1
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McGirr T, Onar O, Jafarnejad SM. Dysregulated ribosome quality control in human diseases. FEBS J 2024. [PMID: 38949989 DOI: 10.1111/febs.17217] [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: 02/12/2024] [Revised: 05/31/2024] [Accepted: 06/20/2024] [Indexed: 07/03/2024]
Abstract
Precise regulation of mRNA translation is of fundamental importance for maintaining homeostasis. Conversely, dysregulated general or transcript-specific translation, as well as abnormal translation events, have been linked to a multitude of diseases. However, driven by the misconception that the transient nature of mRNAs renders their abnormalities inconsequential, the importance of mechanisms that monitor the quality and fidelity of the translation process has been largely overlooked. In recent years, there has been a dramatic shift in this paradigm, evidenced by several seminal discoveries on the role of a key mechanism in monitoring the quality of mRNA translation - namely, Ribosome Quality Control (RQC) - in the maintenance of homeostasis and the prevention of diseases. Here, we will review recent advances in the field and emphasize the biological significance of the RQC mechanism, particularly its implications in human diseases.
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Affiliation(s)
- Tom McGirr
- Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, UK
| | - Okan Onar
- Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, UK
- Department of Biology, Faculty of Science, Ankara University, Turkey
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2
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Levitskaya Z, Ser Z, Koh H, Mei WS, Chee S, Sobota RM, Ghadessy JF. Engineering cell-free systems by chemoproteomic-assisted phenotypic screening. RSC Chem Biol 2024; 5:372-385. [PMID: 38576719 PMCID: PMC10989505 DOI: 10.1039/d4cb00004h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 02/16/2024] [Indexed: 04/06/2024] Open
Abstract
Phenotypic screening is a valuable tool to both understand and engineer complex biological systems. We demonstrate the functionality of this approach in the development of cell-free protein synthesis (CFPS) technology. Phenotypic screening identified numerous compounds that enhanced protein production in yeast lysate CFPS reactions. Notably, many of these were competitive ATP kinase inhibitors, with the exploitation of their inherent substrate promiscuity redirecting ATP flux towards heterologous protein expression. Chemoproteomic-guided strain engineering partially phenocopied drug effects, with a 30% increase in protein yield observed upon deletion of the ATP-consuming SSA1 component of the HSP70 chaperone. Moreover, drug-mediated metabolic rewiring coupled with template optimization generated the highest protein yields in yeast CFPS to date using a hitherto less efficient, but more cost-effective glucose energy regeneration system. Our approach highlights the utility of target-agnostic phenotypic screening and target identification to deconvolute cell-lysate complexity, adding to the expanding repertoire of strategies for improving CFPS.
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Affiliation(s)
- Zarina Levitskaya
- Protein and Peptide Engineering and Research Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR) 8A Biomedical Grove Singapore 138648
| | - Zheng Ser
- Function Proteomics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR) 8A Biomedical Grove Singapore 138648
| | - Hiromi Koh
- Function Proteomics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR) 8A Biomedical Grove Singapore 138648
| | - Wang Shi Mei
- Function Proteomics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR) 8A Biomedical Grove Singapore 138648
| | - Sharon Chee
- Protein and Peptide Engineering and Research Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR) 8A Biomedical Grove Singapore 138648
| | - Radoslaw Mikolaj Sobota
- Function Proteomics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR) 8A Biomedical Grove Singapore 138648
| | - John F Ghadessy
- Protein and Peptide Engineering and Research Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR) 8A Biomedical Grove Singapore 138648
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3
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Gerault MA, Granjeaud S, Camoin L, Nordlund P, Dai L. IMPRINTS.CETSA and IMPRINTS.CETSA.app: an R package and a Shiny application for the analysis and interpretation of IMPRINTS-CETSA data. Brief Bioinform 2024; 25:bbae128. [PMID: 38557673 PMCID: PMC10982947 DOI: 10.1093/bib/bbae128] [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: 10/15/2023] [Revised: 02/10/2024] [Accepted: 03/11/2024] [Indexed: 04/04/2024] Open
Abstract
IMPRINTS-CETSA (Integrated Modulation of Protein Interaction States-Cellular Thermal Shift Assay) provides a highly resolved means to systematically study the interactions of proteins with other cellular components, including metabolites, nucleic acids and other proteins, at the proteome level, but no freely available and user-friendly data analysis software has been reported. Here, we report IMPRINTS.CETSA, an R package that provides the basic data processing framework for robust analysis of the IMPRINTS-CETSA data format, from preprocessing and normalization to visualization. We also report an accompanying R package, IMPRINTS.CETSA.app, which offers a user-friendly Shiny interface for analysis and interpretation of IMPRINTS-CETSA results, with seamless features such as functional enrichment and mapping to other databases at a single site. For the hit generation part, the diverse behaviors of protein modulations have been typically segregated with a two-measure scoring method, i.e. the abundance and thermal stability changes. We present a new algorithm to classify modulated proteins in IMPRINTS-CETSA experiments by a robust single-measure scoring. In this way, both the numerical changes and the statistical significances of the IMPRINTS information can be visualized on a single plot. The IMPRINTS.CETSA and IMPRINTS.CETSA.app R packages are freely available on GitHub at https://github.com/nkdailingyun/IMPRINTS.CETSA and https://github.com/mgerault/IMPRINTS.CETSA.app, respectively. IMPRINTS.CETSA.app is also available as an executable program at https://zenodo.org/records/10636134.
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Affiliation(s)
- Marc-Antoine Gerault
- Department of Oncology and Pathology, Karolinska Institutet, 171 77 Stockholm, Sweden
- Aix-Marseille Univ, INSERM, CNRS, Institut Paoli-Calmettes, CRCM, Marseille Protéomique, F-13009 Marseille, France
| | - Samuel Granjeaud
- Aix-Marseille Univ, INSERM, CNRS, Institut Paoli-Calmettes, CRCM, Marseille Protéomique, F-13009 Marseille, France
| | - Luc Camoin
- Aix-Marseille Univ, INSERM, CNRS, Institut Paoli-Calmettes, CRCM, Marseille Protéomique, F-13009 Marseille, France
| | - Pär Nordlund
- Department of Oncology and Pathology, Karolinska Institutet, 171 77 Stockholm, Sweden
- Institute of Molecular and Cell Biology, A*STAR, 138673, Singapore
| | - Lingyun Dai
- Institute of Molecular and Cell Biology, A*STAR, 138673, Singapore
- Department of Geriatrics, and Shenzhen Clinical Research Centre for Geriatrics, The First Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen 518020, China
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4
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Gao Y, Ma M, Li W, Lei X. Chemoproteomics, A Broad Avenue to Target Deconvolution. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2305608. [PMID: 38095542 PMCID: PMC10885659 DOI: 10.1002/advs.202305608] [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: 08/11/2023] [Revised: 11/29/2023] [Indexed: 12/22/2023]
Abstract
As a vital project of forward chemical genetic research, target deconvolution aims to identify the molecular targets of an active hit compound. Chemoproteomics, either with chemical probe-facilitated target enrichment or probe-free, provides a straightforward and effective approach to profile the target landscape and unravel the mechanisms of action. Canonical methods rely on chemical probes to enable target engagement, enrichment, and identification, whereas click chemistry and photoaffinity labeling techniques improve the efficiency, sensitivity, and spatial accuracy of target recognition. In comparison, recently developed probe-free methods detect protein-ligand interactions without the need to modify the ligand molecule. This review provides a comprehensive overview of different approaches and recent advancements for target identification and highlights the significance of chemoproteomics in investigating biological processes and advancing drug discovery processes.
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Affiliation(s)
- Yihui Gao
- Beijing National Laboratory for Molecular SciencesKey Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of EducationCollege of Chemistry and Molecular EngineeringPeking UniversityBeijing100871China
| | - Mingzhe Ma
- Beijing National Laboratory for Molecular SciencesKey Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of EducationCollege of Chemistry and Molecular EngineeringPeking UniversityBeijing100871China
- Peking‐Tsinghua Center for Life SciencesPeking UniversityBeijing100871China
| | - Wenyang Li
- Beijing National Laboratory for Molecular SciencesKey Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of EducationCollege of Chemistry and Molecular EngineeringPeking UniversityBeijing100871China
| | - Xiaoguang Lei
- Beijing National Laboratory for Molecular SciencesKey Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of EducationCollege of Chemistry and Molecular EngineeringPeking UniversityBeijing100871China
- Peking‐Tsinghua Center for Life SciencesPeking UniversityBeijing100871China
- Academy for Advanced Interdisciplinary StudiesPeking UniversityBeijing100871China
- Institute for Cancer ResearchShenzhen Bay LaboratoryShenzhenChina
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5
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Zhao S, Yang X, Zeng Z, Qian P, Zhao Z, Dai L, Prabhu N, Nordlund P, Tam WL. Deep learning based CETSA feature prediction cross multiple cell lines with latent space representation. Sci Rep 2024; 14:1878. [PMID: 38253642 PMCID: PMC10810365 DOI: 10.1038/s41598-024-51193-6] [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: 07/14/2023] [Accepted: 01/01/2024] [Indexed: 01/24/2024] Open
Abstract
Mass spectrometry-coupled cellular thermal shift assay (MS-CETSA), a biophysical principle-based technique that measures the thermal stability of proteins at the proteome level inside the cell, has contributed significantly to the understanding of drug mechanisms of action and the dissection of protein interaction dynamics in different cellular states. One of the barriers to the wide applications of MS-CETSA is that MS-CETSA experiments must be performed on the specific cell lines of interest, which is typically time-consuming and costly in terms of labeling reagents and mass spectrometry time. In this study, we aim to predict CETSA features in various cell lines by introducing a computational framework called CycleDNN based on deep neural network technology. For a given set of n cell lines, CycleDNN comprises n auto-encoders. Each auto-encoder includes an encoder to convert CETSA features from one cell line into latent features in a latent space [Formula: see text]. It also features a decoder that transforms the latent features back into CETSA features for another cell line. In such a way, the proposed CycleDNN creates a cyclic prediction of CETSA features across different cell lines. The prediction loss, cycle-consistency loss, and latent space regularization loss are used to guide the model training. Experimental results on a public CETSA dataset demonstrate the effectiveness of our proposed approach. Furthermore, we confirm the validity of the predicted MS-CETSA data from our proposed CycleDNN through validation in protein-protein interaction prediction.
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Affiliation(s)
- Shenghao Zhao
- Institute for Infocomm Research (I2R), A*STAR, Singapore, 138632, Singapore
- National University of Singapore (NUS), Singapore, 119077, Singapore
| | - Xulei Yang
- Institute for Infocomm Research (I2R), A*STAR, Singapore, 138632, Singapore.
| | - Zeng Zeng
- Institute for Infocomm Research (I2R), A*STAR, Singapore, 138632, Singapore
| | - Peisheng Qian
- Institute for Infocomm Research (I2R), A*STAR, Singapore, 138632, Singapore
| | - Ziyuan Zhao
- Institute for Infocomm Research (I2R), A*STAR, Singapore, 138632, Singapore
| | - Lingyun Dai
- Institute of Molecular and Cell Biology (IMCB), A*STAR, Singapore, 138632, Singapore
- The Second Clinical Medical College of Jinan University, The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen People's Hospital, Shenzhen, 518020, China
| | - Nayana Prabhu
- Institute of Molecular and Cell Biology (IMCB), A*STAR, Singapore, 138632, Singapore
| | - Pär Nordlund
- Institute of Molecular and Cell Biology (IMCB), A*STAR, Singapore, 138632, Singapore
- Department of Oncology and Pathology, Karolinska Institutet, 171 77, Stockholm, Sweden
| | - Wai Leong Tam
- Genome Institute of Singapore (GIS), A*STAR, Singapore, 138632, Singapore.
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6
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Qu S, Nelson H, Liu X, Semler E, Michell DL, Massick C, Franklin JL, Karijolich J, Weaver AM, Coffey RJ, Liu Q, Vickers KC, Patton JG. 5-Fluorouracil Treatment Represses Pseudouridine-Containing Small RNA Export into Extracellular Vesicles. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.15.575751. [PMID: 38293013 PMCID: PMC10827090 DOI: 10.1101/2024.01.15.575751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
5-fluorouracil (5-FU) has been used for chemotherapy for colorectal and other cancers for over 50 years. The prevailing view of its mechanism of action is inhibition of thymidine synthase leading to defects in DNA replication and repair. However, 5-FU is also incorporated into RNA causing toxicity due to defects in RNA metabolism, inhibition of pseudouridine modification, and altered ribosome function. Here, we examine the impact of 5-FU on the expression and export of small RNAs (sRNAs) into small extracellular vesicles (sEVs). Moreover, we assess the role of 5-FU in regulation of post-transcriptional sRNA modifications (PTxM) using mass spectrometry approaches. EVs are secreted by all cells and contain a variety of proteins and RNAs that can function in cell-cell communication. PTxMs on cellular and extracellular sRNAs provide yet another layer of gene regulation. We found that treatment of the colorectal cancer (CRC) cell line DLD-1 with 5-FU led to surprising differential export of miRNA snRNA, and snoRNA transcripts. Strikingly, 5-FU treatment significantly decreased the levels of pseudouridine on both cellular and secreted EV sRNAs. In contrast, 5-FU exposure led to increased levels of cellular sRNAs containing a variety of methyl-modified bases. Our results suggest that 5-FU exposure leads to altered expression, base modifications, and mislocalization of EV base-modified sRNAs.
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7
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Rudd SG. Targeting pan-essential pathways in cancer with cytotoxic chemotherapy: challenges and opportunities. Cancer Chemother Pharmacol 2023; 92:241-251. [PMID: 37452860 PMCID: PMC10435635 DOI: 10.1007/s00280-023-04562-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 06/22/2023] [Indexed: 07/18/2023]
Abstract
Cytotoxic chemotherapy remains a key modality in cancer treatment. These therapies, successfully used for decades, continue to transform the lives of cancer patients daily. With the high attrition rate of current oncology drug development, combined with the knowledge that most new therapies do not displace standard-of-care treatments and that many healthcare systems cannot afford these new therapies; cytotoxic chemotherapies will remain an important component of cancer therapy for many years to come. The clinical value of these therapies is often under-appreciated within the pre-clinical cancer research community, where this diverse class of agents are often grouped together as non-specific cellular poisons killing tumor cells based solely upon proliferation rate; however, this is inaccurate. This review article seeks to reaffirm the importance of focusing research efforts upon improving our basic understanding of how these drugs work, discussing their ability to target pan-essential pathways in cancer cells, the relationship of this to the chemotherapeutic window, and highlighting basic science approaches that can be employed towards refining their use.
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Affiliation(s)
- Sean G Rudd
- Science For Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden.
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8
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Pang Y, Chen X, Xu B, Zhang Y, Liang S, Hu J, Liu R, Luo X, Wang Y. Engineered multitargeting exosomes carrying miR-323a-3p for CRC therapy. Int J Biol Macromol 2023; 247:125794. [PMID: 37442504 DOI: 10.1016/j.ijbiomac.2023.125794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 07/03/2023] [Accepted: 07/09/2023] [Indexed: 07/15/2023]
Abstract
Colorectal cancer (CRC) is in the forefront of malignancies for its high incidence and mortality. 5-Fluorouracil (5-FU) is one of the most widely used effective drugs for the treatment of CRC. However, there is an urgent need in reducing its systemic side effects and chemoresistance, in order to make 5-FU-based chemotherapy more effective in the treatment of CRC. In this study, engineered CRC cells were established to overexpress miR-323a-3p, which was a tumor suppressor that targeted both EGFR and TYMS. Then miR-323a-3p-loaded exosomes (miR-Exo) were obtained with suitable methods of collection and purification. We found that miR-Exo significantly inhibited CRC cell proliferation and induced apoptosis by the way of targeting EGFR directly in the cells, which eventually led to desirable tumor regression in the cell derived xenograft (CDX) and patient derived xenograft (PDX) tumor mice models. Moreover, we discovered that miR-323a-3p released from miR-Exo directly inhibited the upregulation of thymidylate synthase (TYMS) induced by 5-FU-resistence in CRC cells, resulting in the revival of tumor cytotoxicity from 5-FU. MiR-Exo could effectively induce the CRC cell apoptosis by targeting EGFR and TYMS, and enhance the therapeutic effects of 5-FU on CRC. Our work demonstrates the potency of miR-Exo for advanced CRC biotherapy.
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Affiliation(s)
- Yechun Pang
- Department of General Surgery, Pudong New Area People's Hospital, China; State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xingshi Chen
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Baiying Xu
- Department of General Surgery, Pudong New Area People's Hospital, China
| | - Yuanzhou Zhang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shunshun Liang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jingying Hu
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Rui Liu
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Xiaoying Luo
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Yunfeng Wang
- Department of General Surgery, Pudong New Area People's Hospital, China.
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9
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Chen JK, Merrick KA, Kong YW, Izrael-Tomasevic A, Eng G, Handly ED, Patterson JC, Cannell IG, Suarez-Lopez L, Hosios AM, Dinh A, Kirkpatrick DS, Yu K, Rose CM, Hernandez JM, Hwangbo H, Palmer AC, Vander Heiden MG, Yilmaz ÖH, Yaffe MB. An RNA Damage Response Network Mediates the Lethality of 5-FU in Clinically Relevant Tumor Types. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.28.538590. [PMID: 37162991 PMCID: PMC10168374 DOI: 10.1101/2023.04.28.538590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
5-fluorouracil (5-FU) is a successful and broadly used anti-cancer therapeutic. A major mechanism of action of 5-FU is thought to be through thymidylate synthase (TYMS) inhibition resulting in dTTP depletion and activation of the DNA damage response. This suggests that 5-FU should synergize with other DNA damaging agents. However, we found that combinations of 5-FU and oxaliplatin or irinotecan failed to display any evidence of synergy in clinical trials, and resulted in sub-additive killing in a panel of colorectal cancer (CRC) cell lines. In seeking to understand this antagonism, we unexpectedly found that an RNA damage response during ribosome biogenesis dominates the drug's efficacy in tumor types for which 5-FU shows clinical benefit. 5-FU has an inherent bias for RNA incorporation, and blocking this greatly reduced drug-induced lethality, indicating that accumulation of damaged RNA is more deleterious than the lack of new RNA synthesis. Using 5-FU metabolites that specifically incorporate into either RNA or DNA revealed that CRC cell lines and patient-derived colorectal cancer organoids are inherently more sensitive to RNA damage. This difference held true in cell lines from other tissues in which 5-FU has shown clinical utility, whereas cell lines from tumor tissues that lack clinical 5-FU responsiveness typically showed greater sensitivity to the drug's DNA damage effects. Analysis of changes in the phosphoproteome and ubiquitinome shows RNA damage triggers the selective ubiquitination of multiple ribosomal proteins leading to autophagy-dependent rRNA catabolism and proteasome-dependent degradation of ubiquitinated ribosome proteins. Further, RNA damage response to 5-FU is selectively enhanced by compounds that promote ribosome biogenesis, such as KDM2A inhibitors. These results demonstrate the presence of a strong RNA damage response linked to apoptotic cell death, with clear utility of combinatorially targeting this response in cancer therapy.
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Affiliation(s)
- Jung-Kuei Chen
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Karl A. Merrick
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Yi Wen Kong
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | - George Eng
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Erika D. Handly
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jesse C. Patterson
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ian G. Cannell
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Lucia Suarez-Lopez
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Aaron M. Hosios
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Anh Dinh
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | - Kebing Yu
- Genentech Biotechnology company, South San Francisco, CA 94080, USA
| | | | - Jonathan M. Hernandez
- Surgical Oncology Program, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Haeun Hwangbo
- Curriculum in Bioinformatics and Computational Biology, UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Pharmacology, Computational Medicine Program, and UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Adam C. Palmer
- Department of Pharmacology, Computational Medicine Program, and UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Matthew G. Vander Heiden
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA 02215, USA
| | - Ömer H. Yilmaz
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Michael B. Yaffe
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Surgery, Beth Israel Medical Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
- Surgical Oncology Program, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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10
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Palomar-Siles M, Heldin A, Zhang M, Strandgren C, Yurevych V, van Dinter JT, Engels SAG, Hofman DA, Öhlin S, Meineke B, Bykov VJN, van Heesch S, Wiman KG. Translational readthrough of nonsense mutant TP53 by mRNA incorporation of 5-Fluorouridine. Cell Death Dis 2022; 13:997. [PMID: 36433934 PMCID: PMC9700717 DOI: 10.1038/s41419-022-05431-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 11/08/2022] [Accepted: 11/10/2022] [Indexed: 11/27/2022]
Abstract
TP53 nonsense mutations in cancer produce truncated inactive p53 protein. We show that 5-FU metabolite 5-Fluorouridine (FUr) induces full-length p53 in human tumor cells carrying R213X nonsense mutant TP53. Ribosome profiling visualized translational readthrough at the R213X premature stop codon and demonstrated that FUr-induced readthrough is less permissive for canonical stop codon readthrough compared to aminoglycoside G418. FUr is incorporated into mRNA and can potentially base-pair with guanine, allowing insertion of Arg tRNA at the TP53 R213X UGA premature stop codon and translation of full-length wild-type p53. We confirmed that full-length p53 rescued by FUr triggers tumor cell death by apoptosis. FUr also restored full-length p53 in TP53 R213X mutant human tumor xenografts in vivo. Thus, we demonstrate a novel strategy for therapeutic rescue of nonsense mutant TP53 and suggest that FUr should be explored for treatment of patients with TP53 nonsense mutant tumors.
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Affiliation(s)
- Mireia Palomar-Siles
- grid.4714.60000 0004 1937 0626Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Angelos Heldin
- grid.4714.60000 0004 1937 0626Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Meiqiongzi Zhang
- grid.4714.60000 0004 1937 0626Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Charlotte Strandgren
- grid.4714.60000 0004 1937 0626Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Viktor Yurevych
- grid.487647.ePrincess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Jip T. van Dinter
- grid.487647.ePrincess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Sem A. G. Engels
- grid.487647.ePrincess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Damon A. Hofman
- grid.487647.ePrincess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Susanne Öhlin
- grid.4714.60000 0004 1937 0626Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Birthe Meineke
- grid.4714.60000 0004 1937 0626Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Vladimir J. N. Bykov
- grid.4714.60000 0004 1937 0626Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Sebastiaan van Heesch
- grid.487647.ePrincess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Klas G. Wiman
- grid.4714.60000 0004 1937 0626Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
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11
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Abstract
Knowing that the drug candidate binds to its intended target is a vital part of drug discovery. Thus, several labeled and label-free methods have been developed to study target engagement. In recent years, the cellular thermal shift assay (CETSA) with its variations has been widely adapted to drug discovery workflows. Western blot–based CETSA is used primarily to validate the target binding of a molecule to its target protein whereas CETSA based on bead chemistry detection methods (CETSA HT) has been used to screen molecular libraries to find novel molecules binding to a pre-determined target. Mass spectrometry–based CETSA also known as thermal proteome profiling (TPP) has emerged as a powerful tool for target deconvolution and finding novel binding partners for old and novel molecules. With this technology, it is possible to probe thermal shifts among over 7,000 proteins from one sample and to identify the wanted target binding but also binding to unwanted off-targets known to cause adverse effects. In addition, this proteome-wide method can provide information on the biological process initiated by the ligand binding. The continued development of mass spectrometry labeling reagents, such as isobaric tandem mass tag technology (TMT) continues to increase the throughput of CETSA MS, allowing its use for structure–activity relationship (SAR) studies with a limited number of molecules. In this review, we discussed the differences between different label-free methods to study target engagement, but our focus was on CETSA and recent advances in the CETSA method.
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Affiliation(s)
- Tuomas Aleksi Tolvanen
- Division of Rheumatology, Department of Medicine Solna, Karolinska University Hospital and Karolinska Institute, Stockholm, Sweden.,Pelago Bioscience AB, Solna, Sweden
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Targeting Ribosome Biogenesis in Cancer: Lessons Learned and Way Forward. Cancers (Basel) 2022; 14:cancers14092126. [PMID: 35565259 PMCID: PMC9100539 DOI: 10.3390/cancers14092126] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 04/18/2022] [Accepted: 04/22/2022] [Indexed: 01/05/2023] Open
Abstract
Simple Summary Cells need to produce ribosomes to sustain continuous proliferation and expand in numbers, a feature that is even more prominent in uncontrollably proliferating cancer cells. Certain cancer cell types are expected to depend more on ribosome biogenesis based on their genetic background, and this potential vulnerability can be exploited in designing effective, targeted cancer therapies. This review provides information on anti-cancer molecules that target the ribosome biogenesis machinery and indicates avenues for future research. Abstract Rapid growth and unrestrained proliferation is a hallmark of many cancers. To accomplish this, cancer cells re-wire and increase their biosynthetic and metabolic activities, including ribosome biogenesis (RiBi), a complex, highly energy-consuming process. Several chemotherapeutic agents used in the clinic impair this process by interfering with the transcription of ribosomal RNA (rRNA) in the nucleolus through the blockade of RNA polymerase I or by limiting the nucleotide building blocks of RNA, thereby ultimately preventing the synthesis of new ribosomes. Perturbations in RiBi activate nucleolar stress response pathways, including those controlled by p53. While compounds such as actinomycin D and oxaliplatin effectively disrupt RiBi, there is an ongoing effort to improve the specificity further and find new potent RiBi-targeting compounds with improved pharmacological characteristics. A few recently identified inhibitors have also become popular as research tools, facilitating our advances in understanding RiBi. Here we provide a comprehensive overview of the various compounds targeting RiBi, their mechanism of action, and potential use in cancer therapy. We discuss screening strategies, drug repurposing, and common problems with compound specificity and mechanisms of action. Finally, emerging paths to discovery and avenues for the development of potential biomarkers predictive of therapeutic outcomes across cancer subtypes are also presented.
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NMS-873 Leads to Dysfunctional Glycometabolism in A p97-Independent Manner in HCT116 Colon Cancer Cells. Pharmaceutics 2022; 14:pharmaceutics14040764. [PMID: 35456598 PMCID: PMC9024726 DOI: 10.3390/pharmaceutics14040764] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 03/24/2022] [Accepted: 03/26/2022] [Indexed: 12/28/2022] Open
Abstract
Adenosine triphosphate (ATP)–competitive p97 inhibitor CB-5339, the successor of CB-5083, is being evaluated in Phase 1 clinical trials for anti-cancer therapy. Different modes-of-action p97 inhibitors such as allosteric inhibitors are useful to overcome drug-induced resistance, one of the major problems of targeted therapy. We previously demonstrated that allosteric p97 inhibitor NMS-873 can overcome CB-5083-induced resistance in HCT116. Here we employed chemical proteomics and drug-induced thermal proteome changes to identify drug targets, in combination with drug-resistant cell lines to dissect on- and off-target effects. We found that NMS-873 but not CB-5083 affected glycometabolism. By establishing NMS-873-resistant HCT116 cell lines and performing both cell-based and proteomic analysis, we confirmed that NMS-873 dysregulates glycometabolism in a p97-independent manner. We then used proteome integral solubility alteration with a temperature-based method (PISA T) to identify NDUFAF5 as one of the potential targets of NMS-873 in the mitochondrial complex I. We also demonstrated that glycolysis inhibitor 2-DG enhanced the anti-proliferative effect of NMS-873. The polypharmacology of NMS-873 can be advantageous for anti-cancer therapy for colon cancer.
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