Development, Pharmaceuticals, Bayer AG, Berlin, Germany
| | - Timothy A Lewis
- Center for the Development of Therapeutics, Broad Institute, Cambridge, Massachusetts, USA
| | - Marine Garrido
- Bayer Consumer Care AG, Research and Early Development Oncology, Basel, Switzerland
| | - Stefan Gradl
- Research and Development, Pharmaceuticals, Bayer AG, Berlin, Germany
| | - Henrik Seidel
- Research and Development, Pharmaceuticals, Bayer AG, Berlin, Germany
| | - Yuen-Yi Tseng
- Cancer Program, Broad Institute, Cambridge, Massachusetts, USA
| | - Keith L Ligon
- Department of Pathology, Brigham and Women’s Hospital, Boston Children’s Hospital, Dana Farber Cancer Institute, Boston, Massachusetts, USA
| | - Patrick Y Wen
- Division of Neuro-Oncology, Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts, USA
| | - Matthew Meyerson
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
- Cancer Program, Broad Institute, Cambridge, Massachusetts, USA
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts, USA
| | - Heidi Greulich
- Cancer Program, Broad Institute, Cambridge, Massachusetts, USA
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts, USA
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Kastner P, Chan S. IKAROS Family Transcription Factors in Lymphocyte Differentiation and Function. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1459:33-52. [PMID: 39017838 DOI: 10.1007/978-3-031-62731-6_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/18/2024]
Abstract
The IKAROS family of transcription factors comprises four zinc-finger proteins (IKAROS, HELIOS, AIOLOS, and EOS), which over the last decades have been established to be critical regulators of the development and function of lymphoid cells. These factors act as homo- or heterodimers and are involved both in gene activation and repression. Their function often involves cross-talk with other regulatory circuits, such as the JAK/STAT, NF-κB, and NOTCH pathways. They control lymphocyte differentiation at multiple stages and are notably critical for lymphoid commitment in multipotent hematopoietic progenitors and for T and B cell differentiation downstream of pre-TCR and pre-BCR signaling. They also control many aspects of effector functions in mature B and T cells. They are dysregulated or mutated in multiple pathologies affecting the lymphoid system, which range from leukemia to immunodeficiencies. In this chapter, we review the molecular and physiological function of these factors in lymphocytes and their implications in human pathologies.
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Affiliation(s)
- Philippe Kastner
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch-Graffenstaden, France.
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, Illkirch-Graffenstaden, France.
- Centre National de la Recherche Scientifique (CNRS), UMR7104, Illkirch-Graffenstaden, France.
- Université de Strasbourg, Illkirch-Graffenstaden, France.
- Faculté de Médecine, Université de Strasbourg, Strasbourg, France.
| | - Susan Chan
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch-Graffenstaden, France.
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, Illkirch-Graffenstaden, France.
- Centre National de la Recherche Scientifique (CNRS), UMR7104, Illkirch-Graffenstaden, France.
- Université de Strasbourg, Illkirch-Graffenstaden, France.
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Miyamoto DK, Curnutt NM, Park SM, Stavropoulos A, Kharas MG, Woo CM. Design and Development of IKZF2 and CK1α Dual Degraders. J Med Chem 2023; 66:16953-16979. [PMID: 38085607 PMCID: PMC11302056 DOI: 10.1021/acs.jmedchem.3c01736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2023]
Abstract
Lenalidomide achieves its therapeutic efficacy by recruiting and removing proteins of therapeutic interest through the E3 ligase substrate adapter cereblon. Here, we report the design and characterization of 81 cereblon ligands for their ability to degrade the transcription factor Helios (IKZF2) and casein kinase 1 alpha (CK1α). We identified a key naphthamide scaffold that depleted both intended targets in acute myeloid leukemia MOLM-13 cells. Structure-activity relationship studies for degradation of the desired targets over other targets (IKZF1, GSPT1) afforded an initial lead compound DEG-35. A subsequent scaffold replacement campaign identified DEG-77, which selectively degrades IKZF2 and CK1α, and possesses suitable pharmacokinetic properties, solubility, and selectivity for in vivo studies. Finally, we show that DEG-77 has antiproliferative activity in the diffuse large B cell lymphoma cell line OCI-LY3 and the ovarian cancer cell line A2780 indicating that the dual degrader strategy may have efficacy against additional types of cancer.
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Affiliation(s)
- David K. Miyamoto
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Nicole M. Curnutt
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Sun Mi Park
- Molecular Pharmacology Program and Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Alexios Stavropoulos
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Michael G. Kharas
- Molecular Pharmacology Program and Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Christina M. Woo
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA
- Affiliate member, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
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Spano D, Catara G. Targeting the Ubiquitin-Proteasome System and Recent Advances in Cancer Therapy. Cells 2023; 13:29. [PMID: 38201233 PMCID: PMC10778545 DOI: 10.3390/cells13010029] [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] [Received: 11/13/2023] [Revised: 12/12/2023] [Accepted: 12/20/2023] [Indexed: 01/12/2024] Open
Abstract
Ubiquitination is a reversible post-translational modification based on the chemical addition of ubiquitin to proteins with regulatory effects on various signaling pathways. Ubiquitination can alter the molecular functions of tagged substrates with respect to protein turnover, biological activity, subcellular localization or protein-protein interaction. As a result, a wide variety of cellular processes are under ubiquitination-mediated control, contributing to the maintenance of cellular homeostasis. It follows that the dysregulation of ubiquitination reactions plays a relevant role in the pathogenic states of human diseases such as neurodegenerative diseases, immune-related pathologies and cancer. In recent decades, the enzymes of the ubiquitin-proteasome system (UPS), including E3 ubiquitin ligases and deubiquitinases (DUBs), have attracted attention as novel druggable targets for the development of new anticancer therapeutic approaches. This perspective article summarizes the peculiarities shared by the enzymes involved in the ubiquitination reaction which, when deregulated, can lead to tumorigenesis. Accordingly, an overview of the main pharmacological interventions based on targeting the UPS that are in clinical use or still in clinical trials is provided, also highlighting the limitations of the therapeutic efficacy of these approaches. Therefore, various attempts to circumvent drug resistance and side effects as well as UPS-related emerging technologies in anticancer therapeutics are discussed.
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Affiliation(s)
- Daniela Spano
- Institute for Endocrinology and Experimental Oncology “G. Salvatore”, National Research Council, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Giuliana Catara
- Institute of Biochemistry and Cell Biology, National Research Council, Via Pietro Castellino 111, 80131 Naples, Italy
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120
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Wang Z, Shaabani S, Gao X, Ng YLD, Sapozhnikova V, Mertins P, Krönke J, Dömling A. Direct-to-biology, automated, nano-scale synthesis, and phenotypic screening-enabled E3 ligase modulator discovery. Nat Commun 2023; 14:8437. [PMID: 38114468 PMCID: PMC10730884 DOI: 10.1038/s41467-023-43614-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 11/09/2023] [Indexed: 12/21/2023] Open
Abstract
Thalidomide and its analogs are molecular glues (MGs) that lead to targeted ubiquitination and degradation of key cancer proteins via the cereblon (CRBN) E3 ligase. Here, we develop a direct-to-biology (D2B) approach for accelerated discovery of MGs. In this platform, automated, high throughput, and nano scale synthesis of hundreds of pomalidomide-based MGs was combined with rapid phenotypic screening, enabling an unprecedented fast identification of potent CRBN-acting MGs. The small molecules were further validated by degradation profiling and anti-cancer activity. This revealed E14 as a potent MG degrader targeting IKZF1/3, GSPT1 and 2 with profound effects on a panel of cancer cells. In a more generalized view, integration of automated, nanoscale synthesis with phenotypic assays has the potential to accelerate MGs discovery.
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Affiliation(s)
- Zefeng Wang
- University of Groningen, Department of Drug Design, A. Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Shabnam Shaabani
- University of Groningen, Department of Drug Design, A. Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Xiang Gao
- Department of Internal Medicine III, University Hospital Ulm, 89081, Ulm, Germany
| | - Yuen Lam Dora Ng
- Department of Hematology, Oncology and Cancer Immunology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Valeriia Sapozhnikova
- Department of Hematology, Oncology and Cancer Immunology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- German Cancer Consortium (DKTK) partner site Berlin and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Philipp Mertins
- Max Delbrück Center for Molecular Medicine, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Jan Krönke
- Department of Hematology, Oncology and Cancer Immunology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.
- German Cancer Consortium (DKTK) partner site Berlin and German Cancer Research Center (DKFZ), Heidelberg, Germany.
| | - Alexander Dömling
- University of Groningen, Department of Drug Design, A. Deusinglaan 1, 9713 AV, Groningen, The Netherlands.
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry and Czech Advanced Technology and Research Institute, Palackӯ University in Olomouc, Olomouc, Czech Republic.
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121
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Ng A, Offensperger F, Cisneros JA, Scholes NS, Malik M, Villanti L, Rukavina A, Ferrada E, Hannich JT, Koren A, Kubicek S, Superti-Furga G, Winter GE. Discovery of Molecular Glue Degraders via Isogenic Morphological Profiling. ACS Chem Biol 2023; 18:2464-2473. [PMID: 38098458 PMCID: PMC10764104 DOI: 10.1021/acschembio.3c00598] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 11/11/2023] [Accepted: 11/15/2023] [Indexed: 12/18/2023]
Abstract
Molecular glue degraders (MGDs) are small molecules that degrade proteins of interest via the ubiquitin-proteasome system. While MGDs were historically discovered serendipitously, approaches for MGD discovery now include cell-viability-based drug screens or data mining of public transcriptomics and drug response datasets. These approaches, however, have target spaces restricted to the essential proteins. Here we develop a high-throughput workflow for MGD discovery that also reaches the nonessential proteome. This workflow begins with the rapid synthesis of a compound library by sulfur(VI) fluoride exchange chemistry coupled to a morphological profiling assay in isogenic cell lines that vary in levels of the E3 ligase CRBN. By comparing the morphological changes induced by compound treatment across the isogenic cell lines, we were able to identify FL2-14 as a CRBN-dependent MGD targeting the nonessential protein GSPT2. We envision that this workflow would contribute to the discovery and characterization of MGDs that target a wider range of proteins.
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Affiliation(s)
- Amanda Ng
- CeMM
Research Center for Molecular Medicine of the Austrian Academy of
Sciences, 1090 Vienna, Austria
| | - Fabian Offensperger
- CeMM
Research Center for Molecular Medicine of the Austrian Academy of
Sciences, 1090 Vienna, Austria
| | - Jose A. Cisneros
- CeMM
Research Center for Molecular Medicine of the Austrian Academy of
Sciences, 1090 Vienna, Austria
| | - Natalie S. Scholes
- CeMM
Research Center for Molecular Medicine of the Austrian Academy of
Sciences, 1090 Vienna, Austria
| | - Monika Malik
- CeMM
Research Center for Molecular Medicine of the Austrian Academy of
Sciences, 1090 Vienna, Austria
| | - Ludovica Villanti
- CeMM
Research Center for Molecular Medicine of the Austrian Academy of
Sciences, 1090 Vienna, Austria
| | - Andrea Rukavina
- CeMM
Research Center for Molecular Medicine of the Austrian Academy of
Sciences, 1090 Vienna, Austria
| | - Evandro Ferrada
- CeMM
Research Center for Molecular Medicine of the Austrian Academy of
Sciences, 1090 Vienna, Austria
| | - J. Thomas Hannich
- CeMM
Research Center for Molecular Medicine of the Austrian Academy of
Sciences, 1090 Vienna, Austria
| | - Anna Koren
- CeMM
Research Center for Molecular Medicine of the Austrian Academy of
Sciences, 1090 Vienna, Austria
| | - Stefan Kubicek
- CeMM
Research Center for Molecular Medicine of the Austrian Academy of
Sciences, 1090 Vienna, Austria
| | - Giulio Superti-Furga
- CeMM
Research Center for Molecular Medicine of the Austrian Academy of
Sciences, 1090 Vienna, Austria
- Center
for Physiology and Pharmacology, Medical
University of Vienna, 1090 Vienna, Austria
| | - Georg E. Winter
- CeMM
Research Center for Molecular Medicine of the Austrian Academy of
Sciences, 1090 Vienna, Austria
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122
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Tao AJ, Jiang J, Gadbois GE, Goyal P, Boyle BT, Mumby EJ, Myers SA, English JG, Ferguson FM. A biotin targeting chimera (BioTAC) system to map small molecule interactomes in situ. Nat Commun 2023; 14:8016. [PMID: 38049406 PMCID: PMC10695998 DOI: 10.1038/s41467-023-43507-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 11/12/2023] [Indexed: 12/06/2023] Open
Abstract
Understanding how small molecules bind to specific protein complexes in living cells is critical to understanding their mechanism-of-action. Unbiased chemical biology strategies for direct readout of protein interactome remodelling by small molecules would provide advantages over target-focused approaches, including the ability to detect previously unknown ligand targets and complexes. However, there are few current methods for unbiased profiling of small molecule interactomes. To address this, we envisioned a technology that would combine the sensitivity and live-cell compatibility of proximity labelling coupled to mass spectrometry, with the specificity and unbiased nature of chemoproteomics. In this manuscript, we describe the BioTAC system, a small-molecule guided proximity labelling platform that can rapidly identify both direct and complexed small molecule binding proteins. We benchmark the system against µMap, photoaffinity labelling, affinity purification coupled to mass spectrometry and proximity labelling coupled to mass spectrometry datasets. We also apply the BioTAC system to provide interactome maps of Trametinib and analogues. The BioTAC system overcomes a limitation of current approaches and supports identification of both inhibitor bound and molecular glue bound complexes.
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Affiliation(s)
- Andrew J Tao
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Jiewei Jiang
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Gillian E Gadbois
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Pavitra Goyal
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Bridget T Boyle
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Elizabeth J Mumby
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, 84112, USA
| | - Samuel A Myers
- Laboratory for Immunochemical Circuits, La Jolla Institute for Immunology, La Jolla, CA, 92037, USA
| | - Justin G English
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, 84112, USA.
| | - Fleur M Ferguson
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093, USA.
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, USA.
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123
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Bouguenina H, Scarpino A, O'Hanlon JA, Warne J, Wang HZ, Wah Hak LC, Sadok A, McAndrew PC, Stubbs M, Pierrat OA, Hahner T, Cabry MP, Le Bihan YV, Mitsopoulos C, Sialana FJ, Roumeliotis TI, Burke R, van Montfort RLM, Choudhari J, Chopra R, Caldwell JJ, Collins I. A Degron Blocking Strategy Towards Improved CRL4 CRBN Recruiting PROTAC Selectivity. Chembiochem 2023; 24:e202300351. [PMID: 37418539 DOI: 10.1002/cbic.202300351] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 06/16/2023] [Accepted: 07/03/2023] [Indexed: 07/09/2023]
Abstract
Small molecules inducing protein degradation are important pharmacological tools to interrogate complex biology and are rapidly translating into clinical agents. However, to fully realise the potential of these molecules, selectivity remains a limiting challenge. Herein, we addressed the issue of selectivity in the design of CRL4CRBN recruiting PROteolysis TArgeting Chimeras (PROTACs). Thalidomide derivatives used to generate CRL4CRBN recruiting PROTACs have well described intrinsic monovalent degradation profiles by inducing the recruitment of neo-substrates, such as GSPT1, Ikaros and Aiolos. We leveraged structural insights from known CRL4CRBN neo-substrates to attenuate and indeed remove this monovalent degradation function in well-known CRL4CRBN molecular glues degraders, namely CC-885 and Pomalidomide. We then applied these design principles on a previously published BRD9 PROTAC (dBRD9-A) and generated an analogue with improved selectivity profile. Finally, we implemented a computational modelling pipeline to show that our degron blocking design does not impact PROTAC-induced ternary complex formation. We believe that the tools and principles presented in this work will be valuable to support the development of targeted protein degradation.
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Affiliation(s)
- Habib Bouguenina
- Centre for Cancer Drug Discovery, Institute of Cancer Research, 15 Cotswold Road, Sutton, London, SM2 5NG, UK
| | - Andrea Scarpino
- Centre for Cancer Drug Discovery, Institute of Cancer Research, 15 Cotswold Road, Sutton, London, SM2 5NG, UK
| | - Jack A O'Hanlon
- Centre for Cancer Drug Discovery, Institute of Cancer Research, 15 Cotswold Road, Sutton, London, SM2 5NG, UK
| | - Justin Warne
- Centre for Cancer Drug Discovery, Institute of Cancer Research, 15 Cotswold Road, Sutton, London, SM2 5NG, UK
| | - Hannah Z Wang
- Centre for Cancer Drug Discovery, Institute of Cancer Research, 15 Cotswold Road, Sutton, London, SM2 5NG, UK
| | - Laura Chan Wah Hak
- Centre for Cancer Drug Discovery, Institute of Cancer Research, 15 Cotswold Road, Sutton, London, SM2 5NG, UK
| | - Amine Sadok
- Centre for Cancer Drug Discovery, Institute of Cancer Research, 15 Cotswold Road, Sutton, London, SM2 5NG, UK
- Monte Rosa Therapeutics AG, Aeschenvorstadt 36, 4051, Basel, Switzerland
| | - P Craig McAndrew
- Centre for Cancer Drug Discovery, Institute of Cancer Research, 15 Cotswold Road, Sutton, London, SM2 5NG, UK
| | - Mark Stubbs
- Centre for Cancer Drug Discovery, Institute of Cancer Research, 15 Cotswold Road, Sutton, London, SM2 5NG, UK
| | - Olivier A Pierrat
- Centre for Cancer Drug Discovery, Institute of Cancer Research, 15 Cotswold Road, Sutton, London, SM2 5NG, UK
| | - Tamas Hahner
- Centre for Cancer Drug Discovery, Institute of Cancer Research, 15 Cotswold Road, Sutton, London, SM2 5NG, UK
| | - Marc P Cabry
- Centre for Cancer Drug Discovery, Institute of Cancer Research, 15 Cotswold Road, Sutton, London, SM2 5NG, UK
| | - Yann-Vaï Le Bihan
- Centre for Cancer Drug Discovery, Institute of Cancer Research, 15 Cotswold Road, Sutton, London, SM2 5NG, UK
| | - Costas Mitsopoulos
- Centre for Cancer Drug Discovery, Institute of Cancer Research, 15 Cotswold Road, Sutton, London, SM2 5NG, UK
| | - Fernando J Sialana
- Centre for Cancer Drug Discovery, Institute of Cancer Research, 15 Cotswold Road, Sutton, London, SM2 5NG, UK
- Functional Proteomics Group, The Institute of Cancer Research, Chester Beatty Laboratories, London, SW3 6JB, UK
| | - Theodoros I Roumeliotis
- Centre for Cancer Drug Discovery, Institute of Cancer Research, 15 Cotswold Road, Sutton, London, SM2 5NG, UK
- Functional Proteomics Group, The Institute of Cancer Research, Chester Beatty Laboratories, London, SW3 6JB, UK
| | - Rosemary Burke
- Centre for Cancer Drug Discovery, Institute of Cancer Research, 15 Cotswold Road, Sutton, London, SM2 5NG, UK
| | - Rob L M van Montfort
- Centre for Cancer Drug Discovery, Institute of Cancer Research, 15 Cotswold Road, Sutton, London, SM2 5NG, UK
| | - Jyoti Choudhari
- Functional Proteomics Group, The Institute of Cancer Research, Chester Beatty Laboratories, London, SW3 6JB, UK
| | - Rajesh Chopra
- Centre for Cancer Drug Discovery, Institute of Cancer Research, 15 Cotswold Road, Sutton, London, SM2 5NG, UK
- Apple Tree Partners, The Gridiron Building, Suite 6.05, 1 St Pancras Square, London, N1 C 4AG, UK
| | - John J Caldwell
- Centre for Cancer Drug Discovery, Institute of Cancer Research, 15 Cotswold Road, Sutton, London, SM2 5NG, UK
| | - Ian Collins
- Centre for Cancer Drug Discovery, Institute of Cancer Research, 15 Cotswold Road, Sutton, London, SM2 5NG, UK
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Borsi E, Mazzocchetti G, Dico AF, Vigliotta I, Martello M, Poletti A, Solli V, Armuzzi S, Taurisano B, Kanapari A, Pistis I, Zamagni E, Tacchetti P, Pantani L, Mancuso K, Rocchi S, Rizzello I, Cavo M, Terragna C. High levels of CRBN isoform lacking IMiDs binding domain predicts for a worse response to IMiDs-based upfront therapy in newly diagnosed myeloma patients. Clin Exp Med 2023; 23:5227-5239. [PMID: 37815734 PMCID: PMC10725394 DOI: 10.1007/s10238-023-01205-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 09/22/2023] [Indexed: 10/11/2023]
Abstract
In recent years, the immunoderivative (IMiD) agents have been extensively used for the treatment of multiple myeloma (MM). IMiDs and their newer derivatives CRBN E3 ligase modulator bind the E3 ligase substrate recognition adapter protein cereblon (CRBN), which has been recognized as one of the IMiDs' direct target proteins, and it is essential for the therapeutic effect of these agents.High expression of CRBN was associated with improved clinical response in patients with MM treated with IMiDs, further confirming that the expression of IMiDs' direct target protein CRBN is required for the anti-MM activity. CRBN's central role as a target of IMiDs suggests potential utility as a predictive biomarker of response or resistance to IMiDs therapy. Additionally, the presence of alternatively spliced variants of CRBN in MM cells, especially those lacking the drug-binding domain for IMiDs, raise questions concerning their potential biological function, making difficult the transcript measurement, which leads to inaccurate overestimation of full-length CRBN transcripts. In sight of this, in the present study, we evaluated the CRBN expression, both full-length and spliced isoforms, by using real-time assay data from 87 patients and RNA sequencing data from 50 patients (n = 137 newly diagnosed MM patients), aiming at defining CRBN's role as a predictive biomarker for response to IMiDs-based induction therapy. We found that the expression level of the spliced isoform tends to be higher in not-responding patients, confirming that the presence of a more CRBN spliced transcript predicts for lack of IMiDs response.
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Affiliation(s)
- Enrica Borsi
- IRCCS Azienda Ospedaliero-Universitaria di Bologna-Istituto di Ematologia "Seràgnoli", Bologna, Italy.
| | - Gaia Mazzocchetti
- IRCCS Azienda Ospedaliero-Universitaria di Bologna-Istituto di Ematologia "Seràgnoli", Bologna, Italy
- DIMEC-Dipartimento di Scienze Mediche e Chirurgiche, Università di Bologna, Bologna, Italy
| | | | - Ilaria Vigliotta
- IRCCS Azienda Ospedaliero-Universitaria di Bologna-Istituto di Ematologia "Seràgnoli", Bologna, Italy
| | - Marina Martello
- IRCCS Azienda Ospedaliero-Universitaria di Bologna-Istituto di Ematologia "Seràgnoli", Bologna, Italy
- DIMEC-Dipartimento di Scienze Mediche e Chirurgiche, Università di Bologna, Bologna, Italy
| | - Andrea Poletti
- IRCCS Azienda Ospedaliero-Universitaria di Bologna-Istituto di Ematologia "Seràgnoli", Bologna, Italy
- DIMEC-Dipartimento di Scienze Mediche e Chirurgiche, Università di Bologna, Bologna, Italy
| | - Vincenza Solli
- IRCCS Azienda Ospedaliero-Universitaria di Bologna-Istituto di Ematologia "Seràgnoli", Bologna, Italy
- DIMEC-Dipartimento di Scienze Mediche e Chirurgiche, Università di Bologna, Bologna, Italy
| | - Silvia Armuzzi
- IRCCS Azienda Ospedaliero-Universitaria di Bologna-Istituto di Ematologia "Seràgnoli", Bologna, Italy
- DIMEC-Dipartimento di Scienze Mediche e Chirurgiche, Università di Bologna, Bologna, Italy
| | - Barbara Taurisano
- IRCCS Azienda Ospedaliero-Universitaria di Bologna-Istituto di Ematologia "Seràgnoli", Bologna, Italy
- DIMEC-Dipartimento di Scienze Mediche e Chirurgiche, Università di Bologna, Bologna, Italy
| | - Ajsi Kanapari
- IRCCS Azienda Ospedaliero-Universitaria di Bologna-Istituto di Ematologia "Seràgnoli", Bologna, Italy
- DIMEC-Dipartimento di Scienze Mediche e Chirurgiche, Università di Bologna, Bologna, Italy
| | - Ignazia Pistis
- IRCCS Azienda Ospedaliero-Universitaria di Bologna-Istituto di Ematologia "Seràgnoli", Bologna, Italy
| | - Elena Zamagni
- IRCCS Azienda Ospedaliero-Universitaria di Bologna-Istituto di Ematologia "Seràgnoli", Bologna, Italy
- DIMEC-Dipartimento di Scienze Mediche e Chirurgiche, Università di Bologna, Bologna, Italy
| | - Paola Tacchetti
- IRCCS Azienda Ospedaliero-Universitaria di Bologna-Istituto di Ematologia "Seràgnoli", Bologna, Italy
| | - Lucia Pantani
- IRCCS Azienda Ospedaliero-Universitaria di Bologna-Istituto di Ematologia "Seràgnoli", Bologna, Italy
| | - Katia Mancuso
- IRCCS Azienda Ospedaliero-Universitaria di Bologna-Istituto di Ematologia "Seràgnoli", Bologna, Italy
| | - Serena Rocchi
- IRCCS Azienda Ospedaliero-Universitaria di Bologna-Istituto di Ematologia "Seràgnoli", Bologna, Italy
| | - Ilaria Rizzello
- IRCCS Azienda Ospedaliero-Universitaria di Bologna-Istituto di Ematologia "Seràgnoli", Bologna, Italy
| | - Michele Cavo
- IRCCS Azienda Ospedaliero-Universitaria di Bologna-Istituto di Ematologia "Seràgnoli", Bologna, Italy
- DIMEC-Dipartimento di Scienze Mediche e Chirurgiche, Università di Bologna, Bologna, Italy
| | - Carolina Terragna
- IRCCS Azienda Ospedaliero-Universitaria di Bologna-Istituto di Ematologia "Seràgnoli", Bologna, Italy.
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125
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Kozicka Z. Gluing the pieces together. Science 2023; 382:779-780. [PMID: 37972173 DOI: 10.1126/science.adl4288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
Illuminating the path to degrading troublesome proteins.
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Affiliation(s)
- Zuzanna Kozicka
- Dana-Farber Cancer Institute, Boston, MA, USA
- Friedrich Miescher Institute for Biomedical Research, University of Basel, Basel, Switzerland
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126
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Julio AR, Shikwana F, Truong C, Burton NR, Dominguez E, Turmon AC, Cao J, Backus K. Pervasive aggregation and depletion of host and viral proteins in response to cysteine-reactive electrophilic compounds. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.30.564067. [PMID: 38014036 PMCID: PMC10680658 DOI: 10.1101/2023.10.30.564067] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Protein homeostasis is tightly regulated, with damaged or misfolded proteins quickly eliminated by the proteasome and autophagosome pathways. By co-opting these processes, targeted protein degradation technologies enable pharmacological manipulation of protein abundance. Recently, cysteine-reactive molecules have been added to the degrader toolbox, which offer the benefit of unlocking the therapeutic potential of 'undruggable' protein targets. The proteome-wide impact of these molecules remains to be fully understood and given the general reactivity of many classes of cysteine-reactive electrophiles, on- and off-target effects are likely. Using chemical proteomics, we identified a cysteine-reactive small molecule degrader of the SARS-CoV-2 non- structural protein 14 (nsp14), which effects degradation through direct modification of cysteines in both nsp14 and in host chaperones together with activation of global cell stress response pathways. We find that cysteine-reactive electrophiles increase global protein ubiquitylation, trigger proteasome activation, and result in widespread aggregation and depletion of host proteins, including components of the nuclear pore complex. Formation of stress granules was also found to be a remarkably ubiquitous cellular response to nearly all cysteine-reactive compounds and degraders. Collectively, our study sheds light on complexities of covalent target protein degradation and highlights untapped opportunities in manipulating and characterizing proteostasis processes via deciphering the cysteine-centric regulation of stress response pathways.
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127
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Steinebach C, Bricelj A, Murgai A, Sosič I, Bischof L, Ng YLD, Heim C, Maiwald S, Proj M, Voget R, Feller F, Košmrlj J, Sapozhnikova V, Schmidt A, Zuleeg MR, Lemnitzer P, Mertins P, Hansen FK, Gütschow M, Krönke J, Hartmann MD. Leveraging Ligand Affinity and Properties: Discovery of Novel Benzamide-Type Cereblon Binders for the Design of PROTACs. J Med Chem 2023; 66:14513-14543. [PMID: 37902300 PMCID: PMC10641816 DOI: 10.1021/acs.jmedchem.3c00851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 09/11/2023] [Accepted: 10/05/2023] [Indexed: 10/31/2023]
Abstract
Immunomodulatory imide drugs (IMiDs) such as thalidomide, pomalidomide, and lenalidomide are the most common cereblon (CRBN) recruiters in proteolysis-targeting chimera (PROTAC) design. However, these CRBN ligands induce the degradation of IMiD neosubstrates and are inherently unstable, degrading hydrolytically under moderate conditions. In this work, we simultaneously optimized physiochemical properties, stability, on-target affinity, and off-target neosubstrate modulation features to develop novel nonphthalimide CRBN binders. These efforts led to the discovery of conformationally locked benzamide-type derivatives that replicate the interactions of the natural CRBN degron, exhibit enhanced chemical stability, and display a favorable selectivity profile in terms of neosubstrate recruitment. The utility of the most potent ligands was demonstrated by their transformation into potent degraders of BRD4 and HDAC6 that outperform previously described reference PROTACs. Together with their significantly decreased neomorphic ligase activity on IKZF1/3 and SALL4, these ligands provide opportunities for the design of highly selective and potent chemically inert proximity-inducing compounds.
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Affiliation(s)
| | - Aleša Bricelj
- Faculty
of Pharmacy, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Arunima Murgai
- Department
of Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin
Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, D-12203 Berlin, Germany
| | - Izidor Sosič
- Faculty
of Pharmacy, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Luca Bischof
- Max
Planck Institute for Biology Tübingen, D-72076 Tübingen, Germany
| | - Yuen Lam Dora Ng
- Department
of Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin
Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, D-12203 Berlin, Germany
| | - Christopher Heim
- Max
Planck Institute for Biology Tübingen, D-72076 Tübingen, Germany
| | - Samuel Maiwald
- Max
Planck Institute for Biology Tübingen, D-72076 Tübingen, Germany
| | - Matic Proj
- Faculty
of Pharmacy, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Rabea Voget
- Pharmaceutical
Institute, University of Bonn, D-53121 Bonn, Germany
| | - Felix Feller
- Pharmaceutical
Institute, University of Bonn, D-53121 Bonn, Germany
| | - Janez Košmrlj
- Faculty
of Chemistry and Chemical Technology, University
of Ljubljana, SI 1000 Ljubljana, Slovenia
| | - Valeriia Sapozhnikova
- Department
of Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin
Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, D-12203 Berlin, Germany
- Max
Delbrück
Center for Molecular Medicine, D-13125 Berlin, Germany
- German
Cancer Consortium (DKTK), Partner Site Berlin, DKFZ, D-69120 Heidelberg, Germany
| | - Annika Schmidt
- Department
of Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin
Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, D-12203 Berlin, Germany
| | - Maximilian Rudolf Zuleeg
- Department
of Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin
Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, D-12203 Berlin, Germany
| | - Patricia Lemnitzer
- Department
of Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin
Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, D-12203 Berlin, Germany
| | - Philipp Mertins
- Max
Delbrück
Center for Molecular Medicine, D-13125 Berlin, Germany
- Berlin
Institute of Health, D-10178 Berlin, Germany
| | - Finn K. Hansen
- Pharmaceutical
Institute, University of Bonn, D-53121 Bonn, Germany
| | - Michael Gütschow
- Pharmaceutical
Institute, University of Bonn, D-53121 Bonn, Germany
| | - Jan Krönke
- Department
of Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin
Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, D-12203 Berlin, Germany
- German
Cancer Consortium (DKTK), Partner Site Berlin, DKFZ, D-69120 Heidelberg, Germany
| | - Marcus D. Hartmann
- Max
Planck Institute for Biology Tübingen, D-72076 Tübingen, Germany
- Interfaculty
Institute of Biochemistry, University of
Tübingen, D-72076 Tübingen, Germany
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128
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Giordano Attianese GMP, Ash S, Irving M. Coengineering specificity, safety, and function into T cells for cancer immunotherapy. Immunol Rev 2023; 320:166-198. [PMID: 37548063 DOI: 10.1111/imr.13252] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 07/03/2023] [Indexed: 08/08/2023]
Abstract
Adoptive T-cell transfer (ACT) therapies, including of tumor infiltrating lymphocytes (TILs) and T cells gene-modified to express either a T cell receptor (TCR) or a chimeric antigen receptor (CAR), have demonstrated clinical efficacy for a proportion of patients and cancer-types. The field of ACT has been driven forward by the clinical success of CD19-CAR therapy against various advanced B-cell malignancies, including curative responses for some leukemia patients. However, relapse remains problematic, in particular for lymphoma. Moreover, for a variety of reasons, relative limited efficacy has been demonstrated for ACT of non-hematological solid tumors. Indeed, in addition to pre-infusion challenges including lymphocyte collection and manufacturing, ACT failure can be attributed to several biological processes post-transfer including, (i) inefficient tumor trafficking, infiltration, expansion and retention, (ii) chronic antigen exposure coupled with insufficient costimulation resulting in T-cell exhaustion, (iii) a range of barriers in the tumor microenvironment (TME) mediated by both tumor cells and suppressive immune infiltrate, (iv) tumor antigen heterogeneity and loss, or down-regulation of antigen presentation machinery, (v) gain of tumor intrinsic mechanisms of resistance such as to apoptosis, and (vi) various forms of toxicity and other adverse events in patients. Affinity-optimized TCRs can improve T-cell function and innovative CAR designs as well as gene-modification strategies can be used to coengineer specificity, safety, and function into T cells. Coengineering strategies can be designed not only to directly support the transferred T cells, but also to block suppressive barriers in the TME and harness endogenous innate and adaptive immunity. Here, we review a selection of the remarkable T-cell coengineering strategies, including of tools, receptors, and gene-cargo, that have been developed in recent years to augment tumor control by ACT, more and more of which are advancing to the clinic.
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Affiliation(s)
- Greta Maria Paola Giordano Attianese
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Sarah Ash
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Melita Irving
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
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129
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Senapati D, Sharma V, Rath SK, Rai U, Panigrahi N. Functional implications and therapeutic targeting of androgen response elements in prostate cancer. Biochimie 2023; 214:188-198. [PMID: 37460038 DOI: 10.1016/j.biochi.2023.07.012] [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] [Received: 03/13/2023] [Revised: 06/12/2023] [Accepted: 07/14/2023] [Indexed: 07/29/2023]
Abstract
The androgen receptor (AR) plays an essential role in the growth and progression of prostate cancer (CaP). Ligand-activated AR inside the nucleus binds to the androgen response element (ARE) of the target genes in dimeric form and recruits transcriptional machinery to facilitate gene transcription. Pharmacological compounds that inhibit the AR action either bind to the ligand binding domain (LBD) or interfere with the interactions of AR with other co-regulatory proteins, slowing the progression of the disease. However, the emergence of resistance to conventional treatment makes clinical management of CaP difficult. Resistance has been associated with activation of androgen/AR axis that restores AR transcriptional activity. Activated AR signaling in resistance cases can be mediated by several mechanisms including AR amplification, gain-of-function AR mutations, androgen receptor variant (ARVs), intracrine androgen production, and overexpression of AR coactivators. Importantly, in castration resistant prostate cancer, ARVs lacking the LBD become constitutively active and promote hormone-independent development, underlining the need to concentrate on the other domain or the AR-DNA interface for the identification of novel actionable targets. In this review, we highlight the plasticity of AR-DNA binding and explain how fine-tuning AR's cooperative interactions with DNA translate into developing an alternative strategy to antagonize AR activity.
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Affiliation(s)
- Dhirodatta Senapati
- GITAM School of Pharmacy, GITAM (Deemed to be University), Visakhapatnam, Andhra Pradesh, India.
| | - Vikas Sharma
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Santosh Kumar Rath
- School of Pharmaceuticals and Population Health Informatics, DIT University, Dehradun, Uttarakhand, India
| | - Uddipak Rai
- School of Pharmaceuticals and Population Health Informatics, DIT University, Dehradun, Uttarakhand, India
| | - Naresh Panigrahi
- GITAM School of Pharmacy, GITAM (Deemed to be University), Visakhapatnam, Andhra Pradesh, India
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130
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Jiang Y, Ni S, Xiao B, Jia L. Function, mechanism and drug discovery of ubiquitin and ubiquitin-like modification with multiomics profiling for cancer therapy. Acta Pharm Sin B 2023; 13:4341-4372. [PMID: 37969742 PMCID: PMC10638515 DOI: 10.1016/j.apsb.2023.07.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 05/21/2023] [Accepted: 07/17/2023] [Indexed: 11/17/2023] Open
Abstract
Ubiquitin (Ub) and ubiquitin-like (Ubl) pathways are critical post-translational modifications that determine whether functional proteins are degraded or activated/inactivated. To date, >600 associated enzymes have been reported that comprise a hierarchical task network (e.g., E1-E2-E3 cascade enzymatic reaction and deubiquitination) to modulate substrates, including enormous oncoproteins and tumor-suppressive proteins. Several strategies, such as classical biochemical approaches, multiomics, and clinical sample analysis, were combined to elucidate the functional relations between these enzymes and tumors. In this regard, the fundamental advances and follow-on drug discoveries have been crucial in providing vital information concerning contemporary translational efforts to tailor individualized treatment by targeting Ub and Ubl pathways. Correspondingly, emphasizing the current progress of Ub-related pathways as therapeutic targets in cancer is deemed essential. In the present review, we summarize and discuss the functions, clinical significance, and regulatory mechanisms of Ub and Ubl pathways in tumorigenesis as well as the current progress of small-molecular drug discovery. In particular, multiomics analyses were integrated to delineate the complexity of Ub and Ubl modifications for cancer therapy. The present review will provide a focused and up-to-date overview for the researchers to pursue further studies regarding the Ub and Ubl pathways targeted anticancer strategies.
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Affiliation(s)
| | | | - Biying Xiao
- Cancer Institute, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
| | - Lijun Jia
- Cancer Institute, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
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131
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Long J, Mariossi A, Cao C, Mo Z, Thompson JW, Levine MS, Lemaire LA. Cereblon influences the timing of muscle differentiation in Ciona tadpoles. Proc Natl Acad Sci U S A 2023; 120:e2309989120. [PMID: 37856545 PMCID: PMC10614628 DOI: 10.1073/pnas.2309989120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 09/09/2023] [Indexed: 10/21/2023] Open
Abstract
Thalidomide has a dark history as a teratogen, but in recent years, its derivates have been shown to function as potent chemotherapeutic agents. These drugs bind cereblon (CRBN), the substrate receptor of an E3 ubiquitin ligase complex, and modify its degradation targets. Despite these insights, remarkably little is known about the normal function of cereblon in development. Here, we employ Ciona, a simple invertebrate chordate, to identify endogenous Crbn targets. In Ciona, Crbn is specifically expressed in developing muscles during tail elongation before they acquire contractile activity. Crbn expression is activated by Mrf, the ortholog of MYOD1, a transcription factor important for muscle differentiation. CRISPR/Cas9-mediated mutations of Crbn lead to precocious onset of muscle contractions. By contrast, overexpression of Crbn delays contractions and is associated with decreased expression of contractile protein genes such as troponin. This reduction is possibly due to reduced Mrf protein levels without altering Mrf mRNA levels. Our findings suggest that Mrf and Crbn form a negative feedback loop to control the precision of muscle differentiation during tail elongation.
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Affiliation(s)
- Juanjuan Long
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ08544
| | - Andrea Mariossi
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ08544
| | - Chen Cao
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ08544
| | | | | | - Michael S. Levine
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ08544
- Department of Molecular Biology, Princeton University, Princeton, NJ08544
| | - Laurence A. Lemaire
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ08544
- Department of Biology, Saint Louis University, St. Louis, MO63103
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132
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Ahn G, Riley NM, Kamber RA, Wisnovsky S, Moncayo von Hase S, Bassik MC, Banik SM, Bertozzi CR. Elucidating the cellular determinants of targeted membrane protein degradation by lysosome-targeting chimeras. Science 2023; 382:eadf6249. [PMID: 37856615 PMCID: PMC10766146 DOI: 10.1126/science.adf6249] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 08/31/2023] [Indexed: 10/21/2023]
Abstract
Targeted protein degradation can provide advantages over inhibition approaches in the development of therapeutic strategies. Lysosome-targeting chimeras (LYTACs) harness receptors, such as the cation-independent mannose 6-phosphate receptor (CI-M6PR), to direct extracellular proteins to lysosomes. In this work, we used a genome-wide CRISPR knockout approach to identify modulators of LYTAC-mediated membrane protein degradation in human cells. We found that disrupting retromer genes improved target degradation by reducing LYTAC recycling to the plasma membrane. Neddylated cullin-3 facilitated LYTAC-complex lysosomal maturation and was a predictive marker for LYTAC efficacy. A substantial fraction of cell surface CI-M6PR remains occupied by endogenous M6P-modified glycoproteins. Thus, inhibition of M6P biosynthesis increased the internalization of LYTAC-target complexes. Our findings inform design strategies for next-generation LYTACs and elucidate aspects of cell surface receptor occupancy and trafficking.
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Affiliation(s)
- Green Ahn
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - Nicholas M. Riley
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - Roarke A. Kamber
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Simon Wisnovsky
- Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Salvador Moncayo von Hase
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - Michael C. Bassik
- Sarafan ChEM-H, Stanford University, Stanford, CA 94305, USA
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Steven M. Banik
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - Carolyn R. Bertozzi
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
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133
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Chong PSY, Chooi JY, Lim JSL, Leow ACY, Toh SHM, Azaman I, Koh MY, Teoh PJ, Tan TZ, Chung TH, Chng WJ. Histone Methyltransferase NSD2 Activates PKCα to Drive Metabolic Reprogramming and Lenalidomide Resistance in Multiple Myeloma. Cancer Res 2023; 83:3414-3427. [PMID: 37463241 DOI: 10.1158/0008-5472.can-22-3481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 03/07/2023] [Accepted: 07/14/2023] [Indexed: 07/20/2023]
Abstract
Multiple myeloma cells undergo metabolic reprogramming in response to the hypoxic and nutrient-deprived bone marrow microenvironment. Primary oncogenes in recurrent translocations might be able to drive metabolic heterogeneity to survive the microenvironment that can present new vulnerabilities for therapeutic targeting. t(4;14) translocation leads to the universal overexpression of histone methyltransferase NSD2 that promotes plasma cell transformation through a global increase in H3K36me2. Here, we identified PKCα as an epigenetic target that contributes to the oncogenic potential of NSD2. RNA sequencing of t(4;14) multiple myeloma cell lines revealed a significant enrichment in the regulation of metabolic processes by PKCα, and the glycolytic gene, hexokinase 2 (HK2), was transcriptionally regulated by PKCα in a PI3K/Akt-dependent manner. Loss of PKCα displaced mitochondria-bound HK2 and reversed sensitivity to the glycolytic inhibitor 3-bromopyruvate. In addition, the perturbation of glycolytic flux led to a metabolic shift to a less energetic state and decreased ATP production. Metabolomics analysis indicated lactate as a differential metabolite associated with PKCα. As a result, PKCα conferred resistance to the immunomodulatory drugs (IMiD) lenalidomide in a cereblon-independent manner and could be phenocopied by either overexpression of HK2 or direct supplementation of lactate. Clinically, t(4;14) patients had elevated plasma lactate levels and did not benefit from lenalidomide-based regimens. Altogether, this study provides insights into the epigenetic-metabolism cross-talk in multiple myeloma and highlights the opportunity for therapeutic intervention that leverages the distinct metabolic program in t(4;14) myeloma. SIGNIFICANCE Aberrant glycolysis driven by NSD2-mediated upregulation of PKCα can be therapeutically exploited using metabolic inhibitors with lactate as a biomarker to identify high-risk patients who exhibit poor response towards IMiD-based regimens.
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Affiliation(s)
- Phyllis S Y Chong
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Jing-Yuan Chooi
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Julia S L Lim
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Aaron C Y Leow
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Sabrina Hui Min Toh
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Irfan Azaman
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Mun Yee Koh
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Phaik Ju Teoh
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Tuan Zea Tan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Tae-Hoon Chung
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Wee Joo Chng
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
- Department of Hematology-Oncology, National University Cancer Institute of Singapore, National University Health System, Singapore
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134
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Hassan MM, Li YD, Ma MW, Teng M, Byun WS, Puvar K, Lumpkin R, Sandoval B, Rutter JC, Jin CY, Wang MY, Xu S, Schmoker AM, Cheong H, Groendyke BJ, Qi J, Fischer ES, Ebert BL, Gray NS. Exploration of the Tunability of BRD4 Degradation by DCAF16 Trans-labelling Covalent Glues. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.07.561308. [PMID: 37873358 PMCID: PMC10592706 DOI: 10.1101/2023.10.07.561308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Small molecules that can induce protein degradation by inducing proximity between a desired target and an E3 ligase have the potential to greatly expand the number of proteins that can be manipulated pharmacologically. Current strategies for targeted protein degradation are mostly limited in their target scope to proteins with preexisting ligands. Alternate modalities such as molecular glues, as exemplified by the glutarimide class of ligands for the CUL4CRBN ligase, have been mostly discovered serendipitously. We recently reported a trans-labelling covalent glue mechanism which we named 'Template-assisted covalent modification', where an electrophile decorated small molecule binder of BRD4 was effectively delivered to a cysteine residue on an E3 ligase DCAF16 as a consequence of a BRD4-DCAF16 protein-protein interaction. Herein, we report our medicinal chemistry efforts to evaluate how various electrophilic modifications to the BRD4 binder, JQ1, affect DCAF16 trans-labeling and subsequent BRD4 degradation efficiency. We discovered a decent correlation between the ability of the electrophilic small molecule to induce ternary complex formation between BRD4 and DCAF16 with its ability to induce BRD4 degradation. Moreover, we show that a more solvent-exposed warhead presentation is optimal for DCAF16 recruitment and subsequent BRD4 degradation. Unlike the sensitivity of CUL4CRBN glue degraders to chemical modifications, the diversity of covalent attachments in this class of BRD4 glue degraders suggests a high tolerance and tunability for the BRD4-DCAF16 interaction. This offers a potential new avenue for a rational design of covalent glue degraders by introducing covalent warheads to known binders.
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Affiliation(s)
- Muhammad Murtaza Hassan
- Department of Chemical and Systems Biology, ChEM-H and Stanford Cancer Institute, Stanford School of Medicine, Stanford University, Stanford, CA
| | - Yen-Der Li
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Michelle W. Ma
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA
| | - Mingxing Teng
- Center for Drug Discovery, Department of Pathology & Immunology, and Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX
| | - Woong Sub Byun
- Department of Chemical and Systems Biology, ChEM-H and Stanford Cancer Institute, Stanford School of Medicine, Stanford University, Stanford, CA
| | - Kedar Puvar
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA
| | - Ryan Lumpkin
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA
| | - Brittany Sandoval
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Justine C. Rutter
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Cyrus Y. Jin
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA
| | - Michelle Y. Wang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA
| | - Shawn Xu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Anna M. Schmoker
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA
| | - Hakyung Cheong
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA
| | | | - Jun Qi
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA
| | - Eric S. Fischer
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA
| | - Benjamin L. Ebert
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA
- Howard Hughes Medical Institute, Boston, MA
| | - Nathanael S. Gray
- Department of Chemical and Systems Biology, ChEM-H and Stanford Cancer Institute, Stanford School of Medicine, Stanford University, Stanford, CA
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135
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Daudignon A, Cuccuini W, Bracquemart C, Godon C, Quilichini B, Penther D. Cytogenetics in the management of multiple Myeloma: The guidelines from the Groupe Francophone de Cytogénétique Hématologique (GFCH). Curr Res Transl Med 2023; 71:103427. [PMID: 38035476 DOI: 10.1016/j.retram.2023.103427] [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] [Received: 07/07/2023] [Revised: 10/20/2023] [Accepted: 10/23/2023] [Indexed: 12/02/2023]
Abstract
Multiple myeloma (MM) is characterized by the accumulation of malignant plasma cells (PCs) in the bone marrow. Despite considerable advances in the treatment, MM is considered an incurable chronic disease with a very heterogeneous prognosis, mostly depending on genomic alterations whose complexity evolves over time. The cytogenetic analysis of MM is performed on CD138+ sorted PCs, in order to detect the following high risk cytogenetic abnormalities: t(4;14), 17p/TP53 deletion, 1q21 gain/amplification, 1p32 deletion, as well as t(11;14) because of its therapeutic implication. This minimal panel can be enlarged to detect other recurrent abnormalities, according to the prognostic score chosen by the laboratory. Although the knowledge of the genetic landscape of MM is evolving rapidly with improved molecular technologies, risk scores remain to be refined as they require more time for consensual validation. The GFCH present here the overview of genomics alterations identified in MM and related PCs diseases associated with their prognostic factor, when available, and recommendations from an expert group for identification and characterization of those alterations. This work is the update of previous 2016 recommendations.
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Affiliation(s)
- Agnès Daudignon
- Institut de Génétique Médicale - Hôpital Jeanne de Flandre - CHU de Lille, Lille, France
| | - Wendy Cuccuini
- Laboratoire d'hématologie, Hôpital Saint-Louis -Assistance Publique-Hôpitaux de Paris (APHP), Paris, France
| | - Claire Bracquemart
- Normandie Univ, UNICAEN, CHU de Caen Normandie, Structure Fédérative d'Oncogénétique cyto-moléculaire (MOCAE), Caen, France
| | - Catherine Godon
- Laboratoire d'Hématologie Biologique, CHU Nantes, Nantes, France
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136
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Gonthier K, Weidmann C, Berthiaume L, Jobin C, Lacouture A, Lafront C, Harvey M, Neveu B, Loehr J, Bergeron A, Fradet Y, Lacombe L, Riopel J, Latulippe É, Atallah C, Shum M, Lambert J, Pouliot F, Pelletier M, Audet‐Walsh É. Isocitrate dehydrogenase 1 sustains a hybrid cytoplasmic-mitochondrial tricarboxylic acid cycle that can be targeted for therapeutic purposes in prostate cancer. Mol Oncol 2023; 17:2109-2125. [PMID: 37086156 PMCID: PMC10552900 DOI: 10.1002/1878-0261.13441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 03/07/2023] [Accepted: 04/21/2023] [Indexed: 04/23/2023] Open
Abstract
The androgen receptor (AR) is an established orchestrator of cell metabolism in prostate cancer (PCa), notably by inducing an oxidative mitochondrial program. Intriguingly, AR regulates cytoplasmic isocitrate dehydrogenase 1 (IDH1), but not its mitochondrial counterparts IDH2 and IDH3. Here, we aimed to understand the functional role of IDH1 in PCa. Mouse models, in vitro human PCa cell lines, and human patient-derived organoids (PDOs) were used to study the expression and activity of IDH enzymes in the normal prostate and PCa. Genetic and pharmacological inhibition of IDH1 was then combined with extracellular flux analyses and gas chromatography-mass spectrometry for metabolomic analyses and cancer cell proliferation in vitro and in vivo. In PCa cells, more than 90% of the total IDH activity is mediated through IDH1 rather than its mitochondrial counterparts. This profile seems to originate from the specialized prostate metabolic program, as observed using mouse prostate and PDOs. Pharmacological and genetic inhibition of IDH1 impaired mitochondrial respiration, suggesting that this cytoplasmic enzyme contributes to the mitochondrial tricarboxylic acid cycle (TCA) in PCa. Mass spectrometry-based metabolomics confirmed this hypothesis, showing that inhibition of IDH1 impairs carbon flux into the TCA cycle. Consequently, inhibition of IDH1 decreased PCa cell proliferation in vitro and in vivo. These results demonstrate that PCa cells have a hybrid cytoplasmic-mitochondrial TCA cycle that depends on IDH1. This metabolic enzyme represents a metabolic vulnerability of PCa cells and a potential new therapeutic target.
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Affiliation(s)
- Kevin Gonthier
- Endocrinology – Nephrology Research AxisCHU de Québec‐Université Laval Research CenterCanada
- Department of Molecular Medicine, Faculty of MedicineUniversité LavalQuébecCanada
- Centre de recherche sur le cancer de l'Université LavalQuébecCanada
| | - Cindy Weidmann
- Endocrinology – Nephrology Research AxisCHU de Québec‐Université Laval Research CenterCanada
- Centre de recherche sur le cancer de l'Université LavalQuébecCanada
| | - Line Berthiaume
- Endocrinology – Nephrology Research AxisCHU de Québec‐Université Laval Research CenterCanada
- Centre de recherche sur le cancer de l'Université LavalQuébecCanada
| | - Cynthia Jobin
- Endocrinology – Nephrology Research AxisCHU de Québec‐Université Laval Research CenterCanada
- Department of Molecular Medicine, Faculty of MedicineUniversité LavalQuébecCanada
- Centre de recherche sur le cancer de l'Université LavalQuébecCanada
| | - Aurélie Lacouture
- Endocrinology – Nephrology Research AxisCHU de Québec‐Université Laval Research CenterCanada
- Department of Molecular Medicine, Faculty of MedicineUniversité LavalQuébecCanada
- Centre de recherche sur le cancer de l'Université LavalQuébecCanada
| | - Camille Lafront
- Endocrinology – Nephrology Research AxisCHU de Québec‐Université Laval Research CenterCanada
- Department of Molecular Medicine, Faculty of MedicineUniversité LavalQuébecCanada
- Centre de recherche sur le cancer de l'Université LavalQuébecCanada
| | - Mario Harvey
- Endocrinology – Nephrology Research AxisCHU de Québec‐Université Laval Research CenterCanada
- Centre de recherche sur le cancer de l'Université LavalQuébecCanada
| | - Bertrand Neveu
- Centre de recherche sur le cancer de l'Université LavalQuébecCanada
- Oncology AxisCentre de recherche du CHU de Québec – Université LavalCanada
| | - Jérémy Loehr
- Endocrinology – Nephrology Research AxisCHU de Québec‐Université Laval Research CenterCanada
- Centre de recherche sur le cancer de l'Université LavalQuébecCanada
| | - Alain Bergeron
- Centre de recherche sur le cancer de l'Université LavalQuébecCanada
- Oncology AxisCentre de recherche du CHU de Québec – Université LavalCanada
- Department of Surgery, Faculty of MedicineUniversité LavalQuébecCanada
| | - Yves Fradet
- Centre de recherche sur le cancer de l'Université LavalQuébecCanada
- Oncology AxisCentre de recherche du CHU de Québec – Université LavalCanada
- Department of Surgery, Faculty of MedicineUniversité LavalQuébecCanada
| | - Louis Lacombe
- Centre de recherche sur le cancer de l'Université LavalQuébecCanada
- Oncology AxisCentre de recherche du CHU de Québec – Université LavalCanada
- Department of Surgery, Faculty of MedicineUniversité LavalQuébecCanada
| | - Julie Riopel
- Anatomopathology Service, Department of Laboratory MedicineCHU de Québec – Université LavalCanada
| | - Éva Latulippe
- Department of PathologyCHU de Québec – Université LavalCanada
| | - Chantal Atallah
- Department of PathologyCHU de Québec – Université LavalCanada
| | - Michael Shum
- Endocrinology – Nephrology Research AxisCHU de Québec‐Université Laval Research CenterCanada
- Department of Molecular Medicine, Faculty of MedicineUniversité LavalQuébecCanada
| | - Jean‐Philippe Lambert
- Endocrinology – Nephrology Research AxisCHU de Québec‐Université Laval Research CenterCanada
- Department of Molecular Medicine, Faculty of MedicineUniversité LavalQuébecCanada
- Centre de recherche sur le cancer de l'Université LavalQuébecCanada
- Big Data Research CenterUniversité LavalQuébecQCCanada
| | - Frédéric Pouliot
- Centre de recherche sur le cancer de l'Université LavalQuébecCanada
- Oncology AxisCentre de recherche du CHU de Québec – Université LavalCanada
- Department of Surgery, Faculty of MedicineUniversité LavalQuébecCanada
| | - Martin Pelletier
- Infectious and Immune Disease AxisCHU de Québec‐Université Laval Research CenterCanada
- ARThrite Research CenterUniversité LavalQuébecQCCanada
- Department of Microbiology‐Infectious Diseases and Immunology, Faculty of MedicineUniversité LavalQuébecQCCanada
| | - Étienne Audet‐Walsh
- Endocrinology – Nephrology Research AxisCHU de Québec‐Université Laval Research CenterCanada
- Department of Molecular Medicine, Faculty of MedicineUniversité LavalQuébecCanada
- Centre de recherche sur le cancer de l'Université LavalQuébecCanada
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Basu AA, Zhang C, Riha IA, Magassa A, Ko F, Zhang X. A CRISPR activation screen identifies FBXO22 as an E3 ligase supporting targeted protein degradation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.15.557708. [PMID: 37745578 PMCID: PMC10515933 DOI: 10.1101/2023.09.15.557708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Targeted protein degradation (TPD) represents a potent chemical biology paradigm that leverages the cellular degradation machinery to pharmacologically eliminate specific proteins of interest. Although multiple E3 ligases have been discovered to facilitate TPD, there exists a compelling requirement to diversify the pool of E3 ligases available for such applications. This expansion will broaden the scope of potential protein targets, accommodating those with varying subcellular localizations and expression patterns. In this study, we describe a CRISPR-based transcriptional activation screen focused on human E3 ligases, with the goal of identifying E3 ligases that can facilitate heterobifunctional compound-mediated target degradation. This approach allows us to address the limitations associated with investigating candidate degrader molecules in specific cell lines that either lack or have low levels of the desired E3 ligases. Through this approach, we identified a candidate proteolysis-targeting chimera (PROTAC), 22-SLF, that induces the degradation of FKBP12 when the FBXO22 gene transcription is activated. 22-SLF induced the degradation of endogenous FKBP12 in a FBXO22-dependent manner across multiple cancer cell lines. Subsequent mechanistic investigations revealed that 22-SLF interacts with C227 and/or C228 in FBXO22 to achieve the target degradation. Finally, we demonstrated the versatility of FBXO22-based PROTACs by effectively degrading another endogenous protein BRD4. This study uncovers FBXO22 as an E3 ligase capable of supporting ligand-induced protein degradation through electrophilic PROTACs. The platform we have developed can readily be applied to elucidate protein degradation pathways by identifying E3 ligases that facilitate either small molecule-induced or endogenous protein degradation.
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138
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Shortt J. Mezigdomide and Multiple Myeloma. N Engl J Med 2023; 389:1046-1050. [PMID: 37646699 DOI: 10.1056/nejme2307370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Affiliation(s)
- Jake Shortt
- From the Department of Medicine, School of Clinical Sciences at Monash Health, Faculty of Medicine, Nursing, and Health Sciences, Monash University, and Monash Haematology, Monash Health - both in Clayton, VIC, Australia
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139
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Forster S, Radpour R, Ochsenbein AF. Molecular and immunological mechanisms of clonal evolution in multiple myeloma. Front Immunol 2023; 14:1243997. [PMID: 37744361 PMCID: PMC10516567 DOI: 10.3389/fimmu.2023.1243997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 08/21/2023] [Indexed: 09/26/2023] Open
Abstract
Multiple myeloma (MM) is a hematologic malignancy characterized by the proliferation of clonal plasma cells in the bone marrow (BM). It is known that early genetic mutations in post-germinal center B/plasma cells are the cause of myelomagenesis. The acquisition of additional chromosomal abnormalities and distinct mutations further promote the outgrowth of malignant plasma cell populations that are resistant to conventional treatments, finally resulting in relapsed and therapy-refractory terminal stages of MM. In addition, myeloma cells are supported by autocrine signaling pathways and the tumor microenvironment (TME), which consists of diverse cell types such as stromal cells, immune cells, and components of the extracellular matrix. The TME provides essential signals and stimuli that induce proliferation and/or prevent apoptosis. In particular, the molecular pathways by which MM cells interact with the TME are crucial for the development of MM. To generate successful therapies and prevent MM recurrence, a thorough understanding of the molecular mechanisms that drive MM progression and therapy resistance is essential. In this review, we summarize key mechanisms that promote myelomagenesis and drive the clonal expansion in the course of MM progression such as autocrine signaling cascades, as well as direct and indirect interactions between the TME and malignant plasma cells. In addition, we highlight drug-resistance mechanisms and emerging therapies that are currently tested in clinical trials to overcome therapy-refractory MM stages.
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Affiliation(s)
- Stefan Forster
- Tumor Immunology, Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Ramin Radpour
- Tumor Immunology, Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Adrian F. Ochsenbein
- Tumor Immunology, Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
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140
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Kong NR, Jones LH. Clinical Translation of Targeted Protein Degraders. Clin Pharmacol Ther 2023; 114:558-568. [PMID: 37399310 DOI: 10.1002/cpt.2985] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 06/19/2023] [Indexed: 07/05/2023]
Abstract
Targeted protein degradation (TPD) has emerged as a potentially transformational therapeutic modality with considerable promise. Molecular glue degraders remodel the surface of E3 ligases inducing interactions with neosubstrates resulting in their polyubiquitination and proteasomal degradation. Molecular glues are clinically precedented and have demonstrated the ability to degrade proteins-of-interest (POIs) previously deemed undruggable due to the absence of a traditional small molecule binding pocket. Heterobifunctional proteolysis targeting chimeras (PROTACs) possess ligands for an E3 complex and the POIs, which are chemically linked together, and similarly hijack the ubiquitin machinery to deplete the target. There has been a recent surge in the number of degraders entering clinical trials, particularly directed toward cancer. Nearly all utilize CRL4CRBN as the E3 ligase, and a relatively limited diversity of POIs are currently targeted. In this review, we provide an overview of the degraders in clinical trials and provide a perspective on the lessons learned from their development and emerging human data that will be broadly useful to those working in the TPD field.
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Affiliation(s)
- Nikki R Kong
- Center for Protein Degradation, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | - Lyn H Jones
- Center for Protein Degradation, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
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141
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Li Z, Ma S, Zhang S, Ma Z, Du L, Li M. Degradation of extracellular and membrane proteins in targeted therapy: Status quo and quo vadis. Drug Discov Today 2023; 28:103716. [PMID: 37467880 DOI: 10.1016/j.drudis.2023.103716] [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] [Received: 02/19/2023] [Revised: 06/29/2023] [Accepted: 07/12/2023] [Indexed: 07/21/2023]
Abstract
Targeted protein degradation (TPD) strategies, such as proteolysis-targeting chimeras (PROTACs) only work for intracellular protein degradation because they involve the intracellular protein degradation machinery. Several new technologies have emerged in recent years for TPD of extracellular and membrane proteins. Even though some progress has been demonstrated in the extracellular and membrane protein degradation field, the application of these technologies is still in its infancy. In this review, we survey the therapeutic potential of existing technologies by summarizing and reviewing discoveries and hurdles in extracellular and membrane protein-of-interest (POI) degradation.
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Affiliation(s)
- Zhenzhen Li
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (MOE), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Siyue Ma
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (MOE), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Shuxin Zhang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (MOE), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Zhao Ma
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (MOE), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Lupei Du
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (MOE), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China.
| | - Minyong Li
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (MOE), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China; Helmholtz International Lab, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China.
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142
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Affar M, Bottardi S, Quansah N, Lemarié M, Ramón AC, Affar EB, Milot E. IKAROS: from chromatin organization to transcriptional elongation control. Cell Death Differ 2023:10.1038/s41418-023-01212-2. [PMID: 37620540 DOI: 10.1038/s41418-023-01212-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 07/26/2023] [Accepted: 08/14/2023] [Indexed: 08/26/2023] Open
Abstract
IKAROS is a master regulator of cell fate determination in lymphoid and other hematopoietic cells. This transcription factor orchestrates the association of epigenetic regulators with chromatin, ensuring the expression pattern of target genes in a developmental and lineage-specific manner. Disruption of IKAROS function has been associated with the development of acute lymphocytic leukemia, lymphoma, chronic myeloid leukemia and immune disorders. Paradoxically, while IKAROS has been shown to be a tumor suppressor, it has also been identified as a key therapeutic target in the treatment of various forms of hematological malignancies, including multiple myeloma. Indeed, targeted proteolysis of IKAROS is associated with decreased proliferation and increased death of malignant cells. Although the molecular mechanisms have not been elucidated, the expression levels of IKAROS are variable during hematopoiesis and could therefore be a key determinant in explaining how its absence can have seemingly opposite effects. Mechanistically, IKAROS collaborates with a variety of proteins and complexes controlling chromatin organization at gene regulatory regions, including the Nucleosome Remodeling and Deacetylase complex, and may facilitate transcriptional repression or activation of specific genes. Several transcriptional regulatory functions of IKAROS have been proposed. An emerging mechanism of action involves the ability of IKAROS to promote gene repression or activation through its interaction with the RNA polymerase II machinery, which influences pausing and productive transcription at specific genes. This control appears to be influenced by IKAROS expression levels and isoform production. In here, we summarize the current state of knowledge about the biological roles and mechanisms by which IKAROS regulates gene expression. We highlight the dynamic regulation of this factor by post-translational modifications. Finally, potential avenues to explain how IKAROS destruction may be favorable in the treatment of certain hematological malignancies are also explored.
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Affiliation(s)
- Malik Affar
- Faculty of Medicine, University of Montreal, Montréal, QC, Canada
- Maisonneuve-Rosemont Hospital Research Center, CIUSSS de l'Est-de-l'Île de Montréal, 5415 boulevard de l'Assomption, Montréal, QC, H1T 2M4, Canada
| | - Stefania Bottardi
- Maisonneuve-Rosemont Hospital Research Center, CIUSSS de l'Est-de-l'Île de Montréal, 5415 boulevard de l'Assomption, Montréal, QC, H1T 2M4, Canada
| | - Norreen Quansah
- Maisonneuve-Rosemont Hospital Research Center, CIUSSS de l'Est-de-l'Île de Montréal, 5415 boulevard de l'Assomption, Montréal, QC, H1T 2M4, Canada
| | - Maud Lemarié
- Faculty of Medicine, University of Montreal, Montréal, QC, Canada
- Maisonneuve-Rosemont Hospital Research Center, CIUSSS de l'Est-de-l'Île de Montréal, 5415 boulevard de l'Assomption, Montréal, QC, H1T 2M4, Canada
| | - Ailyn C Ramón
- Faculty of Medicine, University of Montreal, Montréal, QC, Canada
- Maisonneuve-Rosemont Hospital Research Center, CIUSSS de l'Est-de-l'Île de Montréal, 5415 boulevard de l'Assomption, Montréal, QC, H1T 2M4, Canada
| | - El Bachir Affar
- Faculty of Medicine, University of Montreal, Montréal, QC, Canada.
- Maisonneuve-Rosemont Hospital Research Center, CIUSSS de l'Est-de-l'Île de Montréal, 5415 boulevard de l'Assomption, Montréal, QC, H1T 2M4, Canada.
| | - Eric Milot
- Faculty of Medicine, University of Montreal, Montréal, QC, Canada.
- Maisonneuve-Rosemont Hospital Research Center, CIUSSS de l'Est-de-l'Île de Montréal, 5415 boulevard de l'Assomption, Montréal, QC, H1T 2M4, Canada.
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143
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Tao AJ, Jiang J, Gadbois GE, Goyal P, Boyle BT, Mumby EJ, Myers SA, English JG, Ferguson FM. A Biotin Targeting Chimera (BioTAC) System to Map Small Molecule Interactomes in situ. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.21.554211. [PMID: 37662262 PMCID: PMC10473607 DOI: 10.1101/2023.08.21.554211] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Unbiased chemical biology strategies for direct readout of protein interactome remodelling by small molecules provide advantages over target-focused approaches, including the ability to detect previously unknown targets, and the inclusion of chemical off-compete controls leading to high-confidence identifications. We describe the BioTAC system, a small-molecule guided proximity labelling platform, to rapidly identify both direct and complexed small molecule binding proteins. The BioTAC system overcomes a limitation of current approaches, and supports identification of both inhibitor bound and molecular glue bound complexes.
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Affiliation(s)
- Andrew J. Tao
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093
| | - Jiewei Jiang
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093
| | - Gillian E. Gadbois
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093
| | - Pavitra Goyal
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093
| | - Bridget T. Boyle
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093
| | - Elizabeth J. Mumby
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112
| | - Samuel A Myers
- Laboratory for Immunochemical Circuits, La Jolla Institute for Immunology, La Jolla, CA 92037
| | - Justin G. English
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112
| | - Fleur M. Ferguson
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093
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144
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Yamanaka S, Furihata H, Yanagihara Y, Taya A, Nagasaka T, Usui M, Nagaoka K, Shoya Y, Nishino K, Yoshida S, Kosako H, Tanokura M, Miyakawa T, Imai Y, Shibata N, Sawasaki T. Lenalidomide derivatives and proteolysis-targeting chimeras for controlling neosubstrate degradation. Nat Commun 2023; 14:4683. [PMID: 37596276 PMCID: PMC10439208 DOI: 10.1038/s41467-023-40385-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 07/21/2023] [Indexed: 08/20/2023] Open
Abstract
Lenalidomide, an immunomodulatory drug (IMiD), is commonly used as a first-line therapy in many haematological cancers, such as multiple myeloma (MM) and 5q myelodysplastic syndromes (5q MDS), and it functions as a molecular glue for the protein degradation of neosubstrates by CRL4CRBN. Proteolysis-targeting chimeras (PROTACs) using IMiDs with a target protein binder also induce the degradation of target proteins. The targeted protein degradation (TPD) of neosubstrates is crucial for IMiD therapy. However, current IMiDs and IMiD-based PROTACs also break down neosubstrates involved in embryonic development and disease progression. Here, we show that 6-position modifications of lenalidomide are essential for controlling neosubstrate selectivity; 6-fluoro lenalidomide induced the selective degradation of IKZF1, IKZF3, and CK1α, which are involved in anti-haematological cancer activity, and showed stronger anti-proliferative effects on MM and 5q MDS cell lines than lenalidomide. PROTACs using these lenalidomide derivatives for BET proteins induce the selective degradation of BET proteins with the same neosubstrate selectivity. PROTACs also exert anti-proliferative effects in all examined cell lines. Thus, 6-position-modified lenalidomide is a key molecule for selective TPD using thalidomide derivatives and PROTACs.
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Affiliation(s)
- Satoshi Yamanaka
- Division of Cell-Free Sciences, Proteo-Science Center, Ehime University, Matsuyama, 790-8577, Japan
- Division of Proteo-Interactome, Proteo-Science Center, Ehime University, Matsuyama, 790-8577, Japan
| | - Hirotake Furihata
- Division of Cell-Free Sciences, Proteo-Science Center, Ehime University, Matsuyama, 790-8577, Japan
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, 113-8657, Japan
| | - Yuta Yanagihara
- Division of Integrative Pathophysiology, Proteo-Science Center, Ehime University, Toon, 791-0295, Japan
| | - Akihito Taya
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Nagoya, 466-8555, Japan
| | - Takato Nagasaka
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Nagoya, 466-8555, Japan
| | - Mai Usui
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Nagoya, 466-8555, Japan
| | - Koya Nagaoka
- Division of Cell-Free Sciences, Proteo-Science Center, Ehime University, Matsuyama, 790-8577, Japan
| | - Yuki Shoya
- Division of Cell-Free Sciences, Proteo-Science Center, Ehime University, Matsuyama, 790-8577, Japan
| | - Kohei Nishino
- Division of Cell Signaling, Fujii Memorial Institute of Medical Sciences, Tokushima University, Tokushima, 770-8503, Japan
| | - Shuhei Yoshida
- Division of Integrative Pathophysiology, Proteo-Science Center, Ehime University, Toon, 791-0295, Japan
| | - Hidetaka Kosako
- Division of Cell Signaling, Fujii Memorial Institute of Medical Sciences, Tokushima University, Tokushima, 770-8503, Japan
| | - Masaru Tanokura
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, 113-8657, Japan
| | - Takuya Miyakawa
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, 113-8657, Japan
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8502, Japan
| | - Yuuki Imai
- Division of Integrative Pathophysiology, Proteo-Science Center, Ehime University, Toon, 791-0295, Japan
| | - Norio Shibata
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Nagoya, 466-8555, Japan
| | - Tatsuya Sawasaki
- Division of Cell-Free Sciences, Proteo-Science Center, Ehime University, Matsuyama, 790-8577, Japan.
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145
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Teng M, Gray NS. The rise of degrader drugs. Cell Chem Biol 2023; 30:864-878. [PMID: 37494935 DOI: 10.1016/j.chembiol.2023.06.020] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/30/2023] [Accepted: 06/21/2023] [Indexed: 07/28/2023]
Abstract
The cancer genomics revolution has served up a plethora of promising and challenging targets for the drug discovery community. The field of targeted protein degradation (TPD) uses small molecules to reprogram the protein homeostasis system to destroy desired target proteins. In the last decade, remarkable progress has enabled the rational development of degraders for a large number of target proteins, with over 20 molecules targeting more than 12 proteins entering clinical development. While TPD has been fully credentialed by the prior development of immunomodulatory drug (IMiD) class for the treatment of multiple myeloma, the field is poised for a "Gleevec moment" in which robust clinical efficacy of a rationally developed novel degrader against a preselected target is firmly established. Here, we endeavor to provide a high-level evaluation of exciting developments in the field and comment on steps that may realize the full potential of this new therapeutic modality.
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Affiliation(s)
- Mingxing Teng
- Center for Drug Discovery, Department of Pathology & Immunology, and Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Nathanael S Gray
- Department of Chemical and Systems Biology, ChEM-H, Stanford Cancer Institute, School of Medicine, Stanford University, Stanford, CA 94305, USA.
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146
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Shen F, Dassama LMK. Opportunities and challenges of protein-based targeted protein degradation. Chem Sci 2023; 14:8433-8447. [PMID: 37592990 PMCID: PMC10430753 DOI: 10.1039/d3sc02361c] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 07/02/2023] [Indexed: 08/19/2023] Open
Abstract
In the 20 years since the first report of a proteolysis targeting chimeric (PROTAC) molecule, targeted protein degradation (TPD) technologies have attempted to revolutionize the fields of chemical biology and biomedicine by providing exciting research opportunities and potential therapeutics. However, they primarily focus on the use of small molecules to recruit the ubiquitin proteasome system to mediate target protein degradation. This then limits protein targets to cytosolic domains with accessible and suitable small molecule binding pockets. In recent years, biologics such as proteins and nucleic acids have instead been used as binders for targeting proteins, thereby expanding the scope of TPD platforms to include secreted proteins, transmembrane proteins, and soluble but highly disordered intracellular proteins. This perspective summarizes the recent TPD platforms that utilize nanobodies, antibodies, and other proteins as binding moieties to deplete challenging targets, either through the ubiquitin proteasome system or the lysosomal degradation pathway. Importantly, the perspective also highlights opportunities and remaining challenges of current protein-based TPD technologies.
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Affiliation(s)
- Fangfang Shen
- Department of Chemistry, Sarafan ChEM-H Institute, Stanford University USA
| | - Laura M K Dassama
- Department of Chemistry, Sarafan ChEM-H Institute, Stanford University USA
- Department of Microbiology & Immunology, Stanford School of Medicine USA
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147
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Scott EC, Baines AC, Gong Y, Moore R, Pamuk GE, Saber H, Subedee A, Thompson MD, Xiao W, Pazdur R, Rao VA, Schneider J, Beaver JA. Trends in the approval of cancer therapies by the FDA in the twenty-first century. Nat Rev Drug Discov 2023; 22:625-640. [PMID: 37344568 DOI: 10.1038/s41573-023-00723-4] [Citation(s) in RCA: 63] [Impact Index Per Article: 63.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/10/2023] [Indexed: 06/23/2023]
Abstract
The cancer treatment landscape has changed dramatically since the turn of the century, resulting in substantial improvements in outcomes for patients. This Review summarizes trends in the approval of oncology therapeutic products by the United States Food and Drug Administration (FDA) from January 2000 to October 2022, based on a categorization of these products by their mechanism of action and primary target. Notably, the rate of oncology indication approvals has increased in this time, driven by approvals for targeted therapies, as has the rate of introduction of new therapeutic approaches. Kinase inhibitors are the dominant product class by number of approved products and indications, yet immune checkpoint inhibitors have the second most approvals despite not entering the market until 2011. Other trends include a slight increase in the share of approvals for biomarker-defined populations and the emergence of tumour-site-agnostic approvals. Finally, we consider the implications of the trends for the future of oncology therapeutic product development, including the impact of novel therapeutic approaches and technologies.
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Affiliation(s)
- Emma C Scott
- Office of Oncologic Diseases, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA.
| | - Andrea C Baines
- Office of Oncologic Diseases, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
| | - Yutao Gong
- Office of Oncologic Diseases, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
| | - Rodney Moore
- Office of Oncologic Diseases, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
| | - Gulsum E Pamuk
- Office of Oncologic Diseases, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
| | - Haleh Saber
- Office of Oncologic Diseases, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
| | - Ashim Subedee
- Office of Oncologic Diseases, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
- National Cancer Institute, Rockville, MD, USA
| | - Matthew D Thompson
- Office of Oncologic Diseases, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
| | - Wenming Xiao
- Office of Oncologic Diseases, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
| | - Richard Pazdur
- Oncology Center of Excellence, U.S. Food and Drug Administration, Silver Spring, MD, USA
| | - V Ashutosh Rao
- Office of Biotechnology Products, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
| | - Julie Schneider
- Oncology Center of Excellence, U.S. Food and Drug Administration, Silver Spring, MD, USA
| | - Julia A Beaver
- Office of Oncologic Diseases, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
- Oncology Center of Excellence, U.S. Food and Drug Administration, Silver Spring, MD, USA
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148
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Liu X, Ciulli A. Proximity-Based Modalities for Biology and Medicine. ACS CENTRAL SCIENCE 2023; 9:1269-1284. [PMID: 37521793 PMCID: PMC10375889 DOI: 10.1021/acscentsci.3c00395] [Citation(s) in RCA: 36] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Indexed: 08/01/2023]
Abstract
Molecular proximity orchestrates biological function, and blocking existing proximities is an established therapeutic strategy. By contrast, strengthening or creating neoproximity with chemistry enables modulation of biological processes with high selectivity and has the potential to substantially expand the target space. A plethora of proximity-based modalities to target proteins via diverse approaches have recently emerged, opening opportunities for biopharmaceutical innovation. This Outlook outlines the diverse mechanisms and molecules based on induced proximity, including protein degraders, blockers, and stabilizers, inducers of protein post-translational modifications, and agents for cell therapy, and discusses opportunities and challenges that the field must address to mature and unlock translation in biology and medicine.
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Affiliation(s)
- Xingui Liu
- Centre for Targeted Protein
Degradation, Division of Biological Chemistry and Drug Discovery,
School of Life Sciences, University of Dundee, 1 James Lindsay Place, Dundee DD1 5JJ, United Kingdom
| | - Alessio Ciulli
- Centre for Targeted Protein
Degradation, Division of Biological Chemistry and Drug Discovery,
School of Life Sciences, University of Dundee, 1 James Lindsay Place, Dundee DD1 5JJ, United Kingdom
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149
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Chung CI, Yang J, Shu X. Chemogenetic Minitool for Dissecting the Roles of Protein Phase Separation. ACS CENTRAL SCIENCE 2023; 9:1466-1479. [PMID: 37521779 PMCID: PMC10375881 DOI: 10.1021/acscentsci.3c00251] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Indexed: 08/01/2023]
Abstract
Biomolecular condensate is an emerging structural entity that regulates various cellular processes. Recent studies have discovered the phase-separation (PS) capability of several transcription factors (TFs) including YAP/TAZ upon biological stimuli, which provide new mechanisms of gene regulation. However, it remains mostly unanswered as to whether PS from a diffuse state to a phase-separated state promotes gene transcription. To address this question, we have designed a chemogenetic tool, dubbed SPARK-ON, which manipulates the PS of YAP and TAZ without a biological stimulus, forming condensates that are transcriptionally active, containing the DNA-binding partner TEAD, genomic DNA, transcriptional machinery, and nascent RNA. Most importantly, PS of TAZ increases the transcription of its target genes. Therefore, our data indicate that PS promotes gene transcription of TAZ. SPARK-ON is advantageous to current mutagenesis-based approaches that are often problematic when mutagenesis affects the transcriptional activity of a TF. Furthermore, protein abundance levels also affect gene transcription, but PS depends on protein abundance because PS occurs only when the protein level is above a saturation concentration. SPARK-ON decouples PS from protein abundance levels without introducing mutations and thus will find important applications in understanding the biological roles of PS for many TFs and other biomolecular condensates.
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Affiliation(s)
- Chan-I Chung
- Department
of Pharmaceutical Chemistry, University
of California—San Francisco, San Francisco, California 94158, United States
- Cardiovascular
Research Institute, University of California—San
Francisco, San Francisco, California 94158, United States
| | - Junjiao Yang
- Department
of Pharmaceutical Chemistry, University
of California—San Francisco, San Francisco, California 94158, United States
- Cardiovascular
Research Institute, University of California—San
Francisco, San Francisco, California 94158, United States
| | - Xiaokun Shu
- Department
of Pharmaceutical Chemistry, University
of California—San Francisco, San Francisco, California 94158, United States
- Cardiovascular
Research Institute, University of California—San
Francisco, San Francisco, California 94158, United States
- Helen Diller
Family Comprehensive Cancer Center, University
of California—San Francisco, San Francisco, California 94158, United States
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150
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Bouguenina H, Nicolaou S, Le Bihan YV, Bowling EA, Calderon C, Caldwell JJ, Harrington B, Hayes A, McAndrew PC, Mitsopoulos C, Sialana FJ, Scarpino A, Stubbs M, Thapaliya A, Tyagi S, Wang HZ, Wood F, Burke R, Raynaud F, Choudhary J, van Montfort RL, Sadok A, Westbrook TF, Collins I, Chopra R. iTAG an optimized IMiD-induced degron for targeted protein degradation in human and murine cells. iScience 2023; 26:107059. [PMID: 37360684 PMCID: PMC10285648 DOI: 10.1016/j.isci.2023.107059] [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: 04/12/2023] [Revised: 04/18/2023] [Accepted: 06/01/2023] [Indexed: 06/28/2023] Open
Abstract
To address the limitation associated with degron based systems, we have developed iTAG, a synthetic tag based on IMiDs/CELMoDs mechanism of action that improves and addresses the limitations of both PROTAC and previous IMiDs/CeLMoDs based tags. Using structural and sequence analysis, we systematically explored native and chimeric degron containing domains (DCDs) and evaluated their ability to induce degradation. We identified the optimal chimeric iTAG(DCD23 60aa) that elicits robust degradation of targets across cell types and subcellular localizations without exhibiting the well documented "hook effect" of PROTAC-based systems. We showed that iTAG can also induce target degradation by murine CRBN and enabled the exploration of natural neo-substrates that can be degraded by murine CRBN. Hence, the iTAG system constitutes a versatile tool to degrade targets across the human and murine proteome.
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Affiliation(s)
- Habib Bouguenina
- Centre for Cancer Drug Discovery, the Institute of Cancer Research, 15 Cotswold Road, Sutton, London SM2 5NG, UK
| | - Stephanos Nicolaou
- Centre for Cancer Drug Discovery, the Institute of Cancer Research, 15 Cotswold Road, Sutton, London SM2 5NG, UK
| | - Yann-Vaï Le Bihan
- Centre for Cancer Drug Discovery, the Institute of Cancer Research, 15 Cotswold Road, Sutton, London SM2 5NG, UK
| | - Elizabeth A. Bowling
- Therapeutic Innovation Centre (THINC), Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Cheyenne Calderon
- Therapeutic Innovation Centre (THINC), Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - John J. Caldwell
- Centre for Cancer Drug Discovery, the Institute of Cancer Research, 15 Cotswold Road, Sutton, London SM2 5NG, UK
| | - Brinley Harrington
- Therapeutic Innovation Centre (THINC), Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Angela Hayes
- Centre for Cancer Drug Discovery, the Institute of Cancer Research, 15 Cotswold Road, Sutton, London SM2 5NG, UK
| | - P. Craig McAndrew
- Centre for Cancer Drug Discovery, the Institute of Cancer Research, 15 Cotswold Road, Sutton, London SM2 5NG, UK
| | - Costas Mitsopoulos
- Centre for Cancer Drug Discovery, the Institute of Cancer Research, 15 Cotswold Road, Sutton, London SM2 5NG, UK
| | - Fernando Jr. Sialana
- Centre for Cancer Drug Discovery, the Institute of Cancer Research, 15 Cotswold Road, Sutton, London SM2 5NG, UK
- Functional Proteomics Group, The Institute of Cancer Research, Chester Beatty Laboratories, London SW3 6JB, UK
| | - Andrea Scarpino
- Centre for Cancer Drug Discovery, the Institute of Cancer Research, 15 Cotswold Road, Sutton, London SM2 5NG, UK
| | - Mark Stubbs
- Centre for Cancer Drug Discovery, the Institute of Cancer Research, 15 Cotswold Road, Sutton, London SM2 5NG, UK
| | - Arjun Thapaliya
- Centre for Cancer Drug Discovery, the Institute of Cancer Research, 15 Cotswold Road, Sutton, London SM2 5NG, UK
| | - Siddhartha Tyagi
- Therapeutic Innovation Centre (THINC), Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Hannah Z. Wang
- Centre for Cancer Drug Discovery, the Institute of Cancer Research, 15 Cotswold Road, Sutton, London SM2 5NG, UK
| | - Francesca Wood
- Centre for Cancer Drug Discovery, the Institute of Cancer Research, 15 Cotswold Road, Sutton, London SM2 5NG, UK
| | - Rosemary Burke
- Centre for Cancer Drug Discovery, the Institute of Cancer Research, 15 Cotswold Road, Sutton, London SM2 5NG, UK
| | - Florence Raynaud
- Centre for Cancer Drug Discovery, the Institute of Cancer Research, 15 Cotswold Road, Sutton, London SM2 5NG, UK
| | - Jyoti Choudhary
- Functional Proteomics Group, The Institute of Cancer Research, Chester Beatty Laboratories, London SW3 6JB, UK
| | - Rob L.M. van Montfort
- Centre for Cancer Drug Discovery, the Institute of Cancer Research, 15 Cotswold Road, Sutton, London SM2 5NG, UK
| | - Amine Sadok
- Centre for Cancer Drug Discovery, the Institute of Cancer Research, 15 Cotswold Road, Sutton, London SM2 5NG, UK
| | - Thomas F. Westbrook
- Therapeutic Innovation Centre (THINC), Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ian Collins
- Centre for Cancer Drug Discovery, the Institute of Cancer Research, 15 Cotswold Road, Sutton, London SM2 5NG, UK
| | - Rajesh Chopra
- Centre for Cancer Drug Discovery, the Institute of Cancer Research, 15 Cotswold Road, Sutton, London SM2 5NG, UK
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