1
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Krenz B, Lee J, Kannan T, Eilers M. Immune evasion: An imperative and consequence of MYC deregulation. Mol Oncol 2024; 18:2338-2355. [PMID: 38957016 PMCID: PMC11459038 DOI: 10.1002/1878-0261.13695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 05/08/2024] [Accepted: 06/19/2024] [Indexed: 07/04/2024] Open
Abstract
MYC has been implicated in the pathogenesis of a wide range of human tumors and has been described for many years as a transcription factor that regulates genes with pleiotropic functions to promote tumorigenic growth. However, despite extensive efforts to identify specific target genes of MYC that alone could be responsible for promoting tumorigenesis, the field is yet to reach a consensus whether this is the crucial function of MYC. Recent work shifts the view on MYC's function from being a gene-specific transcription factor to an essential stress resilience factor. In highly proliferating cells, MYC preserves cell integrity by promoting DNA repair at core promoters, protecting stalled replication forks, and/or preventing transcription-replication conflicts. Furthermore, an increasing body of evidence demonstrates that MYC not only promotes tumorigenesis by driving cell-autonomous growth, but also enables tumors to evade the host's immune system. In this review, we summarize our current understanding of how MYC impairs antitumor immunity and why this function is evolutionarily hard-wired to the biology of the MYC protein family. We show why the cell-autonomous and immune evasive functions of MYC are mutually dependent and discuss ways to target MYC proteins in cancer therapy.
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Affiliation(s)
- Bastian Krenz
- Department of Biochemistry and Molecular BiologyTheodor Boveri Institute, Biocenter, University of WürzburgWürzburgGermany
- Mildred Scheel Early Career CenterWürzburgGermany
| | - Jongkuen Lee
- Department of Biochemistry and Molecular BiologyTheodor Boveri Institute, Biocenter, University of WürzburgWürzburgGermany
| | - Toshitha Kannan
- Department of Biochemistry and Molecular BiologyTheodor Boveri Institute, Biocenter, University of WürzburgWürzburgGermany
| | - Martin Eilers
- Department of Biochemistry and Molecular BiologyTheodor Boveri Institute, Biocenter, University of WürzburgWürzburgGermany
- Comprehensive Cancer Center MainfrankenWürzburgGermany
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2
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Hluchý M, Blazek D. CDK11, a splicing-associated kinase regulating gene expression. Trends Cell Biol 2024:S0962-8924(24)00161-2. [PMID: 39245599 DOI: 10.1016/j.tcb.2024.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 08/11/2024] [Accepted: 08/12/2024] [Indexed: 09/10/2024]
Abstract
The ability of a cell to properly express its genes depends on optimal transcription and splicing. RNA polymerase II (RNAPII) transcribes protein-coding genes and produces pre-mRNAs, which undergo, largely co-transcriptionally, intron excision by the spliceosome complex. Spliceosome activation is a major control step, leading to a catalytically active complex. Recent work has showed that cyclin-dependent kinase (CDK)11 regulates spliceosome activation via the phosphorylation of SF3B1, a core spliceosome component. Thus, CDK11 arises as a major coordinator of gene expression in metazoans due to its role in the rate-limiting step of pre-mRNA splicing. This review outlines the evolution of CDK11 and SF3B1 and their emerging roles in splicing regulation. It also discusses how CDK11 and its inhibition affect transcription and cell cycle progression.
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Affiliation(s)
- Milan Hluchý
- Central European Institute of Technology (CEITEC), Masaryk University, 62500 Brno, Czech Republic
| | - Dalibor Blazek
- Central European Institute of Technology (CEITEC), Masaryk University, 62500 Brno, Czech Republic.
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3
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Lanfranchi M, Yandiev S, Meyer-Dilhet G, Ellouze S, Kerkhofs M, Dos Reis R, Garcia A, Blondet C, Amar A, Kneppers A, Polvèche H, Plassard D, Foretz M, Viollet B, Sakamoto K, Mounier R, Bourgeois CF, Raineteau O, Goillot E, Courchet J. The AMPK-related kinase NUAK1 controls cortical axons branching by locally modulating mitochondrial metabolic functions. Nat Commun 2024; 15:2487. [PMID: 38514619 PMCID: PMC10958033 DOI: 10.1038/s41467-024-46146-6] [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: 03/25/2023] [Accepted: 02/15/2024] [Indexed: 03/23/2024] Open
Abstract
The cellular mechanisms underlying axonal morphogenesis are essential to the formation of functional neuronal networks. We previously identified the autism-linked kinase NUAK1 as a central regulator of axon branching through the control of mitochondria trafficking. However, (1) the relationship between mitochondrial position, function and axon branching and (2) the downstream effectors whereby NUAK1 regulates axon branching remain unknown. Here, we report that mitochondria recruitment to synaptic boutons supports collateral branches stabilization rather than formation in mouse cortical neurons. NUAK1 deficiency significantly impairs mitochondrial metabolism and axonal ATP concentration, and upregulation of mitochondrial function is sufficient to rescue axonal branching in NUAK1 null neurons in vitro and in vivo. Finally, we found that NUAK1 regulates axon branching through the mitochondria-targeted microprotein BRAWNIN. Our results demonstrate that NUAK1 exerts a dual function during axon branching through its ability to control mitochondrial distribution and metabolic activity.
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Affiliation(s)
- Marine Lanfranchi
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Inserm, Physiopathologie et Génétique du Neurone et du Muscle, UMR5261, U1315, Institut NeuroMyoGène, 69008, Lyon, France
| | - Sozerko Yandiev
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Inserm, Physiopathologie et Génétique du Neurone et du Muscle, UMR5261, U1315, Institut NeuroMyoGène, 69008, Lyon, France
| | - Géraldine Meyer-Dilhet
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Inserm, Physiopathologie et Génétique du Neurone et du Muscle, UMR5261, U1315, Institut NeuroMyoGène, 69008, Lyon, France
| | - Salma Ellouze
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Inserm, Physiopathologie et Génétique du Neurone et du Muscle, UMR5261, U1315, Institut NeuroMyoGène, 69008, Lyon, France
- Univ Lyon, Université Claude Bernard Lyon 1, Inserm, Stem Cell and Brain Research Institute U1208, 69500, Bron, France
| | - Martijn Kerkhofs
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Inserm, Physiopathologie et Génétique du Neurone et du Muscle, UMR5261, U1315, Institut NeuroMyoGène, 69008, Lyon, France
| | - Raphael Dos Reis
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Inserm, Physiopathologie et Génétique du Neurone et du Muscle, UMR5261, U1315, Institut NeuroMyoGène, 69008, Lyon, France
| | - Audrey Garcia
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Inserm, Physiopathologie et Génétique du Neurone et du Muscle, UMR5261, U1315, Institut NeuroMyoGène, 69008, Lyon, France
| | - Camille Blondet
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Inserm, Physiopathologie et Génétique du Neurone et du Muscle, UMR5261, U1315, Institut NeuroMyoGène, 69008, Lyon, France
| | - Alizée Amar
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Inserm, Physiopathologie et Génétique du Neurone et du Muscle, UMR5261, U1315, Institut NeuroMyoGène, 69008, Lyon, France
| | - Anita Kneppers
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Inserm, Physiopathologie et Génétique du Neurone et du Muscle, UMR5261, U1315, Institut NeuroMyoGène, 69008, Lyon, France
| | - Hélène Polvèche
- Laboratoire de Biologie et Modelisation de la Cellule, Ecole Normale Superieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Universite Claude Bernard Lyon 1, 46 allée d'Italie F-69364, Lyon, France
- CECS/AFM, I-STEM, 28 rue Henri Desbruères, F-91100, Corbeil-Essonnes, France
| | - Damien Plassard
- CNRS UMR 7104, INSERM U1258, GenomEast Platform, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg, Illkirch, France
| | - Marc Foretz
- Université Paris Cité, CNRS, Inserm, Institut Cochin, Paris, France
| | - Benoit Viollet
- Université Paris Cité, CNRS, Inserm, Institut Cochin, Paris, France
| | - Kei Sakamoto
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Rémi Mounier
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Inserm, Physiopathologie et Génétique du Neurone et du Muscle, UMR5261, U1315, Institut NeuroMyoGène, 69008, Lyon, France
| | - Cyril F Bourgeois
- Laboratoire de Biologie et Modelisation de la Cellule, Ecole Normale Superieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Universite Claude Bernard Lyon 1, 46 allée d'Italie F-69364, Lyon, France
| | - Olivier Raineteau
- Univ Lyon, Université Claude Bernard Lyon 1, Inserm, Stem Cell and Brain Research Institute U1208, 69500, Bron, France
| | - Evelyne Goillot
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Inserm, Physiopathologie et Génétique du Neurone et du Muscle, UMR5261, U1315, Institut NeuroMyoGène, 69008, Lyon, France
| | - Julien Courchet
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Inserm, Physiopathologie et Génétique du Neurone et du Muscle, UMR5261, U1315, Institut NeuroMyoGène, 69008, Lyon, France.
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4
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Liang H, Luo R, Li G, Zhang W, Zhu D, Wu D, Zhou X, Tong B, Wang B, Feng X, Wang K, Song Y, Yang C. Lysine methylation of PPP1CA by the methyltransferase SUV39H2 disrupts TFEB-dependent autophagy and promotes intervertebral disc degeneration. Cell Death Differ 2023; 30:2135-2150. [PMID: 37605006 PMCID: PMC10482945 DOI: 10.1038/s41418-023-01210-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 08/02/2023] [Accepted: 08/08/2023] [Indexed: 08/23/2023] Open
Abstract
Impaired transcription factor EB (TFEB) function and deficient autophagy activity have been shown to aggravate intervertebral disc (IVD) degeneration (IDD), yet the underlying mechanisms remain less clear. Protein posttranslational modifications (PTMs) are critical for determining TFEB trafficking and transcriptional activity. Here, we demonstrate that TFEB activity is controlled by protein methylation in degenerated nucleus pulposus cells (NPCs), even though TFEB itself is incapable of undergoing methylation. Specifically, protein phosphatase 1 catalytic subunit alpha (PPP1CA), newly identified to dephosphorylate TFEB, contains a K141 mono-methylated site. In degenerated NPCs, increased K141-methylation of PPP1CA disrupts its interaction with TEFB and subsequently blocks TEFB dephosphorylation and nuclear translocation, which eventually leads to autophagy deficiency and NPC senescence. In addition, we found that the PPP1CA-mediated targeting of TFEB is facilitated by the protein phosphatase 1 regulatory subunit 9B (PPP1R9B), which binds with PPP1CA and is also manipulated by K141 methylation. Further proteomic analysis revealed that the protein lysine methyltransferase suppressor of variegation 3-9 homologue 2 (SUV39H2) is responsible for the K141 mono-methylation of PPP1CA. Targeting SUV39H2 effectively mitigates NPC senescence and IDD progression, providing a potential therapeutic strategy for IDD intervention.
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Affiliation(s)
- Huaizhen Liang
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Rongjin Luo
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
- Department of Spine Surgery, Honghui Hospital, Xi'an Jiaotong University, Xi'an, 710054, China
| | - Gaocai Li
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Weifeng Zhang
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Dingchao Zhu
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Di Wu
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Xingyu Zhou
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Bide Tong
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Bingjin Wang
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Xiaobo Feng
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Kun Wang
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Yu Song
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
| | - Cao Yang
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
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5
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Roy A, Sakthikumar S, Kozyrev SV, Nordin J, Pensch R, Mäkeläinen S, Pettersson M, Karlsson EK, Lindblad-Toh K, Forsberg-Nilsson K. Using evolutionary constraint to define novel candidate driver genes in medulloblastoma. Proc Natl Acad Sci U S A 2023; 120:e2300984120. [PMID: 37549291 PMCID: PMC10438395 DOI: 10.1073/pnas.2300984120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 07/07/2023] [Indexed: 08/09/2023] Open
Abstract
Current knowledge of cancer genomics remains biased against noncoding mutations. To systematically search for regulatory noncoding mutations, we assessed mutations in conserved positions in the genome under the assumption that these are more likely to be functional than mutations in positions with low conservation. To this end, we use whole-genome sequencing data from the International Cancer Genome Consortium and combined it with evolutionary constraint inferred from 240 mammals, to identify genes enriched in noncoding constraint mutations (NCCMs), mutations likely to be regulatory in nature. We compare medulloblastoma (MB), which is malignant, to pilocytic astrocytoma (PA), a primarily benign tumor, and find highly different NCCM frequencies between the two, in agreement with the fact that malignant cancers tend to have more mutations. In PA, a high NCCM frequency only affects the BRAF locus, which is the most commonly mutated gene in PA. In contrast, in MB, >500 genes have high levels of NCCMs. Intriguingly, several loci with NCCMs in MB are associated with different ages of onset, such as the HOXB cluster in young MB patients. In adult patients, NCCMs occurred in, e.g., the WASF-2/AHDC1/FGR locus. One of these NCCMs led to increased expression of the SRC kinase FGR and augmented responsiveness of MB cells to dasatinib, a SRC kinase inhibitor. Our analysis thus points to different molecular pathways in different patient groups. These newly identified putative candidate driver mutations may aid in patient stratification in MB and could be valuable for future selection of personalized treatment options.
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Affiliation(s)
- Ananya Roy
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, 751 85Uppsala, Sweden
| | - Sharadha Sakthikumar
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 751 23Uppsala, Sweden
- Broad Institute, Cambridge, MA02142
| | - Sergey V. Kozyrev
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 751 23Uppsala, Sweden
| | - Jessika Nordin
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, 751 85Uppsala, Sweden
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 751 23Uppsala, Sweden
| | - Raphaela Pensch
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 751 23Uppsala, Sweden
| | - Suvi Mäkeläinen
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 751 23Uppsala, Sweden
| | - Mats Pettersson
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 751 23Uppsala, Sweden
| | | | - Elinor K. Karlsson
- Broad Institute, Cambridge, MA02142
- Program in Molecular Medicine, UMass Chan Medical School, Worcester, MA01605
- Program in Bioinformatics and Integrative Biology, UMass Chan Medical School, Worcester, MA01605
| | - Kerstin Lindblad-Toh
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 751 23Uppsala, Sweden
- Broad Institute, Cambridge, MA02142
| | - Karin Forsberg-Nilsson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, 751 85Uppsala, Sweden
- Division of Cancer and Stem Cells, University of Nottingham Biodiscovery Institute, NottinghamNG72RD, United Kingdom
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6
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Whyte D, Skalka G, Walsh P, Wilczynska A, Paul NR, Mitchell C, Nixon C, Clarke W, Bushell M, Morton JP, Murphy DJ, Muthalagu N. NUAK1 governs centrosome replication in pancreatic cancer via MYPT1/PP1β and GSK3β-dependent regulation of PLK4. Mol Oncol 2023; 17:1212-1227. [PMID: 36975767 PMCID: PMC10323901 DOI: 10.1002/1878-0261.13425] [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: 12/06/2022] [Revised: 03/08/2023] [Accepted: 03/24/2023] [Indexed: 03/29/2023] Open
Abstract
The AMP-activated protein kinase (AMPK)-related kinase NUAK1 (NUAK family SNF1-like kinase 1) has emerged as a potential vulnerability in MYC-dependent cancer but the biological roles of NUAK1 in different settings are poorly characterised, and the spectrum of cancer types that exhibit a requirement for NUAK1 is unknown. Unlike canonical oncogenes, NUAK1 is rarely mutated in cancer and appears to function as an obligate facilitator rather than a cancer driver per se. Although numerous groups have developed small-molecule NUAK inhibitors, the circumstances that would trigger their use and the unwanted toxicities that may arise as a consequence of on-target activity are thus undetermined. Reasoning that MYC is a key effector of RAS pathway signalling and the GTPase KRAS is almost uniformly mutated in pancreatic ductal adenocarcinoma (PDAC), we investigated whether this cancer type exhibits a functional requirement for NUAK1. Here, we show that high NUAK1 expression is associated with reduced overall survival in PDAC and that inhibition or depletion of NUAK1 suppresses growth of PDAC cells in culture. We identify a previously unknown role for NUAK1 in regulating accurate centrosome duplication and show that loss of NUAK1 triggers genomic instability. The latter activity is conserved in primary fibroblasts, raising the possibility of undesirable genotoxic effects of NUAK1 inhibition.
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Affiliation(s)
- Declan Whyte
- School of Cancer SciencesUniversity of GlasgowUK
- CRUK Beatson InstituteGlasgowUK
| | - George Skalka
- School of Cancer SciencesUniversity of GlasgowUK
- CRUK Beatson InstituteGlasgowUK
| | - Peter Walsh
- School of Cancer SciencesUniversity of GlasgowUK
- CRUK Beatson InstituteGlasgowUK
| | | | | | | | | | | | - Martin Bushell
- School of Cancer SciencesUniversity of GlasgowUK
- CRUK Beatson InstituteGlasgowUK
| | - Jennifer P. Morton
- School of Cancer SciencesUniversity of GlasgowUK
- CRUK Beatson InstituteGlasgowUK
| | - Daniel J. Murphy
- School of Cancer SciencesUniversity of GlasgowUK
- CRUK Beatson InstituteGlasgowUK
| | - Nathiya Muthalagu
- School of Cancer SciencesUniversity of GlasgowUK
- CRUK Beatson InstituteGlasgowUK
- Present address:
Indian Institute of TechnologyMadrasIndia
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7
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Wang T, Zhao R, Zhi J, Liu Z, Wu A, Yang Z, Wang W, Ni T, Jing L, Yu M. Tox4 regulates transcriptional elongation and reinitiation during murine T cell development. Commun Biol 2023; 6:613. [PMID: 37286708 DOI: 10.1038/s42003-023-04992-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Accepted: 05/30/2023] [Indexed: 06/09/2023] Open
Abstract
HMG protein Tox4 is a regulator of PP1 phosphatases with unknown function in development. Here we show that Tox4 conditional knockout in mice reduces thymic cellularity, partially blocks T cell development, and decreases ratio of CD8 to CD4 through decreasing proliferation and increasing apoptosis of CD8 cells. In addition, single-cell RNA-seq discovered that Tox4 loss also impairs proliferation of the fast-proliferating double positive (DP) blast population within DP cells in part due to downregulation of genes critical for proliferation, notably Cdk1. Moreover, genes with high and low expression level are more dependent on Tox4 than genes with medium expression level. Mechanistically, Tox4 may facilitate transcriptional reinitiation and restrict elongation in a dephosphorylation-dependent manner, a mechanism that is conserved between mouse and human. These results provide insights into the role of TOX4 in development and establish it as an evolutionarily conserved regulator of transcriptional elongation and reinitiation.
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Affiliation(s)
- Talang Wang
- Sheng Yushou Center of Cell Biology and Immunology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Ruoyu Zhao
- Sheng Yushou Center of Cell Biology and Immunology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Department of Pathology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, 200052, China
| | - Junhong Zhi
- Sheng Yushou Center of Cell Biology and Immunology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Ziling Liu
- Sheng Yushou Center of Cell Biology and Immunology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Aiwei Wu
- Sheng Yushou Center of Cell Biology and Immunology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Zimei Yang
- Sheng Yushou Center of Cell Biology and Immunology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Weixu Wang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Sciences and Huashan Hospital, Fudan University, Shanghai, 200438, China
| | - Ting Ni
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Sciences and Huashan Hospital, Fudan University, Shanghai, 200438, China
| | - Lili Jing
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Ming Yu
- Sheng Yushou Center of Cell Biology and Immunology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
- Department of Pathology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, 200052, China.
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8
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Yang L, Zhang Y, Zhang Y, Fan Z. Mechanism and application of ferroptosis in colorectal cancer. Biomed Pharmacother 2023; 158:114102. [PMID: 36528917 DOI: 10.1016/j.biopha.2022.114102] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 11/10/2022] [Accepted: 12/05/2022] [Indexed: 12/23/2022] Open
Abstract
Colorectal cancer (CRC) is the third most common malignant tumor in the world. CRC has high morbidity and mortality rates and it is a serious threat to human health. Ferroptosis is a unique form of iron-dependent oxidative cell death that is usually accompanied by iron accumulation and lipid peroxidation. Ferroptosis has attracted worldwide attention since it was first proposed. It plays an important role in the development of a variety of diseases, such as tumors, ischemia/reperfusion injury, nervous system diseases, and kidney damage, and it may serve as a new therapeutic target. This article reviews the mechanism of ferroptosis and the possibility to target ferroptosis pathways in CRC, providing new ideas for the diagnosis and treatment of CRC.
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Affiliation(s)
- Liu Yang
- Department of General Surgery, The Third People's Hospital of Dalian, Dalian Medical University, Dalian, China; Department of Central Laboratory, The Third People's Hospital of Dalian, Dalian Medical University, Dalian, China; Liaoning Province Key Laboratory of Corneal and Ocular Surface Diseases Research, The Third People's Hospital of Dalian, Dalian, China
| | - Yewei Zhang
- Department of General Surgery, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China.
| | - Yingyi Zhang
- Department of General Surgery, The Third People's Hospital of Dalian, Dalian Medical University, Dalian, China; Department of Central Laboratory, The Third People's Hospital of Dalian, Dalian Medical University, Dalian, China; Liaoning Province Key Laboratory of Corneal and Ocular Surface Diseases Research, The Third People's Hospital of Dalian, Dalian, China.
| | - Zhe Fan
- Department of General Surgery, The Third People's Hospital of Dalian, Dalian Medical University, Dalian, China; Department of Central Laboratory, The Third People's Hospital of Dalian, Dalian Medical University, Dalian, China; Liaoning Province Key Laboratory of Corneal and Ocular Surface Diseases Research, The Third People's Hospital of Dalian, Dalian, China.
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9
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The PNUTS-PP1 complex acts as an intrinsic barrier to herpesvirus KSHV gene expression and replication. Nat Commun 2022; 13:7447. [PMID: 36460671 PMCID: PMC9718767 DOI: 10.1038/s41467-022-35268-4] [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: 05/12/2022] [Accepted: 11/24/2022] [Indexed: 12/03/2022] Open
Abstract
Control of RNA Polymerase II (pol II) elongation is a critical component of gene expression in mammalian cells. The PNUTS-PP1 complex controls elongation rates, slowing pol II after polyadenylation sites to promote termination. The Kaposi's sarcoma-associated herpesvirus (KSHV) co-opts pol II to express its genes, but little is known about its regulation of pol II elongation. We identified PNUTS as a suppressor of a KSHV reporter gene in a genome-wide CRISPR screen. PNUTS depletion enhances global KSHV gene expression and overall viral replication. Mechanistically, PNUTS requires PP1 interaction, binds viral RNAs downstream of polyadenylation sites, and restricts transcription readthrough of viral genes. Surprisingly, PNUTS also represses productive elongation at the 5´ ends of the KSHV reporter and the KSHV T1.4 RNA. From these data, we conclude that PNUTS' activity constitutes an intrinsic barrier to KSHV replication likely by suppressing pol II elongation at promoter-proximal regions.
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10
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Bennison SA, Liu X, Toyo-Oka K. Nuak kinase signaling in development and disease of the central nervous system. Cell Signal 2022; 100:110472. [PMID: 36122883 DOI: 10.1016/j.cellsig.2022.110472] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 09/11/2022] [Accepted: 09/13/2022] [Indexed: 01/14/2023]
Abstract
Protein kinases represent important signaling hubs for a variety of biological functions. Many kinases are traditionally studied for their roles in cancer cell biology, but recent advances in neuroscience research show repurposed kinase function to be important for nervous system development and function. Two members of the AMP-activated protein kinase (AMPK) related family, NUAK1 and NUAK2, have drawn attention in neuroscience due to their mutations in autism spectrum disorder (ASD), attention deficit hyperactivity disorder (ADHD), schizophrenia, and intellectual disability (ID). Furthermore, Nuak kinases have also been implicated in tauopathy and other disorders of aging. This review highlights what is known about the Nuak kinases in nervous system development and disease and explores the possibility of Nuak kinases as targets for therapeutic innovation.
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Affiliation(s)
- Sarah A Bennison
- Department of Neurobiology and Anatomy, Drexel University College of Medicine, Philadelphia, PA 19129, USA
| | - Xiaonan Liu
- Department of Pharmacology and Physiology, Drexel University College of Medicine, Philadelphia, PA 19102, USA
| | - Kazuhito Toyo-Oka
- Department of Neurobiology and Anatomy, Drexel University College of Medicine, Philadelphia, PA 19129, USA.
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11
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Möller S, Saul N, Projahn E, Barrantes I, Gézsi A, Walter M, Antal P, Fuellen G. Gene co-expression analyses of health(span) across multiple species. NAR Genom Bioinform 2022; 4:lqac083. [PMID: 36458022 PMCID: PMC9706456 DOI: 10.1093/nargab/lqac083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 08/20/2022] [Accepted: 10/31/2022] [Indexed: 12/03/2022] Open
Abstract
Health(span)-related gene clusters/modules were recently identified based on knowledge about the cross-species genetic basis of health, to interpret transcriptomic datasets describing health-related interventions. However, the cross-species comparison of health-related observations reveals a lot of heterogeneity, not least due to widely varying health(span) definitions and study designs, posing a challenge for the exploration of conserved healthspan modules and, specifically, their transfer across species. To improve the identification and exploration of conserved/transferable healthspan modules, here we apply an established workflow based on gene co-expression network analyses employing GEO/ArrayExpress data for human and animal models, and perform a comprehensive meta-study of the resulting modules related to health(span), yielding a small set of literature backed health(span) candidate genes. For each experiment, WGCNA (weighted gene correlation network analysis) was used to infer modules of genes which correlate in their expression with a 'health phenotype score' and to determine the most-connected (hub) genes (and their interactions) for each such module. After mapping these hub genes to their human orthologs, 12 health(span) genes were identified in at least two species (ACTN3, ANK1, MRPL18, MYL1, PAXIP1, PPP1CA, SCN3B, SDCBP, SKIV2L, TUBG1, TYROBP, WIPF1), for which enrichment analysis by g:profiler found an association with actin filament-based movement and associated organelles, as well as muscular structures. We conclude that a meta-study of hub genes from co-expression network analyses for the complex phenotype health(span), across multiple species, can yield molecular-mechanistic insights and can direct experimentalists to further investigate the contribution of individual genes and their interactions to health(span).
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Affiliation(s)
- Steffen Möller
- To whom correspondence should be addressed. Tel: +49 381 494 7361; Fax: +49 381 494 7203;
| | - Nadine Saul
- Humboldt-University of Berlin, Institute of Biology, Berlin, Germany
| | - Elias Projahn
- Rostock University Medical Center, Institute for Biostatistics and Informatics in Medicine and Ageing Research, Rostock, Germany
| | - Israel Barrantes
- Rostock University Medical Center, Institute for Biostatistics and Informatics in Medicine and Ageing Research, Rostock, Germany
| | - András Gézsi
- Budapest University of Technology and Economics, Department of Measurement and Information Systems, Budapest, Hungary
| | - Michael Walter
- Rostock University Medical Center, Institute for Clinical Chemistry and Laboratory Medicine, Rostock, Germany
| | - Péter Antal
- Budapest University of Technology and Economics, Department of Measurement and Information Systems, Budapest, Hungary
| | - Georg Fuellen
- Rostock University Medical Center, Institute for Biostatistics and Informatics in Medicine and Ageing Research, Rostock, Germany
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12
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Cytoplasmic forces functionally reorganize nuclear condensates in oocytes. Nat Commun 2022; 13:5070. [PMID: 36038550 PMCID: PMC9424315 DOI: 10.1038/s41467-022-32675-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 08/05/2022] [Indexed: 12/21/2022] Open
Abstract
Cells remodel their cytoplasm with force-generating cytoskeletal motors. Their activity generates random forces that stir the cytoplasm, agitating and displacing membrane-bound organelles like the nucleus in somatic and germ cells. These forces are transmitted inside the nucleus, yet their consequences on liquid-like biomolecular condensates residing in the nucleus remain unexplored. Here, we probe experimentally and computationally diverse nuclear condensates, that include nuclear speckles, Cajal bodies, and nucleoli, during cytoplasmic remodeling of female germ cells named oocytes. We discover that growing mammalian oocytes deploy cytoplasmic forces to timely impose multiscale reorganization of nuclear condensates for the success of meiotic divisions. These cytoplasmic forces accelerate nuclear condensate collision-coalescence and molecular kinetics within condensates. Disrupting the forces decelerates nuclear condensate reorganization on both scales, which correlates with compromised condensate-associated mRNA processing and hindered oocyte divisions that drive female fertility. We establish that cytoplasmic forces can reorganize nuclear condensates in an evolutionary conserved fashion in insects. Our work implies that cells evolved a mechanism, based on cytoplasmic force tuning, to functionally regulate a broad range of nuclear condensates across scales. This finding opens new perspectives when studying condensate-associated pathologies like cancer, neurodegeneration and viral infections. Cytoskeletal activity generates mechanical forces known to agitate and displace membrane-bound organelles in the cytoplasm. In oocytes, Al Jord et al. discover that these cytoplasmic forces functionally remodel nuclear RNA-processing condensates across scales for developmental success.
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13
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Seo MS, Jung KH, Kim K, Lee JE, Han BS, Ko S, Kim JH, Hong S, Lee SH, Hong SS. Discovery of a novel NUAK1 inhibitor against pancreatic cancer. Biomed Pharmacother 2022; 152:113241. [PMID: 35691157 DOI: 10.1016/j.biopha.2022.113241] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 05/31/2022] [Accepted: 06/02/2022] [Indexed: 12/24/2022] Open
Abstract
The novel (nua) kinase family 1 (NUAK1) is an AMPK-related kinase and its expression is associated with tumor malignancy and poor prognosis in several types of cancer, suggesting its potential as a target for cancer therapy. Therefore, the development of NUAK1-targeting inhibitors could improve therapeutic outcomes in cancer. We synthesized KI-301670, a novel NUAK1 inhibitor, and assessed its anticancer effects and mechanism of action in pancreatic cancer. It effectively inhibited pancreatic cancer growth and proliferation, and induced cell cycle arrest, markedly G0/G1 arrest, by increasing the expression of p27 and decreasing expression of p-Rb and E2F1. Additionally, the apoptotic effect of KI-301670 was observed by an increase in cleaved PARP, TUNEL-positive cells, and annexin V cell population, as well as the release of cytochrome c via the loss of mitochondrial membrane potential. KI-301670 inhibited the migration and invasion of pancreatic cancer cells. Mechanistically, KI-301670 effectively inhibited the PI3K/AKT pathway in pancreatic cancer cells. Furthermore, it significantly attenuated tumor growth in a mouse xenograft tumor model. Our results demonstrate that a novel NUAK1 inhibitor, KI-301670, exerts anti-tumor effects by directly suppressing cancer cell growth by affecting the PI3K/AKT pathway, suggesting that it could be a novel therapeutic candidate for pancreatic cancer treatment.
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Affiliation(s)
- Myeong-Seong Seo
- Department of Medicine, College of Medicine, and Program in Biomedical Science & Engineering, Inha University, 3-ga, Sinheung-dong, Jung-gu, Incheon 22332, South Korea
| | - Kyung Hee Jung
- Department of Medicine, College of Medicine, and Program in Biomedical Science & Engineering, Inha University, 3-ga, Sinheung-dong, Jung-gu, Incheon 22332, South Korea
| | - Kewon Kim
- Center for Catalytic Hydrocarbon Functionalization, Institute of Basic Science (IBS) and Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, South Korea
| | - Ji Eun Lee
- Department of Medicine, College of Medicine, and Program in Biomedical Science & Engineering, Inha University, 3-ga, Sinheung-dong, Jung-gu, Incheon 22332, South Korea
| | - Beom Seok Han
- Department of Medicine, College of Medicine, and Program in Biomedical Science & Engineering, Inha University, 3-ga, Sinheung-dong, Jung-gu, Incheon 22332, South Korea
| | - Soyeon Ko
- Department of Medicine, College of Medicine, and Program in Biomedical Science & Engineering, Inha University, 3-ga, Sinheung-dong, Jung-gu, Incheon 22332, South Korea
| | - Jae Ho Kim
- Chemical Kinomics Research Center, Institute of Science and Technology, Seoul 02792, South Korea
| | - Sungwoo Hong
- Center for Catalytic Hydrocarbon Functionalization, Institute of Basic Science (IBS) and Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, South Korea.
| | - So Ha Lee
- Chemical Kinomics Research Center, Institute of Science and Technology, Seoul 02792, South Korea.
| | - Soon-Sun Hong
- Department of Medicine, College of Medicine, and Program in Biomedical Science & Engineering, Inha University, 3-ga, Sinheung-dong, Jung-gu, Incheon 22332, South Korea.
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14
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Liu Z, Wu A, Wu Z, Wang T, Pan Y, Li B, Zhang X, Yu M. TOX4 facilitates promoter-proximal pausing and C-terminal domain dephosphorylation of RNA polymerase II in human cells. Commun Biol 2022; 5:300. [PMID: 35365735 PMCID: PMC8975821 DOI: 10.1038/s42003-022-03214-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 03/02/2022] [Indexed: 11/24/2022] Open
Abstract
TOX4 is one of the regulatory factors of PP1 phosphatases with poorly understood functions. Here we show that chromatin occupancy pattern of TOX4 resembles that of RNA polymerase II (Pol II), and its loss increases cellular level of C-terminal domain (CTD) phosphorylated Pol II but mainly decreases Pol II occupancy on promoters. In addition, elongation rate analyses by 4sUDRB-seq suggest that TOX4 restricts pause release and early elongation but promotes late elongation. Moreover, TT-seq analyses indicate that TOX4 loss mainly decreases transcriptional output. Mechanistically, TOX4 may restrict pause release through facilitating CTD serine 2 and DSIF dephosphorylation, and promote Pol II recycling and reinitiation through facilitating CTD serines 2 and 5 dephosphorylation. Furthermore, among the PP1 phosphatases, TOX4 preferentially binds PP1α and is capable of facilitating Pol II CTD dephosphorylation in vitro. These results lay the foundation for a better understanding of the role of TOX4 in transcriptional regulation. As a role of TOX4, one of the regulatory proteins of PP1 phosphatases, in transcriptional regulation, authors here show that TOX4 restricts pause release and early productive elongation, and promotes Pol II recycling and transcriptional reinitiation.
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Affiliation(s)
- Ziling Liu
- Sheng Yushou Center of Cell Biology and Immunology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200240, Shanghai, China
| | - Aiwei Wu
- Sheng Yushou Center of Cell Biology and Immunology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200240, Shanghai, China
| | - Zhen Wu
- State key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, 200438, Shanghai, China
| | - Talang Wang
- Sheng Yushou Center of Cell Biology and Immunology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200240, Shanghai, China
| | - Yixuan Pan
- Department of Biochemistry and Molecular Cell Biology, Shanghai Jiao Tong University School of Medicine, 200025, Shanghai, China
| | - Bing Li
- Department of Biochemistry and Molecular Cell Biology, Shanghai Jiao Tong University School of Medicine, 200025, Shanghai, China
| | - Xumin Zhang
- State key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, 200438, Shanghai, China
| | - Ming Yu
- Sheng Yushou Center of Cell Biology and Immunology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200240, Shanghai, China. .,Ministry of Education Key Laboratory of Systems Biomedicine, Shanghai Jiao Tong University, 200240, Shanghai, China.
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15
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Lourenco C, Resetca D, Redel C, Lin P, MacDonald AS, Ciaccio R, Kenney TMG, Wei Y, Andrews DW, Sunnerhagen M, Arrowsmith CH, Raught B, Penn LZ. MYC protein interactors in gene transcription and cancer. Nat Rev Cancer 2021; 21:579-591. [PMID: 34188192 DOI: 10.1038/s41568-021-00367-9] [Citation(s) in RCA: 145] [Impact Index Per Article: 48.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/04/2021] [Indexed: 02/07/2023]
Abstract
The transcription factor and oncoprotein MYC is a potent driver of many human cancers and can regulate numerous biological activities that contribute to tumorigenesis. How a single transcription factor can regulate such a diverse set of biological programmes is central to the understanding of MYC function in cancer. In this Perspective, we highlight how multiple proteins that interact with MYC enable MYC to regulate several central control points of gene transcription. These include promoter binding, epigenetic modifications, initiation, elongation and post-transcriptional processes. Evidence shows that a combination of multiple protein interactions enables MYC to function as a potent oncoprotein, working together in a 'coalition model', as presented here. Moreover, as MYC depends on its protein interactome for function, we discuss recent research that emphasizes an unprecedented opportunity to target protein interactors to directly impede MYC oncogenesis.
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Affiliation(s)
| | - Diana Resetca
- Princess Margaret Cancer Centre, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Cornelia Redel
- Princess Margaret Cancer Centre, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Peter Lin
- Princess Margaret Cancer Centre, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Alannah S MacDonald
- Princess Margaret Cancer Centre, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Roberto Ciaccio
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Tristan M G Kenney
- Princess Margaret Cancer Centre, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Yong Wei
- Princess Margaret Cancer Centre, Toronto, ON, Canada
- Biological Sciences, Sunnybrook Research Institute, Toronto, ON, Canada
| | - David W Andrews
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Biological Sciences, Sunnybrook Research Institute, Toronto, ON, Canada
| | - Maria Sunnerhagen
- Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden
| | - Cheryl H Arrowsmith
- Princess Margaret Cancer Centre, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Structural Genomics Consortium, Toronto, ON, Canada
| | - Brian Raught
- Princess Margaret Cancer Centre, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Linda Z Penn
- Princess Margaret Cancer Centre, Toronto, ON, Canada.
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.
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16
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Kim W, LeBlanc B, Matthews WL, Zhang ZY, Zhang Y. Advancements in chemical biology targeting the kinases and phosphatases of RNA polymerase II-mediated transcription. Curr Opin Chem Biol 2021; 63:68-77. [PMID: 33714893 PMCID: PMC8384638 DOI: 10.1016/j.cbpa.2021.02.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 01/21/2021] [Accepted: 02/01/2021] [Indexed: 11/30/2022]
Abstract
Phosphorylation of RNA polymerase II (RNAP II) coordinates the temporal progression of eukaryotic transcription. The development and application of chemical genetic methods have enhanced our ability to investigate the intricate and intertwined pathways regulated by the kinases and phosphatases targeting RNAP II to ensure transcription accuracy and efficiency. Although identifying small molecules that modulate these enzymes has been challenging due to their highly conserved structures, powerful new chemical biology strategies such as targeted covalent inhibitors and small molecule degraders have significantly improved chemical probe specificity. The recent success in discovering phosphatase holoenzyme activators and inhibitors, which demonstrates the feasibility of selective targeting of individual phosphatase complexes, opens up new avenues into the study of transcription. Herein, we summarize how chemical biology is used to delineate kinases' identities involved in RNAP II regulation and new concepts in inhibitor/activator design implemented for kinases/phosphatases involved in modulating RNAP II-mediated transcription.
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Affiliation(s)
- Wantae Kim
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, 78712, USA
| | - Blase LeBlanc
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA
| | - Wendy L Matthews
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA
| | - Zhong-Yin Zhang
- Department of Medicinal Chemistry and Molecular Pharmacology, Department of Chemistry, and Institute for Drug Discovery, Purdue University, West Lafayette, IN, 47907, USA
| | - Yan Zhang
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA; The Institute for Cellular and Molecular Biology. University of Texas at Austin, Austin, TX, 78712, USA.
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17
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van de Vis RAJ, Moustakas A, van der Heide LP. NUAK1 and NUAK2 Fine-Tune TGF-β Signaling. Cancers (Basel) 2021; 13:cancers13133377. [PMID: 34282782 PMCID: PMC8268639 DOI: 10.3390/cancers13133377] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 06/25/2021] [Accepted: 06/30/2021] [Indexed: 01/13/2023] Open
Abstract
Simple Summary TGF-β is a growth factor implicated in a plethora of processes and malignancies, which include cancer and fibrosis. Via binding to its receptor, TGF-β activates a complex intracellular signal transduction pathway, which is controlled by many forms of positive as well as negative feedback. The integrated sum of this feedback determines the outcome and cellular response to TGF-β. In this review, we discuss the role of NUAK1 and NUAK2, a subgroup of the 5′AMP-activated protein kinase family, in providing feedback on intracellular TGF-β signaling. In addition, we discuss how NUAKs mechanistically augment or attenuate the TGF-β response to steer the cell towards a specific output. Understanding the role of NUAKs may aid in developing specific therapeutic agents to combat TGF-β-dependent disease. Abstract Transforming growth factor-β (TGF-β) signaling plays a key role in governing various cellular processes, extending from cell proliferation and apoptosis to differentiation and migration. Due to this extensive involvement in the regulation of cellular function, aberrant TGF-β signaling is frequently implicated in the formation and progression of tumors. Therefore, a full understanding of the mechanisms of TGF-β signaling and its key components will provide valuable insights into how this intricate signaling cascade can shift towards a detrimental course. In this review, we discuss the interplay between TGF-β signaling and the AMP-activated protein kinase (AMPK)-related NUAK kinase family. We highlight the function and regulation of these kinases with focus on the pivotal role NUAK1 and NUAK2 play in regulating TGF-β signaling. Specifically, TGF-β induces the expression of NUAK1 and NUAK2 that regulates TGF-β signaling output in an opposite manner. Besides the focus on the TGF-β pathway, we also present a broader perspective on the expression and signaling interactions of the NUAK kinases to outline the broader functions of these protein kinases.
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Affiliation(s)
- Reinofke A. J. van de Vis
- Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands;
| | - Aristidis Moustakas
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Box 582, SE-75123 Uppsala, Sweden;
| | - Lars P. van der Heide
- Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands;
- Correspondence: ; Tel.: +31-20-5257061
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18
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Krenz B, Gebhardt-Wolf A, Ade CP, Gaballa A, Roehrig F, Vendelova E, Baluapuri A, Eilers U, Gallant P, D'Artista L, Wiegering A, Gasteiger G, Rosenfeldt MT, Bauer S, Zender L, Wolf E, Eilers M. MYC- and MIZ1-Dependent Vesicular Transport of Double-Strand RNA Controls Immune Evasion in Pancreatic Ductal Adenocarcinoma. Cancer Res 2021; 81:4242-4256. [PMID: 34145038 DOI: 10.1158/0008-5472.can-21-1677] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/08/2021] [Accepted: 06/17/2021] [Indexed: 11/16/2022]
Abstract
Deregulated expression of the MYC oncoprotein enables tumor cells to evade immune surveillance, but the mechanisms underlying this surveillance are poorly understood. We show here that endogenous MYC protects pancreatic ductal adenocarcinoma (PDAC) driven by KRASG12D and TP53R172H from eradication by the immune system. Deletion of TANK-binding kinase 1 (TBK1) bypassed the requirement for high MYC expression. TBK1 was active due to the accumulation of double-stranded RNA (dsRNA), which was derived from inverted repetitive elements localized in introns of nuclear genes. Nuclear-derived dsRNA is packaged into extracellular vesicles and subsequently recognized by toll-like receptor 3 (TLR3) to activate TBK1 and downstream MHC class I expression in an autocrine or paracrine manner before being degraded in lysosomes. MYC suppressed loading of dsRNA onto TLR3 and its subsequent degradation via association with MIZ1. Collectively, these findings suggest that MYC and MIZ1 suppress a surveillance pathway that signals perturbances in mRNA processing to the immune system, which facilitates immune evasion in PDAC. SIGNIFICANCE: This study identifies a TBK1-dependent pathway that links dsRNA metabolism to antitumor immunity and shows that suppression of TBK1 is a critical function of MYC in pancreatic ductal adenocarcinoma.
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Affiliation(s)
- Bastian Krenz
- Department of Biochemistry and Molecular Biology, Theodor Boveri Institute, Biocenter, University of Würzburg, Würzburg, Germany
| | - Anneli Gebhardt-Wolf
- Department of Biochemistry and Molecular Biology, Theodor Boveri Institute, Biocenter, University of Würzburg, Würzburg, Germany
| | - Carsten P Ade
- Department of Biochemistry and Molecular Biology, Theodor Boveri Institute, Biocenter, University of Würzburg, Würzburg, Germany
| | - Abdallah Gaballa
- Department of Biochemistry and Molecular Biology, Theodor Boveri Institute, Biocenter, University of Würzburg, Würzburg, Germany
| | - Florian Roehrig
- Comprehensive Cancer Center Mainfranken, Core Unit Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
| | - Emilia Vendelova
- Institute of Systems Immunology, University of Würzburg, Würzburg, Germany
| | - Apoorva Baluapuri
- Department of Biochemistry and Molecular Biology, Cancer Systems Biology Group, Biocenter, University of Würzburg, Würzburg, Germany
| | - Ursula Eilers
- Core Unit High-Content Microscopy, Biocenter, University of Würzburg, Würzburg, Germany
| | - Peter Gallant
- Department of Biochemistry and Molecular Biology, Theodor Boveri Institute, Biocenter, University of Würzburg, Würzburg, Germany
| | - Luana D'Artista
- Department of Medical Oncology and Pneumology (Internal Medicine VIII), University Hospital Tübingen, Tübingen, Germany
| | - Armin Wiegering
- Department of Biochemistry and Molecular Biology, Theodor Boveri Institute, Biocenter, University of Würzburg, Würzburg, Germany.,Department of General, Visceral, Transplant, Vascular and Pediatric Surgery, University Hospital Würzburg, Würzburg, Germany
| | - Georg Gasteiger
- Institute of Systems Immunology, University of Würzburg, Würzburg, Germany
| | | | - Stefan Bauer
- Institute for Immunology, BMFZ, Philipps-University of Marburg, Marburg, Germany
| | - Lars Zender
- Department of Medical Oncology and Pneumology (Internal Medicine VIII), University Hospital Tübingen, Tübingen, Germany
| | - Elmar Wolf
- Department of Biochemistry and Molecular Biology, Cancer Systems Biology Group, Biocenter, University of Würzburg, Würzburg, Germany
| | - Martin Eilers
- Department of Biochemistry and Molecular Biology, Theodor Boveri Institute, Biocenter, University of Würzburg, Würzburg, Germany.
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19
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Curti L, Campaner S. MYC-Induced Replicative Stress: A Double-Edged Sword for Cancer Development and Treatment. Int J Mol Sci 2021; 22:6168. [PMID: 34201047 PMCID: PMC8227504 DOI: 10.3390/ijms22126168] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 05/31/2021] [Accepted: 06/03/2021] [Indexed: 12/15/2022] Open
Abstract
MYC is a transcription factor that controls the expression of a large fraction of cellular genes linked to cell cycle progression, metabolism and differentiation. MYC deregulation in tumors leads to its pervasive genome-wide binding of both promoters and distal regulatory regions, associated with selective transcriptional control of a large fraction of cellular genes. This pairs with alterations of cell cycle control which drive anticipated S-phase entry and reshape the DNA-replication landscape. Under these circumstances, the fine tuning of DNA replication and transcription becomes critical and may pose an intrinsic liability in MYC-overexpressing cancer cells. Here, we will review the current understanding of how MYC controls DNA and RNA synthesis, discuss evidence of replicative and transcriptional stress induced by MYC and summarize preclinical data supporting the therapeutic potential of triggering replicative stress in MYC-driven tumors.
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Affiliation(s)
- Laura Curti
- Center for Genomic Science of IIT@CGS, Fondazione Istituto Italiano di Tecnologia (IIT), 20139 Milan, Italy
| | - Stefano Campaner
- Center for Genomic Science of IIT@CGS, Fondazione Istituto Italiano di Tecnologia (IIT), 20139 Milan, Italy
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20
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Cossa G, Parua PK, Eilers M, Fisher RP. Protein phosphatases in the RNAPII transcription cycle: erasers, sculptors, gatekeepers, and potential drug targets. Genes Dev 2021; 35:658-676. [PMID: 33888562 PMCID: PMC8091971 DOI: 10.1101/gad.348315.121] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
In this review, Cossa et al. discuss the current knowledge and outstanding questions about phosphatases in the context of the RNAPII transcription cycle. The transcription cycle of RNA polymerase II (RNAPII) is governed at multiple points by opposing actions of cyclin-dependent kinases (CDKs) and protein phosphatases, in a process with similarities to the cell division cycle. While important roles of the kinases have been established, phosphatases have emerged more slowly as key players in transcription, and large gaps remain in understanding of their precise functions and targets. Much of the earlier work focused on the roles and regulation of sui generis and often atypical phosphatases—FCP1, Rtr1/RPAP2, and SSU72—with seemingly dedicated functions in RNAPII transcription. Decisive roles in the transcription cycle have now been uncovered for members of the major phosphoprotein phosphatase (PPP) family, including PP1, PP2A, and PP4—abundant enzymes with pleiotropic roles in cellular signaling pathways. These phosphatases appear to act principally at the transitions between transcription cycle phases, ensuring fine control of elongation and termination. Much is still unknown, however, about the division of labor among the PPP family members, and their possible regulation by or of the transcriptional kinases. CDKs active in transcription have recently drawn attention as potential therapeutic targets in cancer and other diseases, raising the prospect that the phosphatases might also present opportunities for new drug development. Here we review the current knowledge and outstanding questions about phosphatases in the context of the RNAPII transcription cycle.
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Affiliation(s)
- Giacomo Cossa
- Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Pabitra K Parua
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Martin Eilers
- Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Robert P Fisher
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
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21
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Landsverk HB, Sandquist LE, Bay LTE, Syljuåsen RG. New link between the RNA polymerase II-CTD and replication stress. Mol Cell Oncol 2021; 8:1910008. [PMID: 34027044 PMCID: PMC8128203 DOI: 10.1080/23723556.2021.1910008] [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] [Indexed: 10/27/2022]
Abstract
Conflicts between transcription and replication are a major source of replication stress. Our recent findings show that proper dephosphorylation of Serine 5 in the carboxy-terminal domain (CTD) of DNA-directed RNA polymerase II subunit RPB1 is needed to prevent such conflicts in human cells.
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Affiliation(s)
- Helga B Landsverk
- Department of Radiation Biology, Institute for Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Lise E Sandquist
- Department of Radiation Biology, Institute for Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Lilli T E Bay
- Department of Radiation Biology, Institute for Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Randi G Syljuåsen
- Department of Radiation Biology, Institute for Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
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22
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Caizzi L, Monteiro-Martins S, Schwalb B, Lysakovskaia K, Schmitzova J, Sawicka A, Chen Y, Lidschreiber M, Cramer P. Efficient RNA polymerase II pause release requires U2 snRNP function. Mol Cell 2021; 81:1920-1934.e9. [PMID: 33689748 DOI: 10.1016/j.molcel.2021.02.016] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 01/07/2021] [Accepted: 02/10/2021] [Indexed: 12/21/2022]
Abstract
Transcription by RNA polymerase II (Pol II) is coupled to pre-mRNA splicing, but the underlying mechanisms remain poorly understood. Co-transcriptional splicing requires assembly of a functional spliceosome on nascent pre-mRNA, but whether and how this influences Pol II transcription remains unclear. Here we show that inhibition of pre-mRNA branch site recognition by the spliceosome component U2 snRNP leads to a widespread and strong decrease in new RNA synthesis from human genes. Multiomics analysis reveals that inhibition of U2 snRNP function increases the duration of Pol II pausing in the promoter-proximal region, impairs recruitment of the pause release factor P-TEFb, and reduces Pol II elongation velocity at the beginning of genes. Our results indicate that efficient release of paused Pol II into active transcription elongation requires the formation of functional spliceosomes and that eukaryotic mRNA biogenesis relies on positive feedback from the splicing machinery to the transcription machinery.
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Affiliation(s)
- Livia Caizzi
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Sara Monteiro-Martins
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Björn Schwalb
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Kseniia Lysakovskaia
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Jana Schmitzova
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Anna Sawicka
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Ying Chen
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Michael Lidschreiber
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Patrick Cramer
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.
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23
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Roeschert I, Poon E, Henssen AG, Garcia HD, Gatti M, Giansanti C, Jamin Y, Ade CP, Gallant P, Schülein-Völk C, Beli P, Richards M, Rosenfeldt M, Altmeyer M, Anderson J, Eggert A, Dobbelstein M, Bayliss R, Chesler L, Büchel G, Eilers M. Combined inhibition of Aurora-A and ATR kinase results in regression of MYCN-amplified neuroblastoma. NATURE CANCER 2021; 2:312-326. [PMID: 33768209 PMCID: PMC7610389 DOI: 10.1038/s43018-020-00171-8] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 12/21/2020] [Indexed: 12/18/2022]
Abstract
Amplification of MYCN is the driving oncogene in a subset of high-risk neuroblastoma. The MYCN protein and the Aurora-A kinase form a complex during S phase that stabilizes MYCN. Here we show that MYCN activates Aurora-A on chromatin, which phosphorylates histone H3 at serine 10 in S phase, promotes the deposition of histone H3.3 and suppresses R-loop formation. Inhibition of Aurora-A induces transcription-replication conflicts and activates the Ataxia telangiectasia and Rad3 related (ATR) kinase, which limits double-strand break accumulation upon Aurora-A inhibition. Combined inhibition of Aurora-A and ATR induces rampant tumor-specific apoptosis and tumor regression in mouse models of neuroblastoma, leading to permanent eradication in a subset of mice. The therapeutic efficacy is due to both tumor cell-intrinsic and immune cell-mediated mechanisms. We propose that targeting the ability of Aurora-A to resolve transcription-replication conflicts is an effective therapy for MYCN-driven neuroblastoma (141 words).
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Affiliation(s)
- Isabelle Roeschert
- Theodor Boveri Institute, Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Evon Poon
- Division of Clinical Studies and Cancer Therapeutics, The Institute of Cancer Research, The Royal Marsden NHS Trust, 15 Cotswold Rd. Belmont, Sutton, Surrey SM2 5NG, UK
| | - Anton G. Henssen
- Experimental and Clinical Research Center, Max Delbrück Center and Charité Berlin, Lindenberger Weg 80, 13125 Berlin, Germany
| | - Heathcliff Dorado Garcia
- Experimental and Clinical Research Center, Max Delbrück Center and Charité Berlin, Lindenberger Weg 80, 13125 Berlin, Germany
| | - Marco Gatti
- Department of Molecular Mechanisms of Disease, University of Zurich, Winterthurerstraße 190, 8057 Zurich, Switzerland
| | - Celeste Giansanti
- Institute of Molecular Oncology, Center of Molecular Biosciences, University of Göttingen, Justus von Liebig Weg 11, 37077 Göttingen, Germany
| | - Yann Jamin
- Divisions of Radiotherapy and Imaging, The Institute of Cancer Research, The Royal Marsden NHS Trust, 15 Cotswold Rd. Belmont, Sutton, Surrey SM2 5NG, UK
| | - Carsten P. Ade
- Theodor Boveri Institute, Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Peter Gallant
- Theodor Boveri Institute, Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Christina Schülein-Völk
- Theodor Boveri Institute, Core Unit High-Content Microscopy, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Petra Beli
- Institute of Molecular Biology, Ackermannweg 4, 55128 Mainz, Germany
| | - Mark Richards
- Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Mathias Rosenfeldt
- Comprehensive Cancer Center Mainfranken, University Hospital Würzburg, Josef-Schneider-Str. 6, 97080 Würzburg, Germany
| | - Matthias Altmeyer
- Department of Molecular Mechanisms of Disease, University of Zurich, Winterthurerstraße 190, 8057 Zurich, Switzerland
| | - John Anderson
- UCL Great Ormond Street Institute of Child Health, 30 Guilford Street London WC1N 1EH, UK
| | - Angelika Eggert
- Experimental and Clinical Research Center, Max Delbrück Center and Charité Berlin, Lindenberger Weg 80, 13125 Berlin, Germany
| | - Matthias Dobbelstein
- Institute of Molecular Oncology, Center of Molecular Biosciences, University of Göttingen, Justus von Liebig Weg 11, 37077 Göttingen, Germany
| | - Richard Bayliss
- Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Louis Chesler
- Division of Clinical Studies and Cancer Therapeutics, The Institute of Cancer Research, The Royal Marsden NHS Trust, 15 Cotswold Rd. Belmont, Sutton, Surrey SM2 5NG, UK
| | - Gabriele Büchel
- Theodor Boveri Institute, Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
- Mildred Scheel Early Career Center, University Hospital Würzburg, Josef-Schneider-Str. 6, 97080 Würzburg, Germany
| | - Martin Eilers
- Theodor Boveri Institute, Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
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24
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Metabolic Effects of Recurrent Genetic Aberrations in Multiple Myeloma. Cancers (Basel) 2021; 13:cancers13030396. [PMID: 33494394 PMCID: PMC7865460 DOI: 10.3390/cancers13030396] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/15/2021] [Accepted: 01/18/2021] [Indexed: 12/17/2022] Open
Abstract
Oncogene activation and malignant transformation exerts energetic, biosynthetic and redox demands on cancer cells due to increased proliferation, cell growth and tumor microenvironment adaptation. As such, altered metabolism is a hallmark of cancer, which is characterized by the reprogramming of multiple metabolic pathways. Multiple myeloma (MM) is a genetically heterogeneous disease that arises from terminally differentiated B cells. MM is characterized by reciprocal chromosomal translocations that often involve the immunoglobulin loci and a restricted set of partner loci, and complex chromosomal rearrangements that are associated with disease progression. Recurrent chromosomal aberrations in MM result in the aberrant expression of MYC, cyclin D1, FGFR3/MMSET and MAF/MAFB. In recent years, the intricate mechanisms that drive cancer cell metabolism and the many metabolic functions of the aforementioned MM-associated oncogenes have been investigated. Here, we discuss the metabolic consequences of recurrent chromosomal translocations in MM and provide a framework for the identification of metabolic changes that characterize MM cells.
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25
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Thng DKH, Toh TB, Chow EKH. Capitalizing on Synthetic Lethality of MYC to Treat Cancer in the Digital Age. Trends Pharmacol Sci 2021; 42:166-182. [PMID: 33422376 DOI: 10.1016/j.tips.2020.11.014] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 11/27/2020] [Accepted: 11/30/2020] [Indexed: 02/06/2023]
Abstract
Deregulation of MYC is among the most frequent oncogenic drivers of cancer. Developing targeted therapies against MYC is, therefore, one of the most critical unmet needs of cancer therapy. Unfortunately, MYC has been labelled as undruggable due to the lack of success in developing clinically relevant MYC-targeted therapies. Synthetic lethality is a promising approach that targets MYC-dependent vulnerabilities in cancer. However, translating the synthetic lethality targets to the clinics is still challenging due to the complex nature of cancers. This review highlights the most promising mechanisms of MYC synthetic lethality and how these discoveries are currently translated into the clinic. Finally, we discuss how in silico computational platforms can improve clinical success of synthetic lethality-based therapy.
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Affiliation(s)
- Dexter Kai Hao Thng
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Tan Boon Toh
- The N.1 Institute for Health, National University of Singapore, Singapore; The Institute for Digital Medicine (WisDM), Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Edward Kai-Hua Chow
- Cancer Science Institute of Singapore, National University of Singapore, Singapore; The N.1 Institute for Health, National University of Singapore, Singapore; The Institute for Digital Medicine (WisDM), Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Department of Biomedical Engineering, National University of Singapore, Singapore.
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26
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Faisal M, Kim JH, Yoo KH, Roh EJ, Hong SS, Lee SH. Development and Therapeutic Potential of NUAKs Inhibitors. J Med Chem 2020; 64:2-25. [PMID: 33356242 DOI: 10.1021/acs.jmedchem.0c00533] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
NUAK isoforms, NUAK1 (ARK5) and NUAK2 (SNARK), are important members of the AMPK family of protein kinases. They are involved in a broad spectrum of physiological and cellular events, and sometimes their biological roles overlap. NUAK isoform dysregulation is associated with numerous pathological disorders, including neurodegeneration, metastatic cancer, and diabetes. Therefore, they are promising therapeutic targets in metabolic diseases and cancers; consequently, various NUAK-targeted inhibitors have been disclosed. The first part of this review comprises a brief discussion of the homology, expression, structure, and characteristics of NUAK isoforms. The second part focuses on NUAK isoforms' involvement in crucial biological operations, including mechanistic findings, highlighting how their abnormal functioning contributes to disease progression and quality of life. The third part summarizes the key findings and applications of targeting NUAK isoforms for treating multiple cancers and neurodegenerative disorders. The final part systematically presents a critical review and analysis of the literature on NUAK isoform inhibitions through small molecules.
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Affiliation(s)
- Muhammad Faisal
- Division of Bio-Medical Science & Technology, KIST School, University of Science and Technology (UST), Hwarangno 14-gil 5, Seongbuk-gu, Seoul 02792, Republic of Korea
| | - Jae Ho Kim
- Chemical Kinomics Research Center, Korea Institute of Science and Technology, Hwarangno 14-gil 5, Seongbuk-gu, Seoul 02792, Republic of Korea
| | - Kyung Ho Yoo
- Chemical Kinomics Research Center, Korea Institute of Science and Technology, Hwarangno 14-gil 5, Seongbuk-gu, Seoul 02792, Republic of Korea
| | - Eun Joo Roh
- Division of Bio-Medical Science & Technology, KIST School, University of Science and Technology (UST), Hwarangno 14-gil 5, Seongbuk-gu, Seoul 02792, Republic of Korea.,Chemical Kinomics Research Center, Korea Institute of Science and Technology, Hwarangno 14-gil 5, Seongbuk-gu, Seoul 02792, Republic of Korea
| | - Soon Sun Hong
- Department of Biomedical Sciences, College of Medicine, and Program in Biomedical Science & Engineering, Inha University, Incheon 22212, Republic of Korea
| | - So Ha Lee
- Chemical Kinomics Research Center, Korea Institute of Science and Technology, Hwarangno 14-gil 5, Seongbuk-gu, Seoul 02792, Republic of Korea
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27
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Khalife J, Fréville A, Gnangnon B, Pierrot C. The Multifaceted Role of Protein Phosphatase 1 in Plasmodium. Trends Parasitol 2020; 37:154-164. [PMID: 33036936 DOI: 10.1016/j.pt.2020.09.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 09/07/2020] [Accepted: 09/08/2020] [Indexed: 11/29/2022]
Abstract
Protein phosphatase type 1 (PP1) forms a wide range of Ser/Thr-specific phosphatase holoenzymes which contain one catalytic subunit (PP1c), present in all eukaryotic cells, associated with variable subunits known as regulatory proteins. It has recently been shown that regulators take a leading role in the organization and the control of PP1 functions. Many studies have addressed the role of these regulators in diverse organisms, including humans, and investigated their link to diseases. In this review we summarize recent advances on the role of PP1c in Plasmodium, its interactome and regulators. As a proof of concept, peptides interfering with the regulator binding capacity of PP1c were shown to inhibit the growth of P. falciparum, suggesting their potential as drug precursors.
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Affiliation(s)
- Jamal Khalife
- Center for Infection and Immunity of Lille, Biology of Apicomplexan Parasites, UMR 9017 CNRS, U1019 INSERM, Université de Lille, Institut Pasteur de Lille, Lille, France.
| | - Aline Fréville
- Center for Infection and Immunity of Lille, Biology of Apicomplexan Parasites, UMR 9017 CNRS, U1019 INSERM, Université de Lille, Institut Pasteur de Lille, Lille, France
| | - Bénédicte Gnangnon
- Center for Infection and Immunity of Lille, Biology of Apicomplexan Parasites, UMR 9017 CNRS, U1019 INSERM, Université de Lille, Institut Pasteur de Lille, Lille, France
| | - Christine Pierrot
- Center for Infection and Immunity of Lille, Biology of Apicomplexan Parasites, UMR 9017 CNRS, U1019 INSERM, Université de Lille, Institut Pasteur de Lille, Lille, France
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28
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Escalona E, Muñoz M, Pincheira R, Elorza ÁA, Castro AF. Cytosolic NUAK1 Enhances ATP Production by Maintaining Proper Glycolysis and Mitochondrial Function in Cancer Cells. Front Oncol 2020; 10:1123. [PMID: 32754444 PMCID: PMC7367139 DOI: 10.3389/fonc.2020.01123] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 06/04/2020] [Indexed: 12/17/2022] Open
Abstract
NUAK1 is an AMPK-related kinase located in the cytosol and the nucleus, whose expression associates with tumor malignancy and poor patient prognosis in several cancers. Accordingly, NUAK1 was associated with metastasis because it promotes cell migration and invasion in different cancer cells. Besides, NUAK1 supports cancer cell survival under metabolic stress and maintains ATP levels in hepatocarcinoma cells, suggesting a role in energy metabolism in cancer. However, the underlying mechanism for this metabolic function, as well as its link to NUAK1 subcellular localization, is unclear. We demonstrated that cytosolic NUAK1 increases ATP levels, which associates with increased mitochondrial respiration, supporting that cytosolic NUAK1 is involved in mitochondrial function regulation in cancer cells. NUAK1 inhibition led to the formation of “donut-like” structures, providing evidence of NUAK1-dependent mitochondrial morphology regulation. Additionally, our results indicated that cytosolic NUAK1 increases the glycolytic capacity of cancer cells under mitochondrial inhibition. Nuclear NUAK1 seems to be involved in the metabolic switch to glycolysis. Altogether, our results suggest that cytosolic NUAK1 participates in mitochondrial ATP production and the maintenance of proper glycolysis in cancer cells. Our current studies support the role of NUAK1 in bioenergetics, mitochondrial homeostasis, glycolysis and metabolic capacities. They suggest different metabolic outcomes depending on its subcellular localization. The identified roles of NUAK1 in cancer metabolism provide a potential mechanism relevant for tumor progression and its association with poor patient prognosis in several cancers. Further studies could shed light on the molecular mechanisms involved in the identified metabolic NUAK1 functions.
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Affiliation(s)
- Emilia Escalona
- Signal Transduction and Cancer Laboratory, Biochemistry and Molecular Biology Department, Faculty of Biological Sciences, Universidad de Concepción, Concepción, Chile
| | - Marcelo Muñoz
- Mitochondrial Medicine Laboratory, Institute of Biomedical Sciences, Faculty of Medicine and Faculty of Life Sciences, Universidad Andres Bello, Santiago, Chile
| | - Roxana Pincheira
- Signal Transduction and Cancer Laboratory, Biochemistry and Molecular Biology Department, Faculty of Biological Sciences, Universidad de Concepción, Concepción, Chile
| | - Álvaro A Elorza
- Mitochondrial Medicine Laboratory, Institute of Biomedical Sciences, Faculty of Medicine and Faculty of Life Sciences, Universidad Andres Bello, Santiago, Chile
| | - Ariel F Castro
- Signal Transduction and Cancer Laboratory, Biochemistry and Molecular Biology Department, Faculty of Biological Sciences, Universidad de Concepción, Concepción, Chile
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29
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Abstract
In this issue of Molecular Cell, Cossa et al. (2020) uncover the basis for a dependency of tumor cells with deregulated MYC on the kinase NUAK1, which acts through PP1 and PNUTS to ensure that splicing keeps up with MYC-driven transcription.
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Affiliation(s)
- Robert P Fisher
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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30
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Hör J, Garriss G, Di Giorgio S, Hack LM, Vanselow JT, Förstner KU, Schlosser A, Henriques-Normark B, Vogel J. Grad-seq in a Gram-positive bacterium reveals exonucleolytic sRNA activation in competence control. EMBO J 2020; 39:e103852. [PMID: 32227509 PMCID: PMC7196914 DOI: 10.15252/embj.2019103852] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 03/03/2020] [Accepted: 03/06/2020] [Indexed: 12/20/2022] Open
Abstract
RNA–protein interactions are the crucial basis for many steps of bacterial gene expression, including post‐transcriptional control by small regulatory RNAs (sRNAs). In stark contrast to recent progress in the analysis of Gram‐negative bacteria, knowledge about RNA–protein complexes in Gram‐positive species remains scarce. Here, we used the Grad‐seq approach to draft a comprehensive landscape of such complexes in Streptococcus pneumoniae, in total determining the sedimentation profiles of ~ 88% of the transcripts and ~ 62% of the proteins of this important human pathogen. Analysis of in‐gradient distributions and subsequent tag‐based protein capture identified interactions of the exoribonuclease Cbf1/YhaM with sRNAs that control bacterial competence for DNA uptake. Unexpectedly, the nucleolytic activity of Cbf1 stabilizes these sRNAs, thereby promoting their function as repressors of competence. Overall, these results provide the first RNA/protein complexome resource of a Gram‐positive species and illustrate how this can be utilized to identify new molecular factors with functions in RNA‐based regulation of virulence‐relevant pathways.
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Affiliation(s)
- Jens Hör
- Institute of Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Geneviève Garriss
- Department of Microbiology, Tumor & Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Silvia Di Giorgio
- Institute of Molecular Infection Biology, University of Würzburg, Würzburg, Germany.,ZB MED-Information Centre for Life Sciences, Cologne, Germany
| | - Lisa-Marie Hack
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Jens T Vanselow
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Würzburg, Germany
| | - Konrad U Förstner
- ZB MED-Information Centre for Life Sciences, Cologne, Germany.,Faculty of Information Science and Communication Studies, TH Köln, Cologne, Germany
| | - Andreas Schlosser
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Würzburg, Germany
| | - Birgitta Henriques-Normark
- Department of Microbiology, Tumor & Cell Biology, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden.,SCELSE and LKC, Nanyang Technological University, NTU, Singapore, Singapore
| | - Jörg Vogel
- Institute of Molecular Infection Biology, University of Würzburg, Würzburg, Germany.,Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
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31
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Baluapuri A, Wolf E, Eilers M. Target gene-independent functions of MYC oncoproteins. Nat Rev Mol Cell Biol 2020; 21:255-267. [PMID: 32071436 DOI: 10.1038/s41580-020-0215-2] [Citation(s) in RCA: 182] [Impact Index Per Article: 45.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/15/2020] [Indexed: 12/13/2022]
Abstract
Oncoproteins of the MYC family are major drivers of human tumorigenesis. Since a large body of evidence indicates that MYC proteins are transcription factors, studying their function has focused on the biology of their target genes. Detailed studies of MYC-dependent changes in RNA levels have provided contrasting models of the oncogenic activity of MYC proteins through either enhancing or repressing the expression of specific target genes, or as global amplifiers of transcription. In this Review, we first summarize the biochemistry of MYC proteins and what is known (or is unclear) about the MYC target genes. We then discuss recent progress in defining the interactomes of MYC and MYCN and how this information affects central concepts of MYC biology, focusing on mechanisms by which MYC proteins modulate transcription. MYC proteins promote transcription termination upon stalling of RNA polymerase II, and we propose that this mechanism enhances the stress resilience of basal transcription. Furthermore, MYC proteins coordinate transcription elongation with DNA replication and cell cycle progression. Finally, we argue that the mechanism by which MYC proteins regulate the transcription machinery is likely to promote tumorigenesis independently of global or relative changes in the expression of their target genes.
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Affiliation(s)
- Apoorva Baluapuri
- Theodor Boveri Institute, Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Am Hubland, Würzburg, Germany
| | - Elmar Wolf
- Theodor Boveri Institute, Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Am Hubland, Würzburg, Germany
| | - Martin Eilers
- Theodor Boveri Institute, Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Am Hubland, Würzburg, Germany.
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