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Laure A, Royet C, Bihel F, Baratte B, Bach S, Peyressatre M, Morris MC. Ethaverine and Papaverine Target Cyclin-Dependent Kinase 5 and Inhibit Lung Cancer Cell Proliferation and Migration. ACS Pharmacol Transl Sci 2024; 7:1377-1385. [PMID: 38751642 PMCID: PMC11091981 DOI: 10.1021/acsptsci.4c00023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 04/11/2024] [Accepted: 04/15/2024] [Indexed: 05/18/2024]
Abstract
CDK5 kinase plays a central role in the regulation of neuronal functions, and its hyperactivation has been associated with neurodegenerative pathologies and more recently with several human cancers, in particular lung cancer. However, ATP-competitive inhibitors targeting CDK5 are poorly selective and suffer limitations, calling for new classes of inhibitors. In a screen for allosteric modulators of CDK5, we identified ethaverine and closely related derivative papaverine and showed that they inhibit cell proliferation and migration of non small cell lung cancer cell lines. Moreover the efficacy of these compounds is significantly enhanced when combined with the ATP-competitive inhibitor roscovitine, suggesting an additive dual mechanism of inhibition targeting CDK5. These compounds do not affect CDK5 stability, but thermodenaturation studies performed with A549 cell extracts infer that they interact with CDK5 in cellulo. Furthermore, the inhibitory potentials of ethaverine and papaverine are reduced in A549 cells treated with siRNA directed against CDK5. Taken together, our results provide unexpected and novel evidence that ethaverine and papaverine constitute promising leads that can be repurposed for targeting CDK5 in lung cancer.
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Affiliation(s)
- Arthur Laure
- Institut
des Biomolécules Max Mousseron, CNRS, UMR 5247, Université de Montpellier, 1919 Route de Mende, 34293 Montpellier, France
| | - Chloé Royet
- Institut
des Biomolécules Max Mousseron, CNRS, UMR 5247, Université de Montpellier, 1919 Route de Mende, 34293 Montpellier, France
| | - Frederic Bihel
- Laboratoire
d’Innovation Thérapeutique, IMS, UMR 7200, CNRS, Université de Strasbourg, 67401 Illkirch, France
| | - Blandine Baratte
- CNRS,
FR2424, Plateforme de criblage KISSf (Kinase Inhibitor Specialized
Screening Facility), Sorbonne Université, Station Biologique de Roscoff, 29680 Roscoff, France
- CNRS,
UMR8227, Integrative Biology of Marine Models Laboratory (LBI2M), Sorbonne Université, Station Biologique de Roscoff, 29680 Roscoff, France
| | - Stéphane Bach
- CNRS,
FR2424, Plateforme de criblage KISSf (Kinase Inhibitor Specialized
Screening Facility), Sorbonne Université, Station Biologique de Roscoff, 29680 Roscoff, France
- CNRS,
UMR8227, Integrative Biology of Marine Models Laboratory (LBI2M), Sorbonne Université, Station Biologique de Roscoff, 29680 Roscoff, France
- Centre
of Excellence for Pharmaceutical Sciences, North-West University, Private Bag X6001, Potchefstroom 2520, South Africa
| | - Marion Peyressatre
- Institut
des Biomolécules Max Mousseron, CNRS, UMR 5247, Université de Montpellier, 1919 Route de Mende, 34293 Montpellier, France
| | - May C. Morris
- Institut
des Biomolécules Max Mousseron, CNRS, UMR 5247, Université de Montpellier, 1919 Route de Mende, 34293 Montpellier, France
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2
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Yetkin-Arik B, Jansen SA, Varderidou-Minasian S, Westendorp B, Skarp KP, Altelaar M, Lindemans CA, Lorenowicz MJ. Mesenchymal stromal/stem cells promote intestinal epithelium regeneration after chemotherapy-induced damage. Stem Cell Res Ther 2024; 15:125. [PMID: 38679715 PMCID: PMC11057078 DOI: 10.1186/s13287-024-03738-9] [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: 10/06/2023] [Accepted: 04/20/2024] [Indexed: 05/01/2024] Open
Abstract
BACKGROUND Allogeneic hematopoietic stem cell transplantation (HSCT) is a curative treatment for leukemia and a range of non-malignant disorders. The success of the therapy is hampered by occurrence of acute graft-versus-host disease (aGvHD); an inflammatory response damaging recipient organs, with gut, liver, and skin being the most susceptible. Intestinal GvHD injury is often a life-threatening complication in patients unresponsive to steroid treatment. Allogeneic mesenchymal stromal/stem cell (MSC) infusions are a promising potential treatment for steroid-resistant aGvHD. Data from our institution and others demonstrate rescue of approximately 40-50% of aGvHD patients with MSCs in Phase I, II studies and minor side effects. Although promising, better understanding of MSC mode of action and patient response to MSC-based therapy is essential to improve this lifesaving treatment. METHODS Single cell human small intestine organoids were embedded in Matrigel, grown for 5 days and treated with busulfan for 48 h. Organoids damaged by treatment with busulfan or control organoids were co-cultured with 5000, 10,000, and 50,000 MSCs for 24 h, 48 h or 7 days and the analyses such as surface area determination, proliferation and apoptosis assessment, RNA sequencing and proteomics were performed. RESULTS Here, we developed a 3D co-culture model of human small intestinal organoids and MSCs, which allows to study the regenerative effects of MSCs on intestinal epithelium in a more physiologically relevant setting than existing in vitro systems. Using this model we mimicked chemotherapy-mediated damage of the intestinal epithelium. The treatment with busulfan, the chemotherapeutic commonly used as conditioning regiment before the HSCT, affected pathways regulating epithelial to mesenchymal transition, proliferation, and apoptosis in small intestinal organoids, as shown by transcriptomic and proteomic analysis. The co-culture of busulfan-treated intestinal organoids with MSCs reversed the effects of busulfan on the transcriptome and proteome of intestinal epithelium, which we also confirmed by functional evaluation of proliferation and apoptosis. CONCLUSIONS Collectively, we demonstrate that our in vitro co-culture system is a new valuable tool to facilitate the investigation of the molecular mechanisms behind the therapeutic effects of MSCs on damaged intestinal epithelium. This could benefit further optimization of the use of MSCs in HSCT patients.
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Affiliation(s)
- B Yetkin-Arik
- Center for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG, Utrecht, The Netherlands
- Regenerative Medicine Center, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
- Centre for Living Technologies, Alliance TU/E, WUR, UU, UMC Utrecht, Princetonlaan 6, 3584 CB, Utrecht, The Netherlands
| | - S A Jansen
- Regenerative Medicine Center, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
- Division of Pediatrics, University Medical Center Utrecht, Utrecht, The Netherlands
- Pediatric Stem Cell Transplantation, Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - S Varderidou-Minasian
- Center for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG, Utrecht, The Netherlands
- Regenerative Medicine Center, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
| | - B Westendorp
- Regenerative Medicine Center, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
- Division Cell Biology, Metabolism and Cancer, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - K-P Skarp
- Biomedical Primate Research Center, Lange Kleiweg 161, 2288 GJ, Rijswijk, The Netherlands
| | - M Altelaar
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research, and Utrecht Institute For Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | - C A Lindemans
- Regenerative Medicine Center, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
- Division of Pediatrics, University Medical Center Utrecht, Utrecht, The Netherlands
- Pediatric Stem Cell Transplantation, Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - M J Lorenowicz
- Center for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG, Utrecht, The Netherlands.
- Regenerative Medicine Center, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands.
- Biomedical Primate Research Center, Lange Kleiweg 161, 2288 GJ, Rijswijk, The Netherlands.
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3
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Figueroa-Navedo AM, Ivanov AR. Experimental and data analysis advances in thermal proteome profiling. CELL REPORTS METHODS 2024; 4:100717. [PMID: 38412830 PMCID: PMC10921035 DOI: 10.1016/j.crmeth.2024.100717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/17/2023] [Accepted: 02/05/2024] [Indexed: 02/29/2024]
Abstract
Method development for mass spectrometry (MS)-based thermal shift proteomic assays have advanced to probe small molecules with known and unknown protein-ligand interaction mechanisms and specificity, which is predominantly used in characterization of drug-protein interactions. In the discovery of target and off-target protein-ligand interactions, a thorough investigation of method development and their impact on the sensitivity and accuracy of protein-small molecule and protein-protein interactions is warranted. In this review, we discuss areas of improvement at each stage of thermal proteome profiling data analysis that includes processing of MS-based data, method development, and their effect on the overall quality of thermal proteome profiles. We also overview the optimization of experimental strategies and prioritization of an increased number of independent biological replicates over the number of evaluated temperatures.
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Affiliation(s)
- Amanda M Figueroa-Navedo
- Barnett Institute of Chemical and Biological Analysis, Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | - Alexander R Ivanov
- Barnett Institute of Chemical and Biological Analysis, Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA.
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4
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Bailey MA, Martyr JG, Hargrove AE, Fitzgerald MC. Stability-Based Proteomics for Investigation of Structured RNA-Protein Interactions. Anal Chem 2024:10.1021/acs.analchem.3c04978. [PMID: 38341805 PMCID: PMC11316846 DOI: 10.1021/acs.analchem.3c04978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/13/2024]
Abstract
RNA-protein interactions are essential to RNA function throughout biology. Identifying the protein interactions associated with a specific RNA, however, is currently hindered by the need for RNA labeling or costly tiling-based approaches. Conventional strategies, which commonly rely on affinity pull-down approaches, are also skewed to the detection of high affinity interactions and frequently miss weaker interactions that may be biologically important. Reported here is the first adaptation of stability-based mass spectrometry methods for the global analysis of RNA-protein interactions. The stability of proteins from rates of oxidation (SPROX) and thermal protein profiling (TPP) methods are used to identify the protein targets of three RNA ligands, the MALAT1 triple helix (TH), a viral stem loop (SL), and an unstructured RNA (PolyU), in LNCaP nuclear lysate. The 315 protein hits with RNA-induced conformational and stability changes detected by TPP and/or SPROX were enriched in previously annotated RNA-binding proteins and included new proteins for hypothesis generation. Also demonstrated are the orthogonality of the SPROX and TPP approaches and the utility of the domain-specific information available with SPROX. This work establishes a novel platform for the global discovery and interrogation of RNA-protein interactions that is generalizable to numerous biological contexts and RNA targets.
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Affiliation(s)
- Morgan A Bailey
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Justin G Martyr
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina 27710, United States
| | - Amanda E Hargrove
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina 27710, United States
| | - Michael C Fitzgerald
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina 27710, United States
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5
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Zhang Q, Liu G, Li Y, Yang B, Guo W, Zhang Y, Pan L, Zhang P, Zhang W, Kong D. Thermal proteome profiling reveals the glial toxicity of dencichine via inhibiting proteasome. Food Chem Toxicol 2023; 182:114146. [PMID: 37923194 DOI: 10.1016/j.fct.2023.114146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 10/13/2023] [Accepted: 10/24/2023] [Indexed: 11/07/2023]
Affiliation(s)
- Qingning Zhang
- Department of Pharmacology of Chinese Materia Medica, Institution of Chinese Integrative Medicine, Hebei Medical University, Shijiazhuang, Hebei, 050017, China
| | - Guangyuan Liu
- Department of Pharmacology of Chinese Materia Medica, Institution of Chinese Integrative Medicine, Hebei Medical University, Shijiazhuang, Hebei, 050017, China
| | - Yahui Li
- Department of Pharmacology of Chinese Materia Medica, Institution of Chinese Integrative Medicine, Hebei Medical University, Shijiazhuang, Hebei, 050017, China
| | - Bingkun Yang
- Department of Pharmacology of Chinese Materia Medica, Institution of Chinese Integrative Medicine, Hebei Medical University, Shijiazhuang, Hebei, 050017, China; School of Pharmacy, Hebei Medical University, Shijiazhuang, Hebei, 050017, China
| | - Wenyan Guo
- Department of Pharmacology of Chinese Materia Medica, Institution of Chinese Integrative Medicine, Hebei Medical University, Shijiazhuang, Hebei, 050017, China
| | - Yuyu Zhang
- Department of Pharmacology of Chinese Materia Medica, Institution of Chinese Integrative Medicine, Hebei Medical University, Shijiazhuang, Hebei, 050017, China
| | - Liangyu Pan
- Department of Pharmacology of Chinese Materia Medica, Institution of Chinese Integrative Medicine, Hebei Medical University, Shijiazhuang, Hebei, 050017, China
| | - Panpan Zhang
- Department of Pharmacology of Chinese Materia Medica, Institution of Chinese Integrative Medicine, Hebei Medical University, Shijiazhuang, Hebei, 050017, China
| | - Wei Zhang
- Department of Pharmacology of Chinese Materia Medica, Institution of Chinese Integrative Medicine, Hebei Medical University, Shijiazhuang, Hebei, 050017, China.
| | - Dezhi Kong
- Department of Pharmacology of Chinese Materia Medica, Institution of Chinese Integrative Medicine, Hebei Medical University, Shijiazhuang, Hebei, 050017, China.
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6
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Zhang M, Kim S, Yang HW. Non-canonical pathway for Rb inactivation and external signaling coordinate cell-cycle entry without CDK4/6 activity. Nat Commun 2023; 14:7847. [PMID: 38030655 PMCID: PMC10687137 DOI: 10.1038/s41467-023-43716-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: 05/17/2023] [Accepted: 11/16/2023] [Indexed: 12/01/2023] Open
Abstract
Cyclin-dependent kinases 4 and 6 (CDK4/6) are critical for initiating cell proliferation by inactivating the retinoblastoma (Rb) protein. However, mammalian cells can bypass CDK4/6 for Rb inactivation. Here we show a non-canonical pathway for Rb inactivation and its interplay with external signals. We find that the non-phosphorylated Rb protein in quiescent cells is intrinsically unstable, offering an alternative mechanism for initiating E2F activity. Nevertheless, this pathway incompletely induces Rb-protein loss, resulting in minimal E2F activity. To trigger cell proliferation, upregulation of mitogenic signaling is required for stabilizing c-Myc, thereby augmenting E2F activity. Concurrently, stress signaling promotes Cip/Kip levels, competitively regulating cell proliferation with mitogenic signaling. In cancer, driver mutations elevate c-Myc levels, facilitating adaptation to CDK4/6 inhibitors. Differentiated cells, despite Rb-protein loss, maintain quiescence through the modulation of c-Myc and Cip/Kip levels. Our findings provide mechanistic insights into an alternative model of cell-cycle entry and the maintenance of quiescence.
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Affiliation(s)
- Mimi Zhang
- Department of Pathology and Cell Biology, Columbia University, New York, NY, 10032, USA
| | - Sungsoo Kim
- Department of Pathology and Cell Biology, Columbia University, New York, NY, 10032, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, 10032, USA
| | - Hee Won Yang
- Department of Pathology and Cell Biology, Columbia University, New York, NY, 10032, USA.
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, 10032, USA.
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7
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Srinivasan V, Asghar MY, Zafar S, Törnquist K, Lindholm D. Proliferation and migration of ML1 follicular thyroid cancer cells are inhibited by IU1 targeting USP14: role of proteasome and autophagy flux. Front Cell Dev Biol 2023; 11:1234204. [PMID: 37711852 PMCID: PMC10499180 DOI: 10.3389/fcell.2023.1234204] [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: 06/03/2023] [Accepted: 08/21/2023] [Indexed: 09/16/2023] Open
Abstract
USP14 is a deubiquitinating enzyme involved in protein degradation by interacting with the proteasome and removal of poly-ubiquitin chains on target proteins. USP14 can influence cellular processes such as cell survival, DNA repair, ER stress, endocytosis, and the inflammatory response. USP14 further plays a role in tumor growth, and the inhibition of USP14 by compounds such as IU1 may affect cancer cell migration and invasion. Here we have studied the mechanisms for the action of IU1 in ML1 follicular thyroid cancer cells, comparing them with control, primary thyroid cells. Treatment with IU1 reduced proliferation of ML1 cells in a concentration-dependent manner, and more prominently than in control cells. IU1 decreased basal migration of ML1 cells, and after stimulation of cells with the bioactive compound, sphingosine-1-phosphate. The sphingosine-1-phosphate receptor 3 was increased in ML1 cells as compared with control thyroid cells, but this was not influenced by IU1. Further studies on the mechanism, revealed that IU1 enhanced the proteasome activity as well as LC3B-dependent autophagy flux in ML1 cells with an opposite effect on control thyroid cells. This indicates that IU1 elicits a cell-type dependent autophagy response, increasing it in ML1 cancer cells. The IU1-mediated stimulation of autophagy and proteasomes can likely contribute to the reduced cell proliferation and migration observed in ML1 cells. The precise set of proteins affected by IU1 in ML1 thyroid and other cancer cells warrant further investigations.
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Affiliation(s)
- Vignesh Srinivasan
- Medicum, Department of Biochemistry and Developmental Biology, Medical Faculty, University of Helsinki, Helsinki, Finland
- Minerva Foundation Institute for Medical Research, Helsinki, Finland
| | - Muhammad Yasir Asghar
- Minerva Foundation Institute for Medical Research, Helsinki, Finland
- Cell and Tissue Dynamics Research Program, Institute of Biotechnology, Helsinki Institute of Life Sciences, University of Helsinki, Helsinki, Finland
| | - Sadia Zafar
- Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
- Department of Pathology, HUSLAB, HUS Diagnostic Center, University of Helsinki, Helsinki University Hospital, Helsinki, Finland
| | - Kid Törnquist
- Minerva Foundation Institute for Medical Research, Helsinki, Finland
- Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, Turku, Finland
| | - Dan Lindholm
- Medicum, Department of Biochemistry and Developmental Biology, Medical Faculty, University of Helsinki, Helsinki, Finland
- Minerva Foundation Institute for Medical Research, Helsinki, Finland
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8
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George AL, Sidgwick FR, Watt JE, Martin MP, Trost M, Marín-Rubio JL, Dueñas ME. Comparison of Quantitative Mass Spectrometric Methods for Drug Target Identification by Thermal Proteome Profiling. J Proteome Res 2023; 22:2629-2640. [PMID: 37439223 PMCID: PMC10407934 DOI: 10.1021/acs.jproteome.3c00111] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Indexed: 07/14/2023]
Abstract
Thermal proteome profiling (TPP) provides a powerful approach to studying proteome-wide interactions of small therapeutic molecules and their target and off-target proteins, complementing phenotypic-based drug screens. Detecting differences in thermal stability due to target engagement requires high quantitative accuracy and consistent detection. Isobaric tandem mass tags (TMTs) are used to multiplex samples and increase quantification precision in TPP analysis by data-dependent acquisition (DDA). However, advances in data-independent acquisition (DIA) can provide higher sensitivity and protein coverage with reduced costs and sample preparation steps. Herein, we explored the performance of different DIA-based label-free quantification approaches compared to TMT-DDA for thermal shift quantitation. Acute myeloid leukemia cells were treated with losmapimod, a known inhibitor of MAPK14 (p38α). Label-free DIA approaches, and particularly the library-free mode in DIA-NN, were comparable of TMT-DDA in their ability to detect target engagement of losmapimod with MAPK14 and one of its downstream targets, MAPKAPK3. Using DIA for thermal shift quantitation is a cost-effective alternative to labeled quantitation in the TPP pipeline.
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Affiliation(s)
- Amy L. George
- Laboratory
for Biological Mass Spectrometry, Biosciences Institute, Newcastle University, Newcastle-upon-Tyne NE2 4HH, U.K.
| | - Frances R. Sidgwick
- Laboratory
for Biological Mass Spectrometry, Biosciences Institute, Newcastle University, Newcastle-upon-Tyne NE2 4HH, U.K.
| | - Jessica E. Watt
- Newcastle
Cancer Centre, Northern Institute for Cancer Research, Medical School, Newcastle University, Paul O’Gorman Building, Framlington Place, Newcastle upon Tyne NE2 4HH, U.K.
| | - Mathew P. Martin
- Newcastle
Cancer Centre, Northern Institute for Cancer Research, Medical School, Newcastle University, Paul O’Gorman Building, Framlington Place, Newcastle upon Tyne NE2 4HH, U.K.
| | - Matthias Trost
- Laboratory
for Biological Mass Spectrometry, Biosciences Institute, Newcastle University, Newcastle-upon-Tyne NE2 4HH, U.K.
| | - José Luis Marín-Rubio
- Laboratory
for Biological Mass Spectrometry, Biosciences Institute, Newcastle University, Newcastle-upon-Tyne NE2 4HH, U.K.
| | - Maria Emilia Dueñas
- Laboratory
for Biological Mass Spectrometry, Biosciences Institute, Newcastle University, Newcastle-upon-Tyne NE2 4HH, U.K.
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9
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Kim SJ, Maric C, Briu LM, Fauchereau F, Baldacci G, Debatisse M, Koundrioukoff S, Cadoret JC. Firing of Replication Origins Is Disturbed by a CDK4/6 Inhibitor in a pRb-Independent Manner. Int J Mol Sci 2023; 24:10629. [PMID: 37445805 DOI: 10.3390/ijms241310629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 06/21/2023] [Accepted: 06/21/2023] [Indexed: 07/15/2023] Open
Abstract
Over the last decade, CDK4/6 inhibitors (palbociclib, ribociclib and abemaciclib) have emerged as promising anticancer drugs. Numerous studies have demonstrated that CDK4/6 inhibitors efficiently block the pRb-E2F pathway and induce cell cycle arrest in pRb-proficient cells. Based on these studies, the inhibitors have been approved by the FDA for treatment of advanced hormonal receptor (HR) positive breast cancers in combination with hormonal therapy. However, some evidence has recently shown unexpected effects of the inhibitors, underlining a need to characterize the effects of CDK4/6 inhibitors beyond pRb. Our study demonstrates how palbociclib impairs origin firing in the DNA replication process in pRb-deficient cell lines. Strikingly, despite the absence of pRb, cells treated with palbociclib synthesize less DNA while showing no cell cycle arrest. Furthermore, this CDK4/6 inhibitor treatment disturbs the temporal program of DNA replication and reduces the density of replication forks. Cells treated with palbociclib show a defect in the loading of the Pre-initiation complex (Pre-IC) proteins on chromatin, indicating a reduced initiation of DNA replication. Our findings highlight hidden effects of palbociclib on the dynamics of DNA replication and of its cytotoxic consequences on cell viability in the absence of pRb. This study provides a potential therapeutic application of palbociclib in combination with other drugs to target genomic instability in pRB-deficient cancers.
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Affiliation(s)
- Su-Jung Kim
- CNRS, Institut Jacques Monod, Université Paris Cité, F-75013 Paris, France
- CNRS UMR9019, Institut Gustave Roussy, 94805 Villejuif, France
| | - Chrystelle Maric
- CNRS, Institut Jacques Monod, Université Paris Cité, F-75013 Paris, France
| | - Lina-Marie Briu
- CNRS, Institut Jacques Monod, Université Paris Cité, F-75013 Paris, France
| | - Fabien Fauchereau
- CNRS, Institut Jacques Monod, Université Paris Cité, F-75013 Paris, France
| | - Giuseppe Baldacci
- CNRS, Institut Jacques Monod, Université Paris Cité, F-75013 Paris, France
| | - Michelle Debatisse
- CNRS UMR9019, Institut Gustave Roussy, 94805 Villejuif, France
- Sorbonne Université, 75005 Paris, France
| | - Stéphane Koundrioukoff
- CNRS UMR9019, Institut Gustave Roussy, 94805 Villejuif, France
- Sorbonne Université, 75005 Paris, France
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10
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Kurata K, Samur MK, Liow P, Wen K, Yamamoto L, Liu J, Morelli E, Gulla A, Tai YT, Qi J, Hideshima T, Anderson KC. BRD9 Degradation Disrupts Ribosome Biogenesis in Multiple Myeloma. Clin Cancer Res 2023; 29:1807-1821. [PMID: 36780189 PMCID: PMC10150249 DOI: 10.1158/1078-0432.ccr-22-3668] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 01/12/2023] [Accepted: 02/09/2023] [Indexed: 02/14/2023]
Abstract
PURPOSE BRD9 is a defining component of the noncanonical SWI/SNF complex, which regulates gene expression by controlling chromatin dynamics. Although recent studies have found an oncogenic role for BRD9 in multiple cancer types including multiple myeloma, its clinical significance and oncogenic mechanism have not yet been elucidated. Here, we sought to identify the clinical and biological impact of BRD9 in multiple myeloma, which may contribute to the development of novel therapeutic strategies. EXPERIMENTAL DESIGN We performed integrated analyses of BRD9 in vitro and in vivo using multiple myeloma cell lines and primary multiple myeloma cells in established preclinical models, which identified the molecular functions of BRD9 contributing to multiple myeloma cell survival. RESULTS We found that high BRD9 expression was a poor prognostic factor in multiple myeloma. Depleting BRD9 by genetic (shRNA) and pharmacologic (dBRD9-A; proteolysis-targeting chimera; BRD9 degrader) approaches downregulated ribosome biogenesis genes, decreased the expression of the master regulator MYC, and disrupted the protein-synthesis maintenance machinery, thereby inhibiting multiple myeloma cell growth in vitro and in vivo in preclinical models. Importantly, we identified that the expression of ribosome biogenesis genes was associated with the disease progression and prognosis of patients with multiple myeloma. Our results suggest that BRD9 promotes gene expression by predominantly occupying the promoter regions of ribosome biogenesis genes and cooperating with BRD4 to enhance the transcriptional function of MYC. CONCLUSIONS Our study identifies and validates BRD9 as a novel therapeutic target in preclinical models of multiple myeloma, which provides the framework for the clinical evaluation of BRD9 degraders to improve patient outcome.
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Affiliation(s)
- Keiji Kurata
- Jerome Lipper Multiple Myeloma Center, LeBow Institute for Myeloma Therapeutics, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Mehmet K. Samur
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, Boston, Massachusetts
| | - Priscilla Liow
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Kenneth Wen
- Jerome Lipper Multiple Myeloma Center, LeBow Institute for Myeloma Therapeutics, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Leona Yamamoto
- Jerome Lipper Multiple Myeloma Center, LeBow Institute for Myeloma Therapeutics, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Jiye Liu
- Jerome Lipper Multiple Myeloma Center, LeBow Institute for Myeloma Therapeutics, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Eugenio Morelli
- Jerome Lipper Multiple Myeloma Center, LeBow Institute for Myeloma Therapeutics, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Annamaria Gulla
- Jerome Lipper Multiple Myeloma Center, LeBow Institute for Myeloma Therapeutics, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
- Candiolo Cancer Institute, FPO-IRCCS, Turin, Italy
| | - Yu-Tzu Tai
- Jerome Lipper Multiple Myeloma Center, LeBow Institute for Myeloma Therapeutics, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Jun Qi
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Teru Hideshima
- Jerome Lipper Multiple Myeloma Center, LeBow Institute for Myeloma Therapeutics, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Kenneth C. Anderson
- Jerome Lipper Multiple Myeloma Center, LeBow Institute for Myeloma Therapeutics, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
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11
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Bailey MA, Tang Y, Park HJ, Fitzgerald MC. Comparative Analysis of Protein Folding Stability-Based Profiling Methods for Characterization of Biological Phenotypes. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:383-393. [PMID: 36802530 PMCID: PMC10164353 DOI: 10.1021/jasms.2c00248] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Recently, a new suite of mass spectrometry-based proteomic methods has been developed that enables evaluation of protein folding stability on the proteomic scale. These methods utilize chemical and thermal denaturation approaches (SPROX and TPP, respectively) as well as proteolysis strategies (DARTS, LiP, and PP) to assess protein folding stability. The analytical capabilities of these technique have been well-established for protein target discovery applications. However, less is known about the relative advantages and disadvantages of using these different strategies to characterize biological phenotypes. Reported here is a comparative study of SPROX, TPP, LiP, and conventional protein expression level measurements using both a mouse model of aging and a mammalian cell culture model of breast cancer. Analyses on proteins in brain tissue cell lysates derived from 1- and 18-month-old mice (n = 4-5 at each time point) and on proteins in cell lysates derived from the MCF-7 and MCF-10A cell lines revealed a majority of the differentially stabilized protein hits in each phenotype analysis had unchanged expression levels. In both phenotype analyses, TPP generated the largest number and fraction of differentially stabilized protein hits. Only a quarter of all the protein hits identified in each phenotype analysis had a differential stability that was detected using multiple techniques. This work also reports the first peptide-level analysis of TPP data, which was required for the correct interpretation of the phenotype analyses performed here. Studies on selected protein stability hits also uncovered phenotype-related functional changes.
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Affiliation(s)
- Morgan A. Bailey
- Department of Chemistry, Duke University, Durham, North Carolina 27708
- These authors contributed equally
| | - Yun Tang
- Department of Chemistry, Duke University, Durham, North Carolina 27708
- These authors contributed equally
| | - Hye-Jin Park
- Department of Chemistry, Duke University, Durham, North Carolina 27708
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12
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Fan X, He Y, Wu G, Chen H, Cheng X, Zhan Y, An C, Chen T, Wang X. Sirt3 activates autophagy to prevent DOX-induced senescence by inactivating PI3K/AKT/mTOR pathway in A549 cells. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2023; 1870:119411. [PMID: 36521686 DOI: 10.1016/j.bbamcr.2022.119411] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 11/27/2022] [Accepted: 12/03/2022] [Indexed: 12/14/2022]
Abstract
Sirtuin 3 (Sirt3), a mitochondrial deacetylase, regulates mitochondrial redox homeostasis and autophagy and is involved in physiological and pathological processes such as aging, cellular metabolism, and tumorigenesis. We here investigate how Sirt3 regulates doxorubicin (DOX)-induced senescence in lung cancer A549 cells. Sirt3 greatly reduced DOX-induced upregulation of senescence marker proteins p53, p16, p21 and SA-β-Gal activity as well as ROS levels. Notably, Sirt3 reversed DOX-induced autophagic flux blockage, as shown by increased p62 degradation and LC3II/LC3I ratio. Importantly, the autophagy inhibitors 3-methyladenine (3-MA) and chloroquine (CQ) partially abolished the antioxidant stress and antiaging effects of Sirt3, while the autophagy activator rapamycin (Rap) potentiated these effects of Sirt3, demonstrating that autophagy mediates the anti-aging effects of Sirt3. Additionally, Sirt3 inhibited the DOX-induced activation of the phosphatidylinositol-3-kinase (PI3K)/AKT/mammalian target of rapamycin (mTOR) signaling pathway, which in turn activated autophagy. The PI3K inhibitor LY294002 promoted the antioxidant stress and antiaging effects of Sirt3, while the AKT activator SC-79 reversed these effects of Sirt3. Taken together, Sirt3 counteracts DOX-induced senescence by improving autophagic flux.
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Affiliation(s)
- Xuhong Fan
- Department of Pain Management, the First Affiliated Hospital of Jinan University, Guangzhou 510630, China
| | - Yuting He
- Department of Pain Management, the First Affiliated Hospital of Jinan University, Guangzhou 510630, China
| | - Guihao Wu
- Department of Pain Management, the First Affiliated Hospital of Jinan University, Guangzhou 510630, China
| | - Hongce Chen
- MOE Key Laboratory of Laser Life Science, Guangdong Provincial Key Laboratory of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou 510631, China
| | - Xuecheng Cheng
- MOE Key Laboratory of Laser Life Science, Guangdong Provincial Key Laboratory of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou 510631, China
| | - Yongtong Zhan
- Department of Pain Management, the First Affiliated Hospital of Jinan University, Guangzhou 510630, China
| | - Chunchun An
- MOE Key Laboratory of Laser Life Science, Guangdong Provincial Key Laboratory of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou 510631, China
| | - Tongsheng Chen
- MOE Key Laboratory of Laser Life Science, Guangdong Provincial Key Laboratory of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou 510631, China
| | - Xiaoping Wang
- Department of Pain Management, the First Affiliated Hospital of Jinan University, Guangzhou 510630, China.
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13
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Marín-Rubio JL, Peltier-Heap RE, Dueñas ME, Heunis T, Dannoura A, Inns J, Scott J, Simpson AJ, Blair HJ, Heidenreich O, Allan JM, Watt JE, Martin MP, Saxty B, Trost M. A Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Assay Identifies Nilotinib as an Inhibitor of Inflammation in Acute Myeloid Leukemia. J Med Chem 2022; 65:12014-12030. [PMID: 36094045 PMCID: PMC9511480 DOI: 10.1021/acs.jmedchem.2c00671] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Inflammatory responses are important in cancer, particularly
in the context of monocyte-rich aggressive myeloid neoplasm. We developed
a label-free cellular phenotypic drug discovery assay to identify
anti-inflammatory drugs in human monocytes derived from acute myeloid
leukemia (AML), by tracking several features ionizing from only 2500
cells using matrix-assisted laser desorption/ionization-time of flight
(MALDI-TOF) mass spectrometry. A proof-of-concept screen showed that
the BCR-ABL inhibitor nilotinib, but not the structurally similar
imatinib, blocks inflammatory responses. In order to identify the
cellular (off-)targets of nilotinib, we performed thermal proteome
profiling (TPP). Unlike imatinib, nilotinib and other later-generation
BCR-ABL inhibitors bind to p38α and inhibit the p38α-MK2/3
signaling axis, which suppressed pro-inflammatory cytokine expression,
cell adhesion, and innate immunity markers in activated monocytes
derived from AML. Thus, our study provides a tool for the discovery
of new anti-inflammatory drugs, which could contribute to the treatment
of inflammation in myeloid neoplasms and other diseases.
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Affiliation(s)
- José Luis Marín-Rubio
- Laboratory for Biological Mass Spectrometry, Biosciences Institute, Newcastle University, Newcastle-upon-Tyne NE2 4HH, UK
| | - Rachel E Peltier-Heap
- Laboratory for Biological Mass Spectrometry, Biosciences Institute, Newcastle University, Newcastle-upon-Tyne NE2 4HH, UK
| | - Maria Emilia Dueñas
- Laboratory for Biological Mass Spectrometry, Biosciences Institute, Newcastle University, Newcastle-upon-Tyne NE2 4HH, UK
| | - Tiaan Heunis
- Laboratory for Biological Mass Spectrometry, Biosciences Institute, Newcastle University, Newcastle-upon-Tyne NE2 4HH, UK.,Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Abeer Dannoura
- Laboratory for Biological Mass Spectrometry, Biosciences Institute, Newcastle University, Newcastle-upon-Tyne NE2 4HH, UK
| | - Joseph Inns
- Laboratory for Biological Mass Spectrometry, Biosciences Institute, Newcastle University, Newcastle-upon-Tyne NE2 4HH, UK
| | - Jonathan Scott
- Translational and Clinical Research Institute, Newcastle University, Newcastle-upon-Tyne NE2 4HH, UK
| | - A John Simpson
- Translational and Clinical Research Institute, Newcastle University, Newcastle-upon-Tyne NE2 4HH, UK.,Respiratory Medicine Unit, Royal Victoria Infirmary, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne NE1 4LP, UK
| | - Helen J Blair
- Translational and Clinical Research Institute, Newcastle University, Herschel Building, Level 6, Brewery Lane, Newcastle upon Tyne NE1 7RU, UK
| | - Olaf Heidenreich
- Translational and Clinical Research Institute, Newcastle University, Herschel Building, Level 6, Brewery Lane, Newcastle upon Tyne NE1 7RU, UK
| | - James M Allan
- Translational and Clinical Research Institute, Newcastle University, Herschel Building, Level 6, Brewery Lane, Newcastle upon Tyne NE1 7RU, UK
| | - Jessica E Watt
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Medical School, Newcastle University, Paul O'Gorman Building, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Mathew P Martin
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Medical School, Newcastle University, Paul O'Gorman Building, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Barbara Saxty
- LifeArc, SBC Open Innovation Campus, Stevenage SG1 2FX, UK
| | - Matthias Trost
- Laboratory for Biological Mass Spectrometry, Biosciences Institute, Newcastle University, Newcastle-upon-Tyne NE2 4HH, UK
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14
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Llop-Hernández À, Verdura S, Cuyàs E, Menendez JA. Nutritional Niches of Cancer Therapy-Induced Senescent Cells. Nutrients 2022; 14:nu14173636. [PMID: 36079891 PMCID: PMC9460569 DOI: 10.3390/nu14173636] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 08/30/2022] [Accepted: 08/31/2022] [Indexed: 11/16/2022] Open
Abstract
Therapy-induced senescence (TIS) is a state of stable proliferative arrest of both normal and neoplastic cells that is triggered by exposure to anticancer treatments. TIS cells acquire a senescence-associated secretory phenotype (SASP), which is pro-inflammatory and actively promotes tumor relapse and adverse side-effects in patients. Here, we hypothesized that TIS cells adapt their scavenging and catabolic ability to overcome the nutritional constraints in their microenvironmental niches. We used a panel of mechanistically-diverse TIS triggers (i.e., bleomycin, doxorubicin, alisertib, and palbociclib) and Biolog Phenotype MicroArrays to identify (among 190 different carbon and nitrogen sources) candidate metabolites that support the survival of TIS cells in limiting nutrient conditions. We provide evidence of distinguishable TIS-associated nutrient consumption profiles involving a core set of shared (e.g., glutamine) and unique (e.g., glucose-1-phosphate, inosine, and uridine) nutritional sources after diverse senescence-inducing interventions. We also observed a trend for an inverse correlation between the intensity of the pro-inflammatory SASP provoked by different TIS agents and diversity of compensatory nutritional niches utilizable by senescent cells. These findings support the detailed exploration of the nutritional niche as a new metabolic dimension to understand and target TIS in cancer.
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Affiliation(s)
| | - Sara Verdura
- Metabolism and Cancer Group, Program Against Cancer Therapeutic Resistance (ProCURE), Catalan Institute of Oncology, 17005 Girona, Spain
| | - Elisabet Cuyàs
- Girona Biomedical Research Institute, 17190 Girona, Spain
- Metabolism and Cancer Group, Program Against Cancer Therapeutic Resistance (ProCURE), Catalan Institute of Oncology, 17005 Girona, Spain
- Correspondence: (E.C.); or (J.A.M.)
| | - Javier A. Menendez
- Girona Biomedical Research Institute, 17190 Girona, Spain
- Metabolism and Cancer Group, Program Against Cancer Therapeutic Resistance (ProCURE), Catalan Institute of Oncology, 17005 Girona, Spain
- Correspondence: (E.C.); or (J.A.M.)
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15
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Artesunate Inhibits the Cell Growth in Colorectal Cancer by Promoting ROS-Dependent Cell Senescence and Autophagy. Cells 2022; 11:cells11162472. [PMID: 36010550 PMCID: PMC9406496 DOI: 10.3390/cells11162472] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 08/01/2022] [Accepted: 08/02/2022] [Indexed: 01/10/2023] Open
Abstract
Although artesunate has been reported to be a promising candidate for colorectal cancer (CRC) treatment, the underlying mechanisms and molecular targets of artesunate are yet to be explored. Here, we report that artesunate acts as a senescence and autophagy inducer to exert its inhibitory effect on CRC in a reactive oxygen species (ROS)-dependent manner. In SW480 and HCT116 cells, artesunate treatment led to mitochondrial dysfunction, drastically promoted mitochondrial ROS generation, and consequently inhibited cell proliferation by causing cell cycle arrest at G0/G1 phase as well as subsequent p16- and p21-mediated cell senescence. Senescent cells underwent endoplasmic reticulum stress (ERS), and the unfolded protein response (UPR) was activated via IRE1α signaling, with upregulated BIP, IRE1α, phosphorylated IRE1α (p-IRE1α), CHOP, and DR5. Further experiments revealed that autophagy was induced by artesunate treatment due to oxidative stress and ER stress. In contrast, N-Acetylcysteine (NAC, an ROS scavenger) and 3-Methyladenine (3-MA, an autophagy inhibitor) restored cell viability and attenuated autophagy in artesunate-treated cells. Furthermore, cellular free Ca2+ levels were increased and could be repressed by NAC, 3-MA, and GSK2350168 (an IRE1α inhibitor). In vivo, artesunate administration reduced the growth of CT26 cell-derived tumors in BALB/c mice. Ki67 and cyclin D1 expression was downregulated in tumor tissue, while p16, p21, p-IRE1α, and LC3B expression was upregulated. Taken together, artesunate induces senescence and autophagy to inhibit cell proliferation in colorectal cancer by promoting excessive ROS generation.
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16
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Lin CY, Yu CJ, Liu CY, Chao TC, Huang CC, Tseng LM, Lai JI. CDK4/6 inhibitors downregulate the ubiquitin-conjugating enzymes UBE2C/S/T involved in the ubiquitin-proteasome pathway in ER + breast cancer. CLINICAL & TRANSLATIONAL ONCOLOGY : OFFICIAL PUBLICATION OF THE FEDERATION OF SPANISH ONCOLOGY SOCIETIES AND OF THE NATIONAL CANCER INSTITUTE OF MEXICO 2022; 24:2120-2135. [PMID: 35917055 DOI: 10.1007/s12094-022-02881-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 06/20/2022] [Indexed: 10/16/2022]
Abstract
Despite significant improvement in therapeutic development in the past decades, breast cancer remains a formidable cause of death for women worldwide. The hormone positive subtype (HR( +)) (also known as luminal type) is the most prevalent category of breast cancer, comprising ~ 70% of patients. The clinical success of the three CDK4/6 inhibitors palbociclib, ribociclib, and abemaciclib has revolutionized the treatment of choice for metastatic HR( +) breast cancer. Accumulating evidence demonstrate that the properties of CDK4/6 inhibitors extend beyond inhibition of the cell cycle, including modulation of immune function, sensitizing PI3K inhibitors, metabolism reprogramming, kinome rewiring, modulation of the proteasome, and many others. The ubiquitin-proteasome pathway (UPP) is a crucial cellular proteolytic system that maintains the homeostasis and turnover of proteins. By transcriptional profiling of the HR( +) breast cancer cell lines MCF7 and T47D treated with Palbociclib, we have uncovered a novel mechanism that demonstrates that the CDK4/6 inhibitors suppress the expression of three ubiquitin-conjugating enzymes UBE2C, UBE2S, UBE2T. Further validation in the HR( +) cell lines show that Palbociclib and ribociclib decrease UBE2C at both the mRNA and protein level, but this phenomenon was not shared with abemaciclib. These three E2 enzymes modulate several E3 ubiquitin ligases, including the APC/C complex which plays a role in G1/S progression. We further demonstrate that the UBE2C/UBE2T expression levels are associated with breast cancer survival, and HR( +) breast cancer cells demonstrate dependence on the UBE2C. Our study suggests a novel link between CDK4/6 inhibitor and UPP pathway, adding to the potential mechanisms of their clinical efficacy in cancer.
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Affiliation(s)
- Chih-Yi Lin
- Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Chung-Jen Yu
- Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Chun-Yu Liu
- School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan.,Division of Medical Oncology, Department of Oncology, Taipei Veterans General Hospital, Taipei, Taiwan.,Division of Transfusion Medicine, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan.,Comprehensive Breast Health Center, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Ta-Chung Chao
- School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan.,Division of Medical Oncology, Department of Oncology, Taipei Veterans General Hospital, Taipei, Taiwan.,Comprehensive Breast Health Center, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Chi-Cheng Huang
- Comprehensive Breast Health Center, Taipei Veterans General Hospital, Taipei, Taiwan.,Division of General Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Ling-Ming Tseng
- School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan.,Comprehensive Breast Health Center, Taipei Veterans General Hospital, Taipei, Taiwan.,Division of General Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Jiun-I Lai
- Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan. .,Division of Medical Oncology, Department of Oncology, Taipei Veterans General Hospital, Taipei, Taiwan. .,Comprehensive Breast Health Center, Taipei Veterans General Hospital, Taipei, Taiwan. .,Center of Immuno-Oncology, Department of Oncology, Taipei Veterans General Hospital, Taipei, Taiwan.
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17
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Yang X, Da Q, Qian P, Veeravalli B, Leong TW, Dai L, Nordlund P, Prabhu N, Zhao Z, Zeng Z. CETSA Feature Based Clustering for Protein Outlier Discovery by Protein-to-Protein Interaction Prediction. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2022; 2022:1659-1662. [PMID: 36085889 DOI: 10.1109/embc48229.2022.9871558] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The Cellular Thermal Shift Assay (CETSA) is a biophysical assay based on the principle of ligand-induced thermal stabilization of target proteins. This technology has revolutionized cell-based target engagement studies and has been used as guidance for drug design. Although many ap-plications of CETSA data have been explored, the correlations between CETSA data and protein-protein interactions (PPI) have barely been touched. In this study, we conduct the first exploration study applying CETSA data for PPI prediction. We use a machine learning method, Decision Tree, to predict PPI scores using proteins' CETSA features. It shows promising results that the predicted PPI scores closely match the ground-truth PPI scores. Furthermore, for a small number of protein pairs, whose PPI score predictions mismatch the ground truth, we use iterative clustering strategy to gradually reduce the number of these pairs. At the end of iterative clustering, the remaining protein pairs may have some unusual properties and are of scientific value for further biological investigation. Our study has demonstrated that PPI is a brand-new application of CETSA data. At the same time, it also manifests that CETSA data can be used as a new data source for PPI exploration study.
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18
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Rampioni Vinciguerra GL, Sonego M, Segatto I, Dall’Acqua A, Vecchione A, Baldassarre G, Belletti B. CDK4/6 Inhibitors in Combination Therapies: Better in Company Than Alone: A Mini Review. Front Oncol 2022; 12:891580. [PMID: 35712501 PMCID: PMC9197541 DOI: 10.3389/fonc.2022.891580] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 04/22/2022] [Indexed: 12/24/2022] Open
Abstract
The cyclin D-CDK4/6 complexes play a pivotal role in controlling the cell cycle. Deregulation in cyclin D-CDK4/6 pathway has been described in many types of cancer and it invariably leads to uncontrolled cell proliferation. Many efforts have been made to develop a target therapy able to inhibit CDK4/6 activity. To date, three selective CDK4/6 small inhibitors have been introduced in the clinic for the treatment of hormone positive advanced breast cancer patients, following the impressive results obtained in phase III clinical trials. However, since their approval, clinical evidences have demonstrated that about 30% of breast cancer is intrinsically resistant to CDK4/6 inhibitors and that prolonged treatment eventually leads to acquired resistance in many patients. So, on one hand, clinical and preclinical studies fully support to go beyond breast cancer and expand the use of CDK4/6 inhibitors in other tumor types; on the other hand, the question of primary and secondary resistance has to be taken into account, since it is now very clear that neoplastic cells rapidly develop adaptive strategies under treatment, eventually resulting in disease progression. Resistance mechanisms so far discovered involve both cell-cycle and non-cell-cycle related escape strategies. Full understanding is yet to be achieved but many different pathways that, if targeted, may lead to reversion of the resistant phenotype, have been already elucidated. Here, we aim to summarize the knowledge in this field, focusing on predictive biomarkers, to recognize intrinsically resistant tumors, and therapeutic strategies, to overcome acquired resistance.
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Affiliation(s)
- Gian Luca Rampioni Vinciguerra
- Division of Molecular Oncology, Centro di Riferimento Oncologico di Aviano (CRO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), National Cancer Institute, Aviano, Italy
- Department of Cancer Biology and Genetics and Comprehensive Cancer Center, The Ohio State University, Columbus, OH, United States
| | - Maura Sonego
- Division of Molecular Oncology, Centro di Riferimento Oncologico di Aviano (CRO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), National Cancer Institute, Aviano, Italy
| | - Ilenia Segatto
- Division of Molecular Oncology, Centro di Riferimento Oncologico di Aviano (CRO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), National Cancer Institute, Aviano, Italy
| | - Alessandra Dall’Acqua
- Division of Molecular Oncology, Centro di Riferimento Oncologico di Aviano (CRO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), National Cancer Institute, Aviano, Italy
| | - Andrea Vecchione
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Psychology, Sant’Andrea Hospital, University of Rome “Sapienza”, Rome, Italy
| | - Gustavo Baldassarre
- Division of Molecular Oncology, Centro di Riferimento Oncologico di Aviano (CRO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), National Cancer Institute, Aviano, Italy
| | - Barbara Belletti
- Division of Molecular Oncology, Centro di Riferimento Oncologico di Aviano (CRO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), National Cancer Institute, Aviano, Italy
- *Correspondence: Barbara Belletti,
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19
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Small Molecule Arranged Thermal Proximity Co aggregation (smarTPCA)-A Novel Approach to Characterize Protein-Protein Interactions in Living Cells by Similar Isothermal Dose-Responses. Int J Mol Sci 2022; 23:ijms23105605. [PMID: 35628420 PMCID: PMC9147192 DOI: 10.3390/ijms23105605] [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: 03/31/2022] [Revised: 05/06/2022] [Accepted: 05/10/2022] [Indexed: 11/17/2022] Open
Abstract
Chemical biology and the application of small molecules has proven to be a potent perturbation strategy, especially for the functional elucidation of proteins, their networks, and regulators. In recent years, the cellular thermal shift assay (CETSA) and its proteome-wide extension, thermal proteome profiling (TPP), have proven to be effective tools for identifying interactions of small molecules with their target proteins, as well as off-targets in living cells. Here, we asked the question whether isothermal dose-response (ITDR) CETSA can be exploited to characterize secondary effects downstream of the primary binding event, such as changes in post-translational modifications or protein-protein interactions (PPI). By applying ITDR-CETSA to MAPK14 kinase inhibitor treatment of living HL-60 cells, we found similar dose-responses for the direct inhibitor target and its known interaction partners MAPKAPK2 and MAPKAPK3. Extension of the dose-response similarity comparison to the proteome wide level using TPP with compound concentration range (TPP-CCR) revealed not only the known MAPK14 interaction partners MAPKAPK2 and MAPKAPK3, but also the potentially new intracellular interaction partner MYLK. We are confident that dose-dependent small molecule treatment in combination with ITDR-CETSA or TPP-CCR similarity assessment will not only allow discrimination between primary and secondary effects, but will also provide a novel method to study PPI in living cells without perturbation by protein modification, which we named "small molecule arranged thermal proximity coaggregation" (smarTPCA).
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20
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Cox D, Ang CS, Nillegoda NB, Reid GE, Hatters DM. Hidden information on protein function in censuses of proteome foldedness. Nat Commun 2022; 13:1992. [PMID: 35422070 PMCID: PMC9010426 DOI: 10.1038/s41467-022-29661-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 03/25/2022] [Indexed: 12/12/2022] Open
Abstract
Methods that assay protein foldedness with proteomics have generated censuses of apparent protein folding stabilities in biological milieu. However, different censuses poorly correlate with each other. Here, we show that the reason for this is that methods targeting foldedness through monitoring amino acid sidechain reactivity also detect changes in conformation and ligand binding, which can be a substantial fraction of the data. We show that the reactivity of only one quarter of cysteine or methionine sidechains in proteins in a urea denaturation curve of mammalian cell lysate can be confidently explained by a two-state unfolding isotherm. Contrary to that expected from unfolding, up to one third of the cysteines decreased reactivity. These cysteines were enriched in proteins with functions relating to unfolded protein stress. One protein, chaperone HSPA8, displayed changes arising from ligand and cofactor binding. Unmasking this hidden information using the approaches outlined here should improve efforts to understand both folding and the remodeling of protein function directly in complex biological settings. Proteomics can define features of proteome foldedness by assessing the reactivity of surface exposed amino acids. Here, the authors show that such exposure patterns yield insight to structural changes in chaperones as they bind to unfolded proteins in urea-denatured mammalian cell lysate.
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21
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Palbociclib regulates intracellular lipids in mammary tumor cells by secreting lipoprotein lipase. Pharmacol Rep 2022; 74:503-512. [DOI: 10.1007/s43440-022-00365-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 03/20/2022] [Accepted: 03/21/2022] [Indexed: 10/18/2022]
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22
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Qi J, Ouyang Z. Targeting CDK4/6 for Anticancer Therapy. Biomedicines 2022; 10:biomedicines10030685. [PMID: 35327487 PMCID: PMC8945444 DOI: 10.3390/biomedicines10030685] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 03/10/2022] [Accepted: 03/14/2022] [Indexed: 12/26/2022] Open
Abstract
Cyclin-dependent kinase 4/6 (CDK4/6) are key regulators of the cell cycle and are deemed as critical therapeutic targets of multiple cancers. Various approaches have been applied to silence CDK4/6 at different levels, i.e., CRISPR to knock out at the DNA level, siRNA to inhibit translation, and drugs that target the protein of interest. Here we summarize the current status in this field, highlighting the mechanisms of small molecular inhibitors treatment and drug resistance. We describe approaches to combat drug resistance, including combination therapy and PROTACs drugs that degrade the kinases. Finally, critical issues and perspectives in the field are outlined.
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Affiliation(s)
- Jiating Qi
- The Second Clinical College, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China;
| | - Zhuqing Ouyang
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
- Correspondence:
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23
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Crozier L, Foy R, Mouery BL, Whitaker RH, Corno A, Spanos C, Ly T, Gowen Cook J, Saurin AT. CDK4/6 inhibitors induce replication stress to cause long-term cell cycle withdrawal. EMBO J 2022; 41:e108599. [PMID: 35037284 PMCID: PMC8922273 DOI: 10.15252/embj.2021108599] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 11/18/2021] [Accepted: 12/21/2021] [Indexed: 12/29/2022] Open
Abstract
CDK4/6 inhibitors arrest the cell cycle in G1-phase. They are approved to treat breast cancer and are also undergoing clinical trials against a range of other tumour types. To facilitate these efforts, it is important to understand why a cytostatic arrest in G1 causes long-lasting effects on tumour growth. Here, we demonstrate that a prolonged G1 arrest following CDK4/6 inhibition downregulates replisome components and impairs origin licencing. Upon release from that arrest, many cells fail to complete DNA replication and exit the cell cycle in a p53-dependent manner. If cells fail to withdraw from the cell cycle following DNA replication problems, they enter mitosis and missegregate chromosomes causing excessive DNA damage, which further limits their proliferative potential. These effects are observed in a range of tumour types, including breast cancer, implying that genotoxic stress is a common outcome of CDK4/6 inhibition. This unanticipated ability of CDK4/6 inhibitors to induce DNA damage now provides a rationale to better predict responsive tumour types and effective combination therapies, as demonstrated by the fact that CDK4/6 inhibition induces sensitivity to chemotherapeutics that also cause replication stress.
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Affiliation(s)
- Lisa Crozier
- Division of Cellular and Systems MedicineJacqui Wood Cancer CentreSchool of MedicineUniversity of DundeeDundeeUK
| | - Reece Foy
- Division of Cellular and Systems MedicineJacqui Wood Cancer CentreSchool of MedicineUniversity of DundeeDundeeUK
| | - Brandon L Mouery
- Curriculum in Genetics and Molecular BiologyUniversity of North Carolina at Chapel HillChapel HillNCUSA
| | - Robert H Whitaker
- Department of Biochemistry and BiophysicsUniversity of North Carolina at Chapel HillChapel HillNCUSA
| | - Andrea Corno
- Division of Cellular and Systems MedicineJacqui Wood Cancer CentreSchool of MedicineUniversity of DundeeDundeeUK
| | - Christos Spanos
- Wellcome Trust Centre for Cell BiologyUniversity of EdinburghEdinburghUK
| | - Tony Ly
- Wellcome Trust Centre for Cell BiologyUniversity of EdinburghEdinburghUK
- Present address:
Centre for Gene Regulation and ExpressionSchool of Life SciencesUniversity of DundeeDundeeUK
| | - Jeanette Gowen Cook
- Department of Biochemistry and BiophysicsUniversity of North Carolina at Chapel HillChapel HillNCUSA
| | - Adrian T Saurin
- Division of Cellular and Systems MedicineJacqui Wood Cancer CentreSchool of MedicineUniversity of DundeeDundeeUK
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24
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Characterization of a small molecule inhibitor of disulfide reductases that induces oxidative stress and lethality in lung cancer cells. Cell Rep 2022; 38:110343. [PMID: 35139387 DOI: 10.1016/j.celrep.2022.110343] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 12/04/2021] [Accepted: 01/14/2022] [Indexed: 12/13/2022] Open
Abstract
Phenotype-based screening can identify small molecules that elicit a desired cellular response, but additional approaches are required to characterize their targets and mechanisms of action. Here, we show that a compound termed LCS3, which selectively impairs the growth of human lung adenocarcinoma (LUAD) cells, induces oxidative stress. To identify the target that mediates this effect, we use thermal proteome profiling (TPP) and uncover the disulfide reductases GSR and TXNRD1 as targets. We confirm through enzymatic assays that LCS3 inhibits disulfide reductase activity through a reversible, uncompetitive mechanism. Further, we demonstrate that LCS3-sensitive LUAD cells are sensitive to the synergistic inhibition of glutathione and thioredoxin pathways. Lastly, a genome-wide CRISPR knockout screen identifies NQO1 loss as a mechanism of LCS3 resistance. This work highlights the ability of TPP to uncover targets of small molecules identified by high-throughput screens and demonstrates the potential therapeutic utility of inhibiting disulfide reductases in LUAD.
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25
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Ruan C, Ning W, Liu Z, Zhang X, Fang Z, Li Y, Dang Y, Xue Y, Ye M. Precipitate-Supported Thermal Proteome Profiling Coupled with Deep Learning for Comprehensive Screening of Drug Target Proteins. ACS Chem Biol 2022; 17:252-262. [PMID: 34989232 DOI: 10.1021/acschembio.1c00936] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Although thermal proteome profiling (TPP) acts as a popular modification-free approach for drug target deconvolution, some key problems are still limiting screening sensitivity. In the prevailing TPP workflow, only the soluble fractions are analyzed after thermal treatment, while the precipitate fractions that also contain abundant information of drug-induced stability shifts are discarded; the sigmoid melting curve fitting strategy used for data processing suffers from discriminations for a part of human proteome with multiple transitions. In this study, a precipitate-supported TPP (PSTPP) assay was presented for unbiased and comprehensive analysis of protein-drug interactions at the proteome level. In PSTPP, only these temperatures where significant precipitation is observed were applied to induce protein denaturation and the complementary information contained in both supernatant fractions and precipitate fractions was used to improve the screening specificity and sensitivity. In addition, a novel image recognition algorithm based on deep learning was developed to recognize the target proteins, which circumvented the problems that exist in the sigmoid curve fitting strategy. PSTPP assay was validated by identifying the known targets of methotrexate, raltitrexed, and SNS-032 with good performance. Using a promiscuous kinase inhibitor, staurosporine, we delineated 99 kinase targets with a specificity up to 83% in K562 cell lysates, which represented a significant improvement over the existing thermal shift methods. Furthermore, the PSTPP strategy was successfully applied to analyze the binding targets of rapamycin, identifying the well-known targets, FKBP1A, as well as revealing a few other potential targets.
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Affiliation(s)
- Chengfei Ruan
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wanshan Ning
- MOE Key Laboratory of Molecular Biophysics, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology (HUST), Wuhan, Hubei 430074, China
| | - Zhen Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
| | - Xiaolei Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
| | - Zheng Fang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanan Li
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
| | - Yongjun Dang
- Center for Novel Target and Therapeutic Intervention, Institute of Life Sciences, Chongqing Medical University, Chongqing 400016, China
| | - Yu Xue
- MOE Key Laboratory of Molecular Biophysics, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology (HUST), Wuhan, Hubei 430074, China
| | - Mingliang Ye
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
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26
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Ei ZZ, Choochuay K, Tubsuwan A, Pinkaew D, Suksomtip M, Vinayanuwattikun C, Chanvorachote P, Chunhacha P. GRP78/BiP determines senescence evasion cell fate after cisplatin-based chemotherapy. Sci Rep 2021; 11:22448. [PMID: 34789798 PMCID: PMC8599848 DOI: 10.1038/s41598-021-01540-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 10/27/2021] [Indexed: 12/29/2022] Open
Abstract
Cisplatin (CDDP) induces senescence characterized by senescence-associated secretory phenotypes (SASP) and the unfolded protein response (UPR). In this study, we investigated the proteins related to the UPR during the senescence cell fate. Strikingly, we found that one of the critical ER-resident proteins, GRP78/BiP, was significantly altered. Here we show that GRP78 levels differentially expressed depending on non-small lung cancer subtypes. GRP78 indeed regulates the evasion of senescence in adenocarcinoma A549 cells, in which the increased GRP78 levels enable them to re-proliferate after CDDP removal. Conversely, GRP78 is downregulated in the senescence H460 cells, making them lacking senescence evasion capability. We observed that the translational regulation critically contributed to the GRP78 protein levels in CDDP-induces senescence. Furthermore, the increased GRP78 level during senescence confers resistance to senolytic drug, Bortezomib, as observed by a twofold increase in IC50 in A549 senescence cells compared to the wild-type. This observation is also consistent in the cells that have undergone genetic manipulation by transfection with pcDNA3.1(+)-GRP78/BiP plasmids and pSpCas9(BB)-2A-Puro containing guide RNA sequence targeting GRP78 exon 3 to induce the overexpression and downregulation of GRP78 in H460 cells, respectively. Our findings reveal a unique role of GRP78 on the senescence evasion cell fate and senolytic drug resistance after cisplatin-based chemotherapy.
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Affiliation(s)
- Zin Zin Ei
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Kanuengnit Choochuay
- Drugs and Cosmetic Excellence Center, Walailak University, Nakhon Si Thammarat, Thailand.,School of Pharmacy, Walailak University, Nakhon Si Thammarat, Thailand
| | - Alisa Tubsuwan
- Thalassemia Research Centre, Institute of Molecular Biosciences, Mahidol University, Nakornpathom, Thailand
| | - Decha Pinkaew
- Division of Cardiology, Department of Medicine, University of Washington, Seattle, WA, 98109, USA
| | - Maneewan Suksomtip
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Chanida Vinayanuwattikun
- Division of Medical Oncology, Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Pithi Chanvorachote
- Department of Pharmacology and Physiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Preedakorn Chunhacha
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, Thailand. .,Preclinical Toxicity and Efficacy Assessment of Medicines and Chemicals Research Clusters, Chulalongkorn University, Bangkok, Thailand.
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27
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Britt HM, Cragnolini T, Thalassinos K. Integration of Mass Spectrometry Data for Structural Biology. Chem Rev 2021; 122:7952-7986. [PMID: 34506113 DOI: 10.1021/acs.chemrev.1c00356] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Mass spectrometry (MS) is increasingly being used to probe the structure and dynamics of proteins and the complexes they form with other macromolecules. There are now several specialized MS methods, each with unique sample preparation, data acquisition, and data processing protocols. Collectively, these methods are referred to as structural MS and include cross-linking, hydrogen-deuterium exchange, hydroxyl radical footprinting, native, ion mobility, and top-down MS. Each of these provides a unique type of structural information, ranging from composition and stoichiometry through to residue level proximity and solvent accessibility. Structural MS has proved particularly beneficial in studying protein classes for which analysis by classic structural biology techniques proves challenging such as glycosylated or intrinsically disordered proteins. To capture the structural details for a particular system, especially larger multiprotein complexes, more than one structural MS method with other structural and biophysical techniques is often required. Key to integrating these diverse data are computational strategies and software solutions to facilitate this process. We provide a background to the structural MS methods and briefly summarize other structural methods and how these are combined with MS. We then describe current state of the art approaches for the integration of structural MS data for structural biology. We quantify how often these methods are used together and provide examples where such combinations have been fruitful. To illustrate the power of integrative approaches, we discuss progress in solving the structures of the proteasome and the nuclear pore complex. We also discuss how information from structural MS, particularly pertaining to protein dynamics, is not currently utilized in integrative workflows and how such information can provide a more accurate picture of the systems studied. We conclude by discussing new developments in the MS and computational fields that will further enable in-cell structural studies.
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Affiliation(s)
- Hannah M Britt
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, United Kingdom
| | - Tristan Cragnolini
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, United Kingdom.,Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, United Kingdom
| | - Konstantinos Thalassinos
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, United Kingdom.,Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, United Kingdom
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28
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Mateus A, Kurzawa N, Perrin J, Bergamini G, Savitski MM. Drug Target Identification in Tissues by Thermal Proteome Profiling. Annu Rev Pharmacol Toxicol 2021; 62:465-482. [PMID: 34499524 DOI: 10.1146/annurev-pharmtox-052120-013205] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Drug target deconvolution can accelerate the drug discovery process by identifying a drug's targets (facilitating medicinal chemistry efforts) and off-targets (anticipating toxicity effects or adverse drug reactions). Multiple mass spectrometry-based approaches have been developed for this purpose, but thermal proteome profiling (TPP) remains to date the only one that does not require compound modification and can be used to identify intracellular targets in living cells. TPP is based on the principle that the thermal stability of a protein can be affected by its interactions. Recent developments of this approach have expanded its applications beyond drugs and cell cultures to studying protein-drug interactions and biological phenomena in tissues. These developments open up the possibility of studying drug treatment or mechanisms of disease in a holistic fashion, which can result in the design of better drugs and lead to a better understanding of fundamental biology. Expected final online publication date for the Annual Review of Pharmacology and Toxicology, Volume 62 is January 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- André Mateus
- Genome Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany;
| | - Nils Kurzawa
- Genome Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany; .,Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany
| | - Jessica Perrin
- Cellzome GmbH, GlaxoSmithKline, 69117 Heidelberg, Germany
| | | | - Mikhail M Savitski
- Genome Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany;
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29
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Malikova AZ, Shcherbakova AS, Konduktorov KA, Zemskaya AS, Dalina AA, Popenko VI, Leonova OG, Morozov AV, Kurochkin NN, Smirnova OA, Kochetkov SN, Kozlov MV. Pre-Senescence Induction in Hepatoma Cells Favors Hepatitis C Virus Replication and Can Be Used in Exploring Antiviral Potential of Histone Deacetylase Inhibitors. Int J Mol Sci 2021; 22:4559. [PMID: 33925399 PMCID: PMC8123837 DOI: 10.3390/ijms22094559] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 04/16/2021] [Accepted: 04/22/2021] [Indexed: 12/22/2022] Open
Abstract
Recent evidence suggests that fibrotic liver injury in patients with chronic hepatitis C correlates with cellular senescence in damaged liver tissue. However, it is still unclear how senescence can affect replication of the hepatitis C virus (HCV). In this work, we report that an inhibitor of cyclin-dependent kinases 4/6, palbociclib, not only induced in hepatoma cells a pre-senescent cellular phenotype, including G1 arrest in the cell cycle, but also accelerated viral replicon multiplication. Importantly, suppression of HCV replication by direct acting antivirals (DAAs) was barely affected by pre-senescence induction, and vice versa, the antiviral activities of host-targeting agents (HTAs), such as inhibitors of human histone deacetylases (HDACi), produced a wide range of reactions-from a dramatic reduction to a noticeable increase. It is very likely that under conditions of the G1 arrest in the cell cycle, HDACi exhibit their actual antiviral potency, since their inherent anticancer activity that complicates the interpretation of test results is minimized.
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30
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Peerzada MN, Hamel E, Bai R, Supuran CT, Azam A. Deciphering the key heterocyclic scaffolds in targeting microtubules, kinases and carbonic anhydrases for cancer drug development. Pharmacol Ther 2021; 225:107860. [PMID: 33895188 DOI: 10.1016/j.pharmthera.2021.107860] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 03/31/2021] [Accepted: 04/06/2021] [Indexed: 12/17/2022]
Abstract
Heterocyclic scaffolds are widely utilized for drug design by taking into account the molecular structure of therapeutic targets that are related to a broad spectrum of ailments, including tumors. Such compounds display various covalent and non-covalent interactions with the specific residues of the target proteins while causing their inhibition. There is a substantial number of heterocyclic compounds approved for cancer treatment, and these compounds function by interacting with different therapeutic targets involved in tumorogenesis. In this review, we trace and emphasize the privileged heterocyclic pharmacophores that have immense potency against several essential chemotherapeutic tumor targets: microtubules, kinases and carbonic anhydrases. Potent compounds currently undergoing pre-clinical and clinical studies have also been assessed for ascertaining the effective class of chemical scaffolds that have significant therapeutic potential against multiple malignancies. In addition, we also describe briefly the role of heterocyclic compounds in various chemotherapy regimens. The optimized molecular hybridization of delineated motifs may result in the discovery of more active anticancer therapeutics and circumvent the development of resistance by specific targets in the future.
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Affiliation(s)
- Mudasir Nabi Peerzada
- Medicinal Chemistry Research Laboratory, Department of Chemistry, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Ernest Hamel
- Molecular Pharmacology Branch, Developmental Therapeutics Program, Division of Cancer Treatment and Diagnosis, Frederick National Laboratory for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Ruoli Bai
- Molecular Pharmacology Branch, Developmental Therapeutics Program, Division of Cancer Treatment and Diagnosis, Frederick National Laboratory for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Claudiu T Supuran
- Department of NEUROFARBA, Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, Polo Scientifico, Via U. Schiff 6, 50019 Sesto Fiorentino, Florence, Italy.
| | - Amir Azam
- Medicinal Chemistry Research Laboratory, Department of Chemistry, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India.
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31
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Patel NH, Bloukh S, Alwohosh E, Alhesa A, Saleh T, Gewirtz DA. Autophagy and senescence in cancer therapy. Adv Cancer Res 2021; 150:1-74. [PMID: 33858594 DOI: 10.1016/bs.acr.2021.01.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Tumor cells can undergo diverse responses to cancer therapy. While apoptosis represents the most desirable outcome, tumor cells can alternatively undergo autophagy and senescence. Both autophagy and senescence have the potential to make complex contributions to tumor cell survival via both cell autonomous and cell non-autonomous pathways. The induction of autophagy and senescence in tumor cells, preclinically and clinically, either individually or concomitantly, has generated interest in the utilization of autophagy modulating and senolytic therapies to target autophagy and senescence, respectively. This chapter summarizes the current evidence for the promotion of autophagy and senescence as fundamental responses to cancer therapy and discusses the complexity of their functional contributions to cell survival and disease outcomes. We also highlight current modalities designed to exploit autophagy and senescence in efforts to improve the efficacy of cancer therapy.
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Affiliation(s)
- Nipa H Patel
- Department of Pharmacology and Toxicology and Medicine, Virginia Commonwealth University, Richmond, VA, United States; Massey Cancer Center, Goodwin Research Laboratories, Virginia Commonwealth University, Richmond, VA, United States
| | - Sarah Bloukh
- Department of Basic Medical Sciences, Faculty of Medicine, The Hashemite University, Zarqa, Jordan
| | - Enas Alwohosh
- Department of Basic Medical Sciences, Faculty of Medicine, The Hashemite University, Zarqa, Jordan
| | - Ahmad Alhesa
- Department of Basic Medical Sciences, Faculty of Medicine, The Hashemite University, Zarqa, Jordan
| | - Tareq Saleh
- Department of Basic Medical Sciences, Faculty of Medicine, The Hashemite University, Zarqa, Jordan
| | - David A Gewirtz
- Department of Pharmacology and Toxicology and Medicine, Virginia Commonwealth University, Richmond, VA, United States; Massey Cancer Center, Goodwin Research Laboratories, Virginia Commonwealth University, Richmond, VA, United States.
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32
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Carnero Corrales MA, Zinken S, Konstantinidis G, Rafehi M, Abdelrahman A, Wu YW, Janning P, Müller CE, Laraia L, Waldmann H. Thermal proteome profiling identifies the membrane-bound purinergic receptor P2X4 as a target of the autophagy inhibitor indophagolin. Cell Chem Biol 2021; 28:1750-1757.e5. [PMID: 33725479 DOI: 10.1016/j.chembiol.2021.02.017] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 01/21/2021] [Accepted: 02/23/2021] [Indexed: 12/11/2022]
Abstract
Signaling pathways are frequently activated through signal-receiving membrane proteins, and the discovery of small molecules targeting these receptors may yield insights into their biology. However, due to their intrinsic properties, membrane protein targets often cannot be identified by means of established approaches, in particular affinity-based proteomics, calling for the exploration of new methods. Here, we report the identification of indophagolin as representative member of an indoline-based class of autophagy inhibitors through a target-agnostic phenotypic assay. Thermal proteome profiling and subsequent biochemical validation identified the purinergic receptor P2X4 as a target of indophagolin, and subsequent investigations suggest that indophagolin targets further purinergic receptors. These results demonstrate that thermal proteome profiling may enable the de novo identification of membrane-bound receptors as cellular targets of bioactive small molecules.
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Affiliation(s)
- Marjorie A Carnero Corrales
- Max Planck Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Straße 11, 44227 Dortmund, Germany; Technische Universität Dortmund, Faculty of Chemistry and Chemical Biology, Otto-Hahn-Straße 6, 44227 Dortmund, Germany
| | - Sarah Zinken
- Max Planck Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Straße 11, 44227 Dortmund, Germany; Technische Universität Dortmund, Faculty of Chemistry and Chemical Biology, Otto-Hahn-Straße 6, 44227 Dortmund, Germany
| | - Georgios Konstantinidis
- Chemical Genomics Center of the Max Planck Society, Otto-Hahn-Straße 15, 44227 Dortmund, Germany
| | - Muhammad Rafehi
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Sciences Bonn (PSB), Pharmaceutical Chemistry I, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
| | - Aliaa Abdelrahman
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Sciences Bonn (PSB), Pharmaceutical Chemistry I, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
| | - Yao-Wen Wu
- Chemical Genomics Center of the Max Planck Society, Otto-Hahn-Straße 15, 44227 Dortmund, Germany
| | - Petra Janning
- Max Planck Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Straße 11, 44227 Dortmund, Germany; Technische Universität Dortmund, Faculty of Chemistry and Chemical Biology, Otto-Hahn-Straße 6, 44227 Dortmund, Germany
| | - Christa E Müller
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Sciences Bonn (PSB), Pharmaceutical Chemistry I, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
| | - Luca Laraia
- Max Planck Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Straße 11, 44227 Dortmund, Germany; Department of Chemistry, Technical University of Denmark, Kemitorvet 207, Room 124, 2800 Kongens Lyngby, Denmark.
| | - Herbert Waldmann
- Max Planck Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Straße 11, 44227 Dortmund, Germany; Technische Universität Dortmund, Faculty of Chemistry and Chemical Biology, Otto-Hahn-Straße 6, 44227 Dortmund, Germany.
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33
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Functional heterogeneity in senescence. Biochem Soc Trans 2021; 48:765-773. [PMID: 32369550 PMCID: PMC7329341 DOI: 10.1042/bst20190109] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 04/06/2020] [Accepted: 04/08/2020] [Indexed: 12/22/2022]
Abstract
Senescence is a tumour suppressor mechanism which is cell-intrinsically activated in the context of cellular stress. Senescence can further be propagated to neighbouring cells, a process called secondary senescence induction. Secondary senescence was initially shown as a paracrine response to the secretion of cytokines from primary senescent cells. More recently, juxtacrine Notch signalling has been implicated in mediating secondary senescence induction. Primary and secondary senescent induction results in distinct transcriptional outcomes. In addition, cell type and the stimulus in which senescence is induced can lead to variations in the phenotype of the senescence response. It is unclear whether heterogeneous senescent end-points are associated with distinct cellular function in situ, presenting functional heterogeneity. Thus, understanding senescence heterogeneity could prove to be important when devising ways of targeting senescent cells by senolytics, senostatics or senogenics. In this review, we discuss a role for functional heterogeneity in senescence in tissue- and cell-type specific manners, highlighting potential differences in senescence outcomes of primary and secondary senescence.
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34
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Ernst P, Heidel FH. Molecular Mechanisms of Senescence and Implications for the Treatment of Myeloid Malignancies. Cancers (Basel) 2021; 13:612. [PMID: 33557090 PMCID: PMC7913823 DOI: 10.3390/cancers13040612] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 01/30/2021] [Accepted: 02/01/2021] [Indexed: 01/07/2023] Open
Abstract
Senescence is a cellular state that is involved in aging-associated diseases but may also prohibit the development of pre-cancerous lesions and tumor growth. Senescent cells are actively secreting chemo- and cytokines, and this senescence-associated secretory phenotype (SASP) can contribute to both early anti-tumorigenic and long-term pro-tumorigenic effects. Recently, complex mechanisms of cellular senescence and their influence on cellular processes have been defined in more detail and, therefore, facilitate translational development of targeted therapies. In this review, we aim to discuss major molecular pathways involved in cellular senescence and potential therapeutic strategies, with a specific focus on myeloid malignancies.
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Affiliation(s)
- Philipp Ernst
- Internal Medicine 2, Hematology and Oncology, Jena University Hospital, 07747 Jena, Germany;
- Research Program “Else Kröner-Forschungskolleg AntiAge“, Jena University Hospital, 07747 Jena, Germany
| | - Florian H. Heidel
- Internal Medicine C, Hematology and Oncology, Stem Cell Transplantation and Palliative Care, Greifswald University Medicine, 17475 Greifswald, Germany
- Leibniz Institute on Aging, Fritz-Lipmann Institute, 07745 Jena, Germany
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35
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Sun J, Prabhu N, Tang J, Yang F, Jia L, Guo J, Xiao K, Tam WL, Nordlund P, Dai L. Recent advances in proteome-wide label-free target deconvolution for bioactive small molecules. Med Res Rev 2021; 41:2893-2926. [PMID: 33533067 DOI: 10.1002/med.21788] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 01/04/2021] [Accepted: 01/20/2021] [Indexed: 01/01/2023]
Abstract
Small-molecule drugs modulate biological processes and disease states through engagement of target proteins in cells. Assessing drug-target engagement on a proteome-wide scale is of utmost importance in better understanding the molecular mechanisms of action of observed beneficial and adverse effects, as well as in developing next generation tool compounds and drugs with better efficacies and specificities. However, systematic assessment of drug-target engagement has been an arduous task. With the continuous development of mass spectrometry-based proteomics instruments and techniques, various chemical proteomics approaches for drug target deconvolution (i.e., the identification of molecular target for drugs) have emerged. Among these, the label-free target deconvolution approaches that do not involve the chemical modification of compounds of interest, have gained increased attention in the community. Here we provide an overview of the basic principles and recent biological applications of the most important label-free methods including the cellular thermal shift assay, pulse proteolysis, chemical denaturant and protein precipitation, stability of proteins from rates of oxidation, drug affinity responsive target stability, limited proteolysis, and solvent-induced protein precipitation. The state-of-the-art technical implications and future outlook for the label-free approaches are also discussed.
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Affiliation(s)
- Jichao Sun
- Department of Urology, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen Urology Minimally Invasive Engineering Center, Shenzhen, Guangdong, China.,Department of Geriatrics, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China
| | - Nayana Prabhu
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Jun Tang
- Department of Urology, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen Urology Minimally Invasive Engineering Center, Shenzhen, Guangdong, China.,Integrated Chinese and Western Medicine Postdoctoral Research Station, Jinan University, Guangzhou, Guangdong, China
| | - Fan Yang
- Department of Geriatrics, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China.,Integrated Chinese and Western Medicine Postdoctoral Research Station, Jinan University, Guangzhou, Guangdong, China
| | - Lin Jia
- College of Pharmacy, Shenzhen Technology University, Shenzhen, Guangdong, China
| | - Jinan Guo
- Department of Urology, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen Urology Minimally Invasive Engineering Center, Shenzhen, Guangdong, China
| | - Kefeng Xiao
- Department of Urology, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen Urology Minimally Invasive Engineering Center, Shenzhen, Guangdong, China
| | - Wai Leong Tam
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.,Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Pär Nordlund
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.,Department of Oncology and Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Lingyun Dai
- Department of Urology, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen Urology Minimally Invasive Engineering Center, Shenzhen, Guangdong, China.,Department of Geriatrics, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China.,Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
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Ha J, Park H, Park J, Park SB. Recent advances in identifying protein targets in drug discovery. Cell Chem Biol 2020; 28:394-423. [PMID: 33357463 DOI: 10.1016/j.chembiol.2020.12.001] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 11/11/2020] [Accepted: 11/30/2020] [Indexed: 02/06/2023]
Abstract
Phenotype-based screening has emerged as an alternative route for discovering new chemical entities toward first-in-class therapeutics. However, clarifying their mode of action has been a significant bottleneck for drug discovery. For target protein identification, conventionally bioactive small molecules are conjugated onto solid supports and then applied to isolate target proteins from whole proteome. This approach requires a high binding affinity between bioactive small molecules and their target proteins. Besides, the binding affinity can be significantly hampered after structural modifications of bioactive molecules with linkers. To overcome these limitations, two major strategies have recently been pursued: (1) the covalent conjugation between small molecules and target proteins using photoactivatable moieties or electrophiles, and (2) label-free target identification through monitoring target engagement by tracking the thermal, proteolytic, or chemical stability of target proteins. This review focuses on recent advancements in target identification from covalent capturing to label-free strategies.
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Affiliation(s)
- Jaeyoung Ha
- Department of Biophysics and Chemical Biology, Seoul National University, Seoul 08826, Korea
| | - Hankum Park
- CRI Center for Chemical Proteomics, Department of Chemistry, Seoul National University, Seoul 08826, Korea
| | - Jongmin Park
- Department of Chemistry, Kangwon National University, Chuncheon 24341, Korea.
| | - Seung Bum Park
- Department of Biophysics and Chemical Biology, Seoul National University, Seoul 08826, Korea; CRI Center for Chemical Proteomics, Department of Chemistry, Seoul National University, Seoul 08826, Korea.
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Tampere M, Pettke A, Salata C, Wallner O, Koolmeister T, Cazares-Körner A, Visnes T, Hesselman MC, Kunold E, Wiita E, Kalderén C, Lightowler M, Jemth AS, Lehtiö J, Rosenquist Å, Warpman-Berglund U, Helleday T, Mirazimi A, Jafari R, Puumalainen MR. Novel Broad-Spectrum Antiviral Inhibitors Targeting Host Factors Essential for Replication of Pathogenic RNA Viruses. Viruses 2020; 12:E1423. [PMID: 33322045 PMCID: PMC7762994 DOI: 10.3390/v12121423] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 11/26/2020] [Accepted: 12/07/2020] [Indexed: 12/14/2022] Open
Abstract
Recent RNA virus outbreaks such as Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and Ebola virus (EBOV) have caused worldwide health emergencies highlighting the urgent need for new antiviral strategies. Targeting host cell pathways supporting viral replication is an attractive approach for development of antiviral compounds, especially with new, unexplored viruses where knowledge of virus biology is limited. Here, we present a strategy to identify host-targeted small molecule inhibitors using an image-based phenotypic antiviral screening assay followed by extensive target identification efforts revealing altered cellular pathways upon antiviral compound treatment. The newly discovered antiviral compounds showed broad-range antiviral activity against pathogenic RNA viruses such as SARS-CoV-2, EBOV and Crimean-Congo hemorrhagic fever virus (CCHFV). Target identification of the antiviral compounds by thermal protein profiling revealed major effects on proteostasis pathways and disturbance in interactions between cellular HSP70 complex and viral proteins, illustrating the supportive role of HSP70 on many RNA viruses across virus families. Collectively, this strategy identifies new small molecule inhibitors with broad antiviral activity against pathogenic RNA viruses, but also uncovers novel virus biology urgently needed for design of new antiviral therapies.
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Affiliation(s)
- Marianna Tampere
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden; (M.T.); (A.P.); (O.W.); (T.K.); (A.C.-K.); (T.V.); (M.C.H.); (E.K.); (E.W.); (C.K.); (M.L.); (A.-S.J.); (J.L.); (Å.R.); (U.W.-B.); (T.H.); (R.J.)
- National Veterinary Institute, SE-756 51 Uppsala, Sweden;
| | - Aleksandra Pettke
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden; (M.T.); (A.P.); (O.W.); (T.K.); (A.C.-K.); (T.V.); (M.C.H.); (E.K.); (E.W.); (C.K.); (M.L.); (A.-S.J.); (J.L.); (Å.R.); (U.W.-B.); (T.H.); (R.J.)
| | - Cristiano Salata
- Department of Microbiology, Public Health Agency of Sweden, 171 65 Stockholm, Sweden;
- Department of Molecular Medicine, University of Padova, 35121 Padova, Italy
| | - Olov Wallner
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden; (M.T.); (A.P.); (O.W.); (T.K.); (A.C.-K.); (T.V.); (M.C.H.); (E.K.); (E.W.); (C.K.); (M.L.); (A.-S.J.); (J.L.); (Å.R.); (U.W.-B.); (T.H.); (R.J.)
| | - Tobias Koolmeister
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden; (M.T.); (A.P.); (O.W.); (T.K.); (A.C.-K.); (T.V.); (M.C.H.); (E.K.); (E.W.); (C.K.); (M.L.); (A.-S.J.); (J.L.); (Å.R.); (U.W.-B.); (T.H.); (R.J.)
| | - Armando Cazares-Körner
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden; (M.T.); (A.P.); (O.W.); (T.K.); (A.C.-K.); (T.V.); (M.C.H.); (E.K.); (E.W.); (C.K.); (M.L.); (A.-S.J.); (J.L.); (Å.R.); (U.W.-B.); (T.H.); (R.J.)
| | - Torkild Visnes
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden; (M.T.); (A.P.); (O.W.); (T.K.); (A.C.-K.); (T.V.); (M.C.H.); (E.K.); (E.W.); (C.K.); (M.L.); (A.-S.J.); (J.L.); (Å.R.); (U.W.-B.); (T.H.); (R.J.)
| | - Maria Carmen Hesselman
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden; (M.T.); (A.P.); (O.W.); (T.K.); (A.C.-K.); (T.V.); (M.C.H.); (E.K.); (E.W.); (C.K.); (M.L.); (A.-S.J.); (J.L.); (Å.R.); (U.W.-B.); (T.H.); (R.J.)
| | - Elena Kunold
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden; (M.T.); (A.P.); (O.W.); (T.K.); (A.C.-K.); (T.V.); (M.C.H.); (E.K.); (E.W.); (C.K.); (M.L.); (A.-S.J.); (J.L.); (Å.R.); (U.W.-B.); (T.H.); (R.J.)
| | - Elisee Wiita
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden; (M.T.); (A.P.); (O.W.); (T.K.); (A.C.-K.); (T.V.); (M.C.H.); (E.K.); (E.W.); (C.K.); (M.L.); (A.-S.J.); (J.L.); (Å.R.); (U.W.-B.); (T.H.); (R.J.)
| | - Christina Kalderén
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden; (M.T.); (A.P.); (O.W.); (T.K.); (A.C.-K.); (T.V.); (M.C.H.); (E.K.); (E.W.); (C.K.); (M.L.); (A.-S.J.); (J.L.); (Å.R.); (U.W.-B.); (T.H.); (R.J.)
| | - Molly Lightowler
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden; (M.T.); (A.P.); (O.W.); (T.K.); (A.C.-K.); (T.V.); (M.C.H.); (E.K.); (E.W.); (C.K.); (M.L.); (A.-S.J.); (J.L.); (Å.R.); (U.W.-B.); (T.H.); (R.J.)
| | - Ann-Sofie Jemth
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden; (M.T.); (A.P.); (O.W.); (T.K.); (A.C.-K.); (T.V.); (M.C.H.); (E.K.); (E.W.); (C.K.); (M.L.); (A.-S.J.); (J.L.); (Å.R.); (U.W.-B.); (T.H.); (R.J.)
| | - Janne Lehtiö
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden; (M.T.); (A.P.); (O.W.); (T.K.); (A.C.-K.); (T.V.); (M.C.H.); (E.K.); (E.W.); (C.K.); (M.L.); (A.-S.J.); (J.L.); (Å.R.); (U.W.-B.); (T.H.); (R.J.)
| | - Åsa Rosenquist
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden; (M.T.); (A.P.); (O.W.); (T.K.); (A.C.-K.); (T.V.); (M.C.H.); (E.K.); (E.W.); (C.K.); (M.L.); (A.-S.J.); (J.L.); (Å.R.); (U.W.-B.); (T.H.); (R.J.)
| | - Ulrika Warpman-Berglund
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden; (M.T.); (A.P.); (O.W.); (T.K.); (A.C.-K.); (T.V.); (M.C.H.); (E.K.); (E.W.); (C.K.); (M.L.); (A.-S.J.); (J.L.); (Å.R.); (U.W.-B.); (T.H.); (R.J.)
| | - Thomas Helleday
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden; (M.T.); (A.P.); (O.W.); (T.K.); (A.C.-K.); (T.V.); (M.C.H.); (E.K.); (E.W.); (C.K.); (M.L.); (A.-S.J.); (J.L.); (Å.R.); (U.W.-B.); (T.H.); (R.J.)
| | - Ali Mirazimi
- National Veterinary Institute, SE-756 51 Uppsala, Sweden;
- Unit of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute and Karolinska University Hospital, 17177 Stockholm, Sweden
| | - Rozbeh Jafari
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden; (M.T.); (A.P.); (O.W.); (T.K.); (A.C.-K.); (T.V.); (M.C.H.); (E.K.); (E.W.); (C.K.); (M.L.); (A.-S.J.); (J.L.); (Å.R.); (U.W.-B.); (T.H.); (R.J.)
| | - Marjo-Riitta Puumalainen
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden; (M.T.); (A.P.); (O.W.); (T.K.); (A.C.-K.); (T.V.); (M.C.H.); (E.K.); (E.W.); (C.K.); (M.L.); (A.-S.J.); (J.L.); (Å.R.); (U.W.-B.); (T.H.); (R.J.)
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Hendrychová D, Jorda R, Kryštof V. How selective are clinical CDK4/6 inhibitors? Med Res Rev 2020; 41:1578-1598. [PMID: 33300617 DOI: 10.1002/med.21769] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 09/28/2020] [Accepted: 11/29/2020] [Indexed: 12/29/2022]
Abstract
Pharmacological inhibition of cyclin-dependent kinase 4/6 (CDK4/6) has emerged as an efficient approach for treating breast cancer, and its clinical potential is expanding to other cancers. CDK4/6 inhibitors were originally believed to act by arresting proliferation in the G1 phase, but it is gradually becoming clear that the cellular response to these compounds is far more complex than this. Multiple context-dependent mechanisms of action are emerging, involving modulation of quiescence, senescence, autophagy, cellular metabolism, and enhanced tumor cell immunogenicity. These mechanisms may be driven by interactions with unexpected targets. We review cellular responses to the Food and Drug Administration-approved CDK4/6 inhibitors palbociclib, ribociclib, and abemaciclib, and summarize available knowledge of other drugs undergoing clinical trials, including data on their off-target landscapes. We emphasize the importance of comprehensively characterizing drugs' selectivity profiles to maximize their clinical efficacy and safety and to facilitate their repurposing to treat additional diseases based on their target spectrum.
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Affiliation(s)
- Denisa Hendrychová
- Department of Experimental Biology, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - Radek Jorda
- Department of Experimental Biology, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - Vladimír Kryštof
- Department of Experimental Biology, Faculty of Science, Palacký University, Olomouc, Czech Republic
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Engler M, Fidan M, Nandi S, Cirstea IC. Senescence in RASopathies, a possible novel contributor to a complex pathophenoype. Mech Ageing Dev 2020; 194:111411. [PMID: 33309600 DOI: 10.1016/j.mad.2020.111411] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 11/17/2020] [Accepted: 11/23/2020] [Indexed: 01/07/2023]
Abstract
Senescence is a biological process that induces a permanent cell cycle arrest and a specific gene expression program in response to various stressors. Following studies over the last few decades, the concept of senescence has evolved from an antiproliferative mechanism in cancer (oncogene-induced senescence) to a critical component of physiological processes associated with embryonic development, tissue regeneration, ageing and its associated diseases. In somatic cells, oncogenic mutations in RAS-MAPK pathway genes are associated with oncogene-induced senescence and cancer, while germline mutations in the same pathway are linked to a group of monogenic developmental disorders generally termed RASopathies. Here, we consider that in these disorders, senescence induction may result in opposing outcomes, a tumour protective effect and a possible contributor to a premature ageing phenotype identified in Costello syndrome, which belongs to the RASopathy group. In this review, we will highlight the role of senescence in organismal homeostasis and we will describe the current knowledge about senescence in RASopathies. Additionally, we provide a perspective on examples of experimentally characterised RASopathy mutations that, alone or in combination with various stressors, may also trigger an age-dependent chronic senescence, possibly contributing to the age-dependent worsening of RASopathy pathophenotype and the reduction of lifespan.
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Affiliation(s)
- Melanie Engler
- Institute of Comparative Molecular Endocrinology, Ulm University, Helmholtzstr. 8/1, 89081, Ulm, Germany
| | - Miray Fidan
- Institute of Comparative Molecular Endocrinology, Ulm University, Helmholtzstr. 8/1, 89081, Ulm, Germany
| | - Sayantan Nandi
- Institute of Comparative Molecular Endocrinology, Ulm University, Helmholtzstr. 8/1, 89081, Ulm, Germany
| | - Ion Cristian Cirstea
- Institute of Comparative Molecular Endocrinology, Ulm University, Helmholtzstr. 8/1, 89081, Ulm, Germany.
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Marinelli O, Romagnoli E, Maggi F, Nabissi M, Amantini C, Morelli MB, Santoni M, Battelli N, Santoni G. Exploring treatment with Ribociclib alone or in sequence/combination with Everolimus in ER +HER2 -Rb wild-type and knock-down in breast cancer cell lines. BMC Cancer 2020; 20:1119. [PMID: 33213401 PMCID: PMC7678099 DOI: 10.1186/s12885-020-07619-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 11/06/2020] [Indexed: 11/10/2022] Open
Abstract
Background Breast cancer (BC) is the second most common type of cancer worldwide. Among targeted therapies for Hormone Receptor-positive (HR+) and Human Epidermal growth factor Receptor 2-negative (HER2−) BC, the Cyclin-Dependent Kinases (CDK4/6) are targeted by inhibitors such as Ribociclib (Rib); however, resistance to CDK4/6 inhibitors frequently develops. The aim of this work is to assess in vitro activity of Rib and Everolimus (Eve) in HR+HER2− MCF-7 and HR−HER2−BT-549 BC cell lines. Methods HR+HER2− MCF-7 and HR−HER2− BT-549 BC cell lines were treated with increasing concentration of Rib and Eve (up to 80 μg/mL) for 48–72 h. Subsequently, HR+HER2− MCF-7 cells were silenced for Retinoblastoma (Rb) gene, and thus, the effect of Rib in sequential or concurrent schedule with Eve for the treatment of both Rb wild type or Rb knock-down MCF-7 in vitro was evaluated. Cell viability of HR+HER2− MCF-7cells treated with sequential and concurrent dosing schedule was analyzed by MTT assay. Moreover, cell cycle phases, cell death and senescence were evaluated by cytofluorimetric analysis after treatment with Rib or Eve alone or in combination. Results The sequential treatment didn’t produce a significant increase of cytotoxicity, compared to Rib alone. Instead, the cotreatment synergized to increase the cytotoxicity compared to Rib alone. The cotreatment reduced the percentage of cells in S and G2/M phases and induced apoptosis. Rib triggered senescence and Eve completely reversed this effect in Rb wild type BC cells. Rib also showed Rb-independent effects as shown by results in Rb knock-down MCF-7. Conclusion Overall, the Rib/Eve concurrent therapy augmented the in vitro cytotoxic effect, compared to Rib/Eve sequential therapy or single treatments. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-020-07619-1.
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Affiliation(s)
| | | | - Federica Maggi
- School of Pharmacy, University of Camerino, 62032, Camerino, MC, Italy.,Department of Molecular Medicine, University of Rome Sapienza, Rome, Italy
| | - Massimo Nabissi
- School of Pharmacy, University of Camerino, 62032, Camerino, MC, Italy
| | - Consuelo Amantini
- School of Bioscience and Veterinary Medicine, University of Camerino, Camerino, MC, Italy
| | | | - Matteo Santoni
- Medical Oncology Unit, Hospital of Macerata, Macerata, Italy
| | - Nicola Battelli
- Medical Oncology Unit, Hospital of Macerata, Macerata, Italy
| | - Giorgio Santoni
- School of Pharmacy, University of Camerino, 62032, Camerino, MC, Italy.
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Heunis T, Lamoliatte F, Marín-Rubio JL, Dannoura A, Trost M. Technical report: Targeted proteomic analysis reveals enrichment of atypical ubiquitin chains in contractile murine tissues. J Proteomics 2020; 229:103963. [PMID: 32898700 PMCID: PMC7567960 DOI: 10.1016/j.jprot.2020.103963] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 08/14/2020] [Accepted: 08/24/2020] [Indexed: 12/03/2022]
Abstract
Ubiquitylation is an elaborate post-translational modification involved in all biological processes. Its pleotropic effect is driven by the ability to form complex polyubiquitin chain architectures that can influence biological functions. In this study, we optimised sample preparation and chromatographic separation of Ubiquitin peptides for Absolute Quantification by Parallel Reaction Monitoring (Ub-AQUA-PRM). Using this refined Ub-AQUA-PRM assay, we were able to quantify all ubiquitin chain types in 10-min LC-MS/MS runs. We used this method to determine the ubiquitin chain-linkage composition in murine bone marrow-derived macrophages and different mouse tissues. We could show tissue-specific differences in ubiquitin levels in murine tissues, with polyubiquitin chain types contributing a small proportion to the total pool of ubiquitin. Interestingly, we observed enrichment of atypical (K33) ubiquitin chains in heart and muscle. Our approach enabled high-throughput screening of ubiquitin chain-linkage composition in different murine tissues and highlighted a possible role for atypical ubiquitylation in contractile tissues. Significance Large knowledge gaps exist in our understanding of ubiquitin chain-linkage composition in mammalian tissues. Defining this in vivo ubiquitin chain-linkage landscape could reveal the functional importance of different ubiquitin chain types in tissues. In this study, we refined the previously described Ub-AQUA-PRM assay to enable quantification of all ubiquitin chain types in a high-throughput manner. Using this assay, we provided new data on the ubiquitin chain-linkage composition in primary murine macrophages and tissues, and revealed an enrichment of atypical ubiquitin chains in contractile tissues. Our approach should thus enable rapid, high-throughput screening of ubiquitin chain-linkage composition in different sample types, as demonstrated in murine primary cells and tissues.
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Affiliation(s)
- Tiaan Heunis
- Biosciences Institute, Newcastle University, NE2 4HH Newcastle upon Tyne, United Kingdom
| | - Frederic Lamoliatte
- Biosciences Institute, Newcastle University, NE2 4HH Newcastle upon Tyne, United Kingdom
| | - José Luis Marín-Rubio
- Biosciences Institute, Newcastle University, NE2 4HH Newcastle upon Tyne, United Kingdom
| | - Abeer Dannoura
- Biosciences Institute, Newcastle University, NE2 4HH Newcastle upon Tyne, United Kingdom
| | - Matthias Trost
- Biosciences Institute, Newcastle University, NE2 4HH Newcastle upon Tyne, United Kingdom.
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Lyu J, Ruan C, Zhang X, Wang Y, Li K, Ye M. Microparticle-Assisted Precipitation Screening Method for Robust Drug Target Identification. Anal Chem 2020; 92:13912-13921. [PMID: 32933243 DOI: 10.1021/acs.analchem.0c02756] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
While thermal proteome profiling (TPP) shines in the field of drug target screening by analyzing the soluble fraction of the proteome samples treated at high temperature, the counterpart, the insoluble precipitate, has been overlooked for a long time. The analysis of the precipitate is hampered by the inefficient sample processing procedure. Herein, we propose a novel method, termed microparticle-assisted precipitation screening (MAPS), for drug target identification. The MAPS method exploits the principle that drug-bound proteins will be more resistant to thermal unfolding similar to the classic TPP method, but the process of protein precipitation is assisted by microparticles. Upon heating, proteins unfold and aggregate on the surface of the microparticles. The introduction of a microparticle simplifies the whole sample preparation workflow. The proteins that precipitate on the microparticles are subjected to washing, alkylation, and digestion. The whole sample preparation is processed conveniently on the surface of the microparticles without any transfer. With the assistance of microparticles, sample loss is minimized. The MAPS method is compatible with minute amounts of initial proteins. MAPS was applied to screen the targets of several well-studied drugs and the known target proteins were successfully identified with high confidence and specificity. To investigate the specificity of the method, MAPS was applied to screen the targets of the pan-kinase inhibitor, staurosporine, and 32 protein kinases (specificity of 80%) were identified using only 20 μg of initial proteins of each sample. MAPS is an unbiased robust method for drug target screening, filling the vacancy of stability-based target screening using a precipitate.
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Affiliation(s)
- Jiawen Lyu
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chengfei Ruan
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaolei Zhang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yan Wang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kejia Li
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mingliang Ye
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
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43
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Dai L, Li Z, Chen D, Jia L, Guo J, Zhao T, Nordlund P. Target identification and validation of natural products with label-free methodology: A critical review from 2005 to 2020. Pharmacol Ther 2020; 216:107690. [PMID: 32980441 DOI: 10.1016/j.pharmthera.2020.107690] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 09/22/2020] [Accepted: 09/22/2020] [Indexed: 02/08/2023]
Abstract
Natural products (NPs) have been an important source of therapeutic drugs in clinic use and contributed many chemical probes for research. The usefulness of NPs is however often marred by the incomplete understanding of their direct cellular targets. A number of experimental methods for drug target identification have been developed over the years. One class of methods, termed "label-free" methodology, exploits the energetic and biophysical features accompanying the association of macromolecules with drugs and other compounds in their native forms. Herein we review the working principles, assay implementations, and key applications of the most important approaches, and also give examples where they have been applied to NPs. We also assess the key advantages and limitations of each method. Furthermore, we address when and how the label-free methodology can be particularly useful considering some of the unique features of NP chemistry and bioactivation.
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Affiliation(s)
- Lingyun Dai
- Department of Urology, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen Urology Minimally Invasive Engineering Center, Shenzhen 518020, Guangdong, China; Department of Geriatrics, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen 518020, Guangdong, China; Institute of Molecular and Cell Biology, A*STAR, Singapore 138673, Singapore.
| | - Zhijie Li
- Department of Urology, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen Urology Minimally Invasive Engineering Center, Shenzhen 518020, Guangdong, China; Department of Geriatrics, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen 518020, Guangdong, China
| | - Dan Chen
- Institute of Molecular and Cell Biology, A*STAR, Singapore 138673, Singapore
| | - Lin Jia
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong 999077, China
| | - Jinan Guo
- Department of Urology, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen Urology Minimally Invasive Engineering Center, Shenzhen 518020, Guangdong, China
| | - Tianyun Zhao
- Institute of Molecular and Cell Biology, A*STAR, Singapore 138673, Singapore
| | - Pär Nordlund
- Institute of Molecular and Cell Biology, A*STAR, Singapore 138673, Singapore; Department of Oncology and Pathology, Karolinska Institutet, 171 77 Stockholm, Sweden.
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44
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Li J, Zhou Y, Yan Y, Zheng Z, Hu Y, Wu W. Sulforaphane-cysteine downregulates CDK4 /CDK6 and inhibits tubulin polymerization contributing to cell cycle arrest and apoptosis in human glioblastoma cells. Aging (Albany NY) 2020; 12:16837-16851. [PMID: 32860670 PMCID: PMC7521484 DOI: 10.18632/aging.103537] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 04/27/2020] [Indexed: 01/24/2023]
Abstract
Here we demonstrated that sulforaphane-cysteine (SFN-Cys) regulated cell cycle-related protein expressions in G0/G1 and G2/M phases of U87MG cells via High Performance Liquid Chromatography-Mass Spectrometry/Mass Spectrometry (HPLC-MS/MS) and proteomics analysis. Further, mRNA products of CDK4, CDK6 and α-tubulin were significantly higher in glioblastoma than those in normal tissues, and these results were significantly correlated to pathological grades and clinical prognosis via analyzing TCGA and CGGA databases. Furthermore, Western blot showed that SFN-Cys downregulated CDK4, CDK6 and p-Rb in a dose-dependent manner and these results were reversed by p-ERK1/2 blocker PD98059 in U87MG and U373MG cells. The reductions of CDK4, CDK6 and p-Rb were reversed by proteasome inhibitor MG132; similarly, the upregulation of 26S proteasome by SFN-Cys was reversed by PD98059. Interestingly, SFN-Cys decreased CDK4 and CDK6 by phosphorylated ERK1/2-caused proteasomal degradation resulting in decreased Rb phosphorylation contributing to cell cycle arrest in G0/G1 phase. Besides, Western blot showed that SFN-Cys downregulated α-tubulin resulting in microtubule disruption and aggregation, and cell cycle arrest in G2/M phase and apoptosis. These results might help us understand the molecular etiology of glioblastoma progression to establish brand-new anti-cancer therapies.
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Affiliation(s)
- Juntao Li
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, China,Beijing Key Laboratory for Tumor Invasion and Metastasis, Capital Medical University, Beijing, China
| | - Yan Zhou
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, China,Beijing Key Laboratory for Tumor Invasion and Metastasis, Capital Medical University, Beijing, China
| | - Yuting Yan
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, China,Beijing Key Laboratory for Tumor Invasion and Metastasis, Capital Medical University, Beijing, China
| | - Zhongnan Zheng
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, China,Beijing Key Laboratory for Tumor Invasion and Metastasis, Capital Medical University, Beijing, China
| | - Yabin Hu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, China,Beijing Key Laboratory for Tumor Invasion and Metastasis, Capital Medical University, Beijing, China
| | - Wei Wu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, China,Beijing Key Laboratory for Tumor Invasion and Metastasis, Capital Medical University, Beijing, China
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45
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Wagner V, Gil J. Senescence as a therapeutically relevant response to CDK4/6 inhibitors. Oncogene 2020; 39:5165-5176. [PMID: 32541838 PMCID: PMC7610384 DOI: 10.1038/s41388-020-1354-9] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 05/26/2020] [Accepted: 06/03/2020] [Indexed: 12/19/2022]
Abstract
Cyclin-dependent kinases 4 and 6 (CDK4/6) phosphorylate and inhibit retinoblastoma (RB) family proteins. Hyperphosphorylated RB releases E2F transcription factors, activating a transcriptional program that initiates S phase. Due to the critical role that this pathway has in regulating cell cycle progression, inhibiting CDK4/6 is an attractive therapeutic strategy. Indeed, CDK4/6 inhibitors in combination with antiestrogens produce a significant benefit in patients with ER+/HER2- breast cancer. Clinical trials are currently investigating if the use of CDK4/6 inhibitors alone or in combination can be extended to other cancer types. Inhibition of CDK4/6 can result in different cell fates such as quiescence, senescence, or apoptosis. Senescence is a stress response that can be induced by stimuli that include oncogenic activation, chemotherapy, irradiation, and targeted therapies such as CDK4/6 inhibitors. Senescent cells undergo a stable cell cycle arrest and produce a bioactive secretome that remodels their microenvironment and engages the immune system. In this review, we analyze the therapeutic relevance of senescence induction by CDK4/6 inhibitors. We also discuss how different therapies, including checkpoint inhibitors and drugs targeting MEK or PI3K, can be used in combination with CDK4/6 inhibitors to reinforce or exploit senescence. Recently, a lot of effort has been put into identifying compounds that selectively kill senescent cells (termed senolytics). Thus, sequential treatment with senolytics might be an additional strategy to potentiate the antitumor effects of CDK4/6 inhibitors.
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Affiliation(s)
- Verena Wagner
- MRC London Institute of Medical Sciences (LMS), Du Cane Road, London, W12 0NN, UK
- Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Jesús Gil
- MRC London Institute of Medical Sciences (LMS), Du Cane Road, London, W12 0NN, UK.
- Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, Du Cane Road, London, W12 0NN, UK.
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46
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Li J, Van Vranken JG, Paulo JA, Huttlin EL, Gygi SP. Selection of Heating Temperatures Improves the Sensitivity of the Proteome Integral Solubility Alteration Assay. J Proteome Res 2020; 19:2159-2166. [PMID: 32243163 DOI: 10.1021/acs.jproteome.0c00063] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The thermal shift assay is a robust method of discovering protein-ligand interactions by measuring the alterations in protein thermal stability under various conditions. Several thermal shift assays have been developed and their throughput has been advanced greatly by the rapid progress in tandem mass tag-based quantitative proteomics. A recent paper by Gaetani et al. ( J. Proteome Res. 2019, 18 (11), 4027-4037) introduced the proteome integral solubility alteration (PISA) assay, further increasing throughput and simplifying the data analysis. Both ΔSm (a proxy of the difference between areas under the melting curves) and fold changes (ratios between integral samples) are readouts of the PISA assay and positively related to ΔTm (shift in melting temperatures). Here, we show that the magnitudes of these readouts are inherently small in PISA assay, which is a challenge for quantitation. Both simulation and experimental results show that the selection of a subset of heating temperatures ameliorates the small difference problem and improves the sensitivity of the PISA assay.
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Affiliation(s)
- Jiaming Li
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Jonathan G Van Vranken
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Edward L Huttlin
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
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Saleh T, Bloukh S, Carpenter VJ, Alwohoush E, Bakeer J, Darwish S, Azab B, Gewirtz DA. Therapy-Induced Senescence: An "Old" Friend Becomes the Enemy. Cancers (Basel) 2020; 12:cancers12040822. [PMID: 32235364 PMCID: PMC7226427 DOI: 10.3390/cancers12040822] [Citation(s) in RCA: 154] [Impact Index Per Article: 38.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 03/21/2020] [Accepted: 03/25/2020] [Indexed: 01/10/2023] Open
Abstract
For the past two decades, cellular senescence has been recognized as a central component of the tumor cell response to chemotherapy and radiation. Traditionally, this form of senescence, termed Therapy-Induced Senescence (TIS), was linked to extensive nuclear damage precipitated by classical genotoxic chemotherapy. However, a number of other forms of therapy have also been shown to induce senescence in tumor cells independently of direct genomic damage. This review attempts to provide a comprehensive summary of both conventional and targeted anticancer therapeutics that have been shown to induce senescence in vitro and in vivo. Still, the utility of promoting senescence as a therapeutic endpoint remains under debate. Since senescence represents a durable form of growth arrest, it might be argued that senescence is a desirable outcome of cancer therapy. However, accumulating evidence suggesting that cells have the capacity to escape from TIS would support an alternative conclusion, that senescence provides an avenue whereby tumor cells can evade the potentially lethal action of anticancer drugs, allowing the cells to enter a temporary state of dormancy that eventually facilitates disease recurrence, often in a more aggressive state. Furthermore, TIS is now strongly connected to tumor cell remodeling, potentially to tumor dormancy, acquiring more ominous malignant phenotypes and accounts for several untoward adverse effects of cancer therapy. Here, we argue that senescence represents a barrier to effective anticancer treatment, and discuss the emerging efforts to identify and exploit agents with senolytic properties as a strategy for elimination of the persistent residual surviving tumor cell population, with the goal of mitigating the tumor-promoting influence of the senescent cells and to thereby reduce the likelihood of cancer relapse.
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Affiliation(s)
- Tareq Saleh
- Department of Basic Medical Sciences, Faculty of Medicine, The Hashemite University, Zarqa 13133, Jordan; (T.S.); (S.D.)
| | - Sarah Bloukh
- Department of Pathology, Microbiology and Forensic Medicine, School of Medicine, The University of Jordan, Amman 11942, Jordan; (S.B.); (E.A.); (J.B.); (B.A.)
| | - Valerie J. Carpenter
- Department of Pharmacology and Toxicology, School of Medicine, Virginia Commonwealth University, Richmond, VA 23284, USA;
| | - Enas Alwohoush
- Department of Pathology, Microbiology and Forensic Medicine, School of Medicine, The University of Jordan, Amman 11942, Jordan; (S.B.); (E.A.); (J.B.); (B.A.)
| | - Jomana Bakeer
- Department of Pathology, Microbiology and Forensic Medicine, School of Medicine, The University of Jordan, Amman 11942, Jordan; (S.B.); (E.A.); (J.B.); (B.A.)
| | - Sarah Darwish
- Department of Basic Medical Sciences, Faculty of Medicine, The Hashemite University, Zarqa 13133, Jordan; (T.S.); (S.D.)
| | - Belal Azab
- Department of Pathology, Microbiology and Forensic Medicine, School of Medicine, The University of Jordan, Amman 11942, Jordan; (S.B.); (E.A.); (J.B.); (B.A.)
- Department of Human and Molecular Genetics, School of Medicine, Virginia Commonwealth University, Richmond, VA 23284, USA
| | - David A. Gewirtz
- Department of Pharmacology and Toxicology, School of Medicine, Virginia Commonwealth University, Richmond, VA 23284, USA;
- Correspondence:
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48
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Huang JX, Coukos JS, Moellering RE. Interaction profiling methods to map protein and pathway targets of bioactive ligands. Curr Opin Chem Biol 2020; 54:76-84. [PMID: 32146330 DOI: 10.1016/j.cbpa.2020.02.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 01/17/2020] [Accepted: 02/05/2020] [Indexed: 01/08/2023]
Abstract
Recent advances in -omic profiling technologies have ushered in an era where we no longer want to merely measure the presence or absence of a biomolecule of interest, but instead hope to understand its function and interactions within larger signaling networks. Here, we review several emerging proteomic technologies capable of detecting protein interaction networks in live cells and their integration to draft holistic maps of proteins that respond to diverse stimuli, including bioactive small molecules. Moreover, we provide a conceptual framework to combine so-called 'top-down' and 'bottom-up' interaction profiling methods and ensuing proteomic profiles to directly identify binding targets of small molecule ligands, as well as for unbiased discovery of proteins and pathways that may be directly bound or influenced by those first responders. The integrated, interaction-based profiling methods discussed here have the potential to provide a unique and dynamic view into cellular signaling networks for both basic and translational biological studies.
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Affiliation(s)
- Jun X Huang
- Department of Chemistry, The University of Chicago, 929 E. 57th Street, Chicago, IL, 60637, USA; Institute for Genomics and Systems Biology, The University of Chicago, 929 E. 57th Street, Chicago, IL, 60637, USA
| | - John S Coukos
- Department of Chemistry, The University of Chicago, 929 E. 57th Street, Chicago, IL, 60637, USA; Institute for Genomics and Systems Biology, The University of Chicago, 929 E. 57th Street, Chicago, IL, 60637, USA
| | - Raymond E Moellering
- Department of Chemistry, The University of Chicago, 929 E. 57th Street, Chicago, IL, 60637, USA; Institute for Genomics and Systems Biology, The University of Chicago, 929 E. 57th Street, Chicago, IL, 60637, USA.
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49
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Lyu J, Wang K, Ye M. Modification-free approaches to screen drug targets at proteome level. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2019.06.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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50
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Cabrera A, Wiebelhaus N, Quan B, Ma R, Meng H, Fitzgerald MC. Comparative Analysis of Mass-Spectrometry-Based Proteomic Methods for Protein Target Discovery Using a One-Pot Approach. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:217-226. [PMID: 32031398 PMCID: PMC7441748 DOI: 10.1021/jasms.9b00041] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Recently, several mass-spectrometry- and protein-denaturation-based proteomic methods have been developed to facilitate protein target discovery efforts in drug mode-of-action studies. These methods, which include the stability of proteins from rates of oxidation (SPROX), pulse proteolysis (PP), chemical denaturation and protein precipitation (CPP), and thermal proteome profiling (TPP) techniques, have been used in an increasing number of applications in recent years. However, while the advantages and disadvantages to using these different techniques have been reviewed, the analytical characteristics of these methods have not been directly compared. Reported here is such a direct comparison using the well-studied immunosuppressive drug, cyclosporine A (CsA), and the proteins in a yeast cell lysate. Also described is a one-pot strategy that can be utilized with each technique to streamline data acquisition and analysis. We find that there are benefits to utilizing all four strategies for protein target discovery including increased proteomic coverage and reduced false positive rates that approach 0%. Moreover, the one-pot strategy described here makes such an experiment feasible, because of the 10-fold reduction in reagent costs and instrument time it affords.
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Affiliation(s)
- Aurora Cabrera
- Department of Chemistry, Duke University, Durham, North Carolina 27708
| | - Nancy Wiebelhaus
- Department of Chemistry, Duke University, Durham, North Carolina 27708
| | - Baiyi Quan
- Department of Chemistry, Duke University, Durham, North Carolina 27708
| | - Renze Ma
- Department of Chemistry, Duke University, Durham, North Carolina 27708
| | - He Meng
- Department of Chemistry, Duke University, Durham, North Carolina 27708
| | - Michael C. Fitzgerald
- Department of Chemistry, Duke University, Durham, North Carolina 27708
- Address Reprint Requests To: Professor Michael C. Fitzgerald, Department of Chemistry, Box 90346, Duke University, Durham, North Carolina 27708-0346, Tel: 919-660-1547, Fax: 919-660-1605,
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