1
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Prekovic S, Chalkiadakis T, Roest M, Roden D, Lutz C, Schuurman K, Opdam M, Hoekman L, Abbott N, Tesselaar T, Wajahat M, Dwyer AR, Mayayo‐Peralta I, Gomez G, Altelaar M, Beijersbergen R, Győrffy B, Young L, Linn S, Jonkers J, Tilley W, Hickey T, Vareslija D, Swarbrick A, Zwart W. Luminal breast cancer identity is determined by loss of glucocorticoid receptor activity. EMBO Mol Med 2023; 15:e17737. [PMID: 37902007 PMCID: PMC10701603 DOI: 10.15252/emmm.202317737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 09/27/2023] [Accepted: 10/04/2023] [Indexed: 10/31/2023] Open
Abstract
Glucocorticoid receptor (GR) is a transcription factor that plays a crucial role in cancer biology. In this study, we utilized an in silico-designed GR activity signature to demonstrate that GR relates to the proliferative capacity of numerous primary cancer types. In breast cancer, the GR activity status determines luminal subtype identity and has implications for patient outcomes. We reveal that GR engages with estrogen receptor (ER), leading to redistribution of ER on the chromatin. Notably, GR activation leads to upregulation of the ZBTB16 gene, encoding for a transcriptional repressor, which controls growth in ER-positive breast cancer and associates with prognosis in luminal A patients. In relation to ZBTB16's repressive nature, GR activation leads to epigenetic remodeling and loss of histone acetylation at sites proximal to cancer-driving genes. Based on these findings, epigenetic inhibitors reduce viability of ER-positive breast cancer cells that display absence of GR activity. Our findings provide insights into how GR controls ER-positive breast cancer growth and may have implications for patients' prognostication and provide novel therapeutic candidates for breast cancer treatment.
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Affiliation(s)
- Stefan Prekovic
- Division of Oncogenomics, Oncode InstituteThe Netherlands Cancer InstituteAmsterdamThe Netherlands
- Center for Molecular MedicineUMC UtrechtUtrechtThe Netherlands
| | | | - Merel Roest
- Division of Oncogenomics, Oncode InstituteThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Daniel Roden
- Cancer Ecosystems ProgramGarvan Institute of Medical ResearchDarlinghurstNSWAustralia
- School of Clinical Medicine, Faculty of Medicine and HealthUNSW SydneySydneyNSWAustralia
| | - Catrin Lutz
- Division of Molecular Pathology, Oncode InstituteThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Karianne Schuurman
- Division of Oncogenomics, Oncode InstituteThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Mark Opdam
- Division of Molecular Pathology, Oncode InstituteThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Liesbeth Hoekman
- Mass Spectrometry/Proteomics FacilityThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Nina Abbott
- Division of Oncogenomics, Oncode InstituteThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Tanja Tesselaar
- Division of Oncogenomics, Oncode InstituteThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Maliha Wajahat
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical SchoolUniversity of AdelaideAdelaideSAAustralia
| | - Amy R Dwyer
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical SchoolUniversity of AdelaideAdelaideSAAustralia
| | - Isabel Mayayo‐Peralta
- Division of Oncogenomics, Oncode InstituteThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Gabriela Gomez
- School of Pharmacy and Biomolecular SciencesThe Royal College of Surgeons University of Medicine and Health SciencesDublinIreland
| | - Maarten Altelaar
- Mass Spectrometry/Proteomics FacilityThe Netherlands Cancer InstituteAmsterdamThe Netherlands
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical SciencesUtrecht UniversityUtrechtThe Netherlands
| | - Roderick Beijersbergen
- Division of Molecular Carcinogenesis and Robotics and Screening CentreNetherlands Cancer InstituteAmsterdamThe Netherlands
| | - Balázs Győrffy
- TTK Cancer Biomarker Research GroupInstitute of EnzymologyBudapestHungary
- Department of Bioinformatics and 2nd Department of PediatricsSemmelweis UniversityBudapestHungary
| | - Leonie Young
- Endocrine Oncology Research Group, Department of SurgeryThe Royal College of Surgeons University of Medicine and Health SciencesDublinIreland
- Beaumont RCSI Cancer CentreBeaumont HospitalDublinIreland
| | - Sabine Linn
- Division of Molecular Pathology, Oncode InstituteThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Jos Jonkers
- Division of Molecular Pathology, Oncode InstituteThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Wayne Tilley
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical SchoolUniversity of AdelaideAdelaideSAAustralia
- Freemasons Centre for Male Health and WellbeingUniversity of AdelaideAdelaideSAAustralia
| | - Theresa Hickey
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical SchoolUniversity of AdelaideAdelaideSAAustralia
| | - Damir Vareslija
- School of Pharmacy and Biomolecular SciencesThe Royal College of Surgeons University of Medicine and Health SciencesDublinIreland
- Beaumont RCSI Cancer CentreBeaumont HospitalDublinIreland
| | - Alexander Swarbrick
- Cancer Ecosystems ProgramGarvan Institute of Medical ResearchDarlinghurstNSWAustralia
- School of Clinical Medicine, Faculty of Medicine and HealthUNSW SydneySydneyNSWAustralia
| | - Wilbert Zwart
- Division of Oncogenomics, Oncode InstituteThe Netherlands Cancer InstituteAmsterdamThe Netherlands
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Department of Biomedical EngineeringEindhoven University of TechnologyEindhovenThe Netherlands
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2
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Maresca M, van den Brand T, Li H, Teunissen H, Davies J, de Wit E. Pioneer activity distinguishes activating from non-activating SOX2 binding sites. EMBO J 2023; 42:e113150. [PMID: 37691488 PMCID: PMC10577566 DOI: 10.15252/embj.2022113150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 07/17/2023] [Accepted: 07/22/2023] [Indexed: 09/12/2023] Open
Abstract
Genome-wide transcriptional activity involves the binding of many transcription factors (TFs) to thousands of sites in the genome. Pioneer TFs are a class of TFs that maintain open chromatin and allow non-pioneer TFs access to their target sites. Determining which TF binding sites directly drive transcription remains a challenge. Here, we use acute protein depletion of the pioneer TF SOX2 to establish its functionality in maintaining chromatin accessibility. We show that thousands of accessible sites are lost within an hour of protein depletion, indicating rapid turnover of these sites in the absence of the pioneer factor. To understand the relationship with transcription, we performed nascent transcription analysis and found that open chromatin sites that are maintained by SOX2 are highly predictive of gene expression, in contrast to all other SOX2 binding sites. We use CRISPR-Cas9 genome editing in the Klf2 locus to functionally validate a predicted regulatory element. We conclude that the regulatory activity of SOX2 is exerted mainly at sites where it maintains accessibility and that other binding sites are largely dispensable for gene regulation.
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Affiliation(s)
- Michela Maresca
- Division of Gene RegulationThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Teun van den Brand
- Division of Gene RegulationThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Hangpeng Li
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of MedicineUniversity of OxfordOxfordUK
| | - Hans Teunissen
- Division of Gene RegulationThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - James Davies
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of MedicineUniversity of OxfordOxfordUK
| | - Elzo de Wit
- Division of Gene RegulationThe Netherlands Cancer InstituteAmsterdamThe Netherlands
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3
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Carrillo‐Carrasco VP, Hernandez‐Garcia J, Mutte SK, Weijers D. The birth of a giant: evolutionary insights into the origin of auxin responses in plants. EMBO J 2023; 42:e113018. [PMID: 36786017 PMCID: PMC10015382 DOI: 10.15252/embj.2022113018] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 01/20/2023] [Accepted: 01/25/2023] [Indexed: 02/15/2023] Open
Abstract
The plant signaling molecule auxin is present in multiple kingdoms of life. Since its discovery, a century of research has been focused on its action as a phytohormone. In land plants, auxin regulates growth and development through transcriptional and non-transcriptional programs. Some of the molecular mechanisms underlying these responses are well understood, mainly in Arabidopsis. Recently, the availability of genomic and transcriptomic data of green lineages, together with phylogenetic inference, has provided the basis to reconstruct the evolutionary history of some components involved in auxin biology. In this review, we follow the evolutionary trajectory that allowed auxin to become the "giant" of plant biology by focusing on bryophytes and streptophyte algae. We consider auxin biosynthesis, transport, physiological, and molecular responses, as well as evidence supporting the role of auxin as a chemical messenger for communication within ecosystems. Finally, we emphasize that functional validation of predicted orthologs will shed light on the conserved properties of auxin biology among streptophytes.
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Affiliation(s)
| | | | - Sumanth K Mutte
- Laboratory of BiochemistryWageningen UniversityWageningenthe Netherlands
| | - Dolf Weijers
- Laboratory of BiochemistryWageningen UniversityWageningenthe Netherlands
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4
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Fuderer M, van der Heide O, Liu H, van den Berg CAT, Sbrizzi A. Efficient performance analysis and optimization of transient-state sequences for multiparametric magnetic resonance imaging. NMR Biomed 2023; 36:e4864. [PMID: 36321222 PMCID: PMC10078474 DOI: 10.1002/nbm.4864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 10/11/2022] [Accepted: 10/30/2022] [Indexed: 06/16/2023]
Abstract
In transient-state multiparametric MRI sequences such as Magnetic Resonance Spin TomogrAphy in Time-domain (MR-STAT), MR fingerprinting, or hybrid-state imaging, the flip angle pattern of the RF excitation varies over the sequence. This gives considerable freedom to choose an optimal pattern of flip angles. For pragmatic reasons, most optimization methodologies choose for a single-voxel approach (i.e., without taking the spatial encoding scheme into account). Particularly in MR-STAT, the context of spatial encoding is important. In the current study, we present a methodology, called BLock Analysis of a K-space-domain Jacobian (BLAKJac), which is sufficiently fast to optimize a sequence in the context of a predetermined phase-encoding pattern. Based on MR-STAT acquisitions and reconstructions, we show that sequences optimized using BLAKJac are more reliable in terms of actually achieved precision than conventional single-voxel-optimized sequences. In addition, BLAKJac provides analytical tools that give insights into the performance of the sequence in a very limited computation time. Our experiments are based on MR-STAT, but the theory is equally valid for other transient-state multiparametric methods.
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Affiliation(s)
- Miha Fuderer
- Radiotherapy, Imaging DivisionUniversity Medical Center UtrechtUtrechtthe Netherlands
| | - Oscar van der Heide
- Radiotherapy, Imaging DivisionUniversity Medical Center UtrechtUtrechtthe Netherlands
| | - Hongyan Liu
- Radiotherapy, Imaging DivisionUniversity Medical Center UtrechtUtrechtthe Netherlands
| | | | - Alessandro Sbrizzi
- Radiotherapy, Imaging DivisionUniversity Medical Center UtrechtUtrechtthe Netherlands
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5
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Gasperini C, Tuntevski K, Beatini S, Pelizzoli R, Lo Van A, Mangoni D, Cossu RM, Pascarella G, Bianchini P, Bielefeld P, Scarpato M, Pons‐Espinal M, Sanges R, Diaspro A, Fitzsimons CP, Carninci P, Gustincich S, De Pietri Tonelli D. Piwil2 (Mili) sustains neurogenesis and prevents cellular senescence in the postnatal hippocampus. EMBO Rep 2023; 24:e53801. [PMID: 36472244 PMCID: PMC9900342 DOI: 10.15252/embr.202153801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 10/25/2022] [Accepted: 11/10/2022] [Indexed: 12/12/2022] Open
Abstract
Adult neural progenitor cells (aNPCs) ensure lifelong neurogenesis in the mammalian hippocampus. Proper regulation of aNPC fate has thus important implications for brain plasticity and healthy aging. Piwi proteins and the small noncoding RNAs interacting with them (piRNAs) have been proposed to control memory and anxiety, but the mechanism remains elusive. Here, we show that Piwil2 (Mili) is essential for proper neurogenesis in the postnatal mouse hippocampus. RNA sequencing of aNPCs and their differentiated progeny reveal that Mili and piRNAs are dynamically expressed in neurogenesis. Depletion of Mili and piRNAs in the adult hippocampus impairs aNPC differentiation toward a neural fate, induces senescence, and generates reactive glia. Transcripts modulated upon Mili depletion bear sequences complementary or homologous to piRNAs and include repetitive elements and mRNAs encoding essential proteins for proper neurogenesis. Our results provide evidence of a critical role for Mili in maintaining fitness and proper fate of aNPCs, underpinning a possible involvement of the piRNA pathway in brain plasticity and successful aging.
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Affiliation(s)
- Caterina Gasperini
- Neurobiology of miRNA LaboratoryIstituto Italiano di TecnologiaGenoaItaly
| | - Kiril Tuntevski
- Neurobiology of miRNA LaboratoryIstituto Italiano di TecnologiaGenoaItaly
- The Open University Affiliated Research Centre at Istituto Italiano di Tecnologia (ARC@IIT)GenoaItaly
| | - Silvia Beatini
- Neurobiology of miRNA LaboratoryIstituto Italiano di TecnologiaGenoaItaly
| | - Roberta Pelizzoli
- Neurobiology of miRNA LaboratoryIstituto Italiano di TecnologiaGenoaItaly
| | - Amanda Lo Van
- Neurobiology of miRNA LaboratoryIstituto Italiano di TecnologiaGenoaItaly
| | - Damiano Mangoni
- Central RNA LaboratoryIstituto Italiano di TecnologiaGenoaItaly
| | - Rosa M Cossu
- Central RNA LaboratoryIstituto Italiano di TecnologiaGenoaItaly
| | - Giovanni Pascarella
- Division of Genomic TechnologiesRIKEN Center for Life Science TechnologiesYokohamaJapan
| | - Paolo Bianchini
- Nanoscopy, CHT ErzelliIstituto Italiano di TecnologiaGenoaItaly
| | - Pascal Bielefeld
- Swammerdam Institute for Life Sciences, Faculty of ScienceUniversity of AmsterdamAmsterdamThe Netherlands
| | | | | | - Remo Sanges
- Central RNA LaboratoryIstituto Italiano di TecnologiaGenoaItaly
- Area of NeuroscienceSISSATriesteItaly
| | - Alberto Diaspro
- Nanoscopy, CHT ErzelliIstituto Italiano di TecnologiaGenoaItaly
| | - Carlos P Fitzsimons
- Swammerdam Institute for Life Sciences, Faculty of ScienceUniversity of AmsterdamAmsterdamThe Netherlands
| | - Piero Carninci
- Division of Genomic TechnologiesRIKEN Center for Life Science TechnologiesYokohamaJapan
- Human TechnopoleMilanItaly
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6
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Grönloh MLB, Arts JJG, Palacios Martínez S, van der Veen AA, Kempers L, van Steen ACI, Roelofs JJTH, Nolte MA, Goedhart J, van Buul JD. Endothelial transmigration hotspots limit vascular leakage through heterogeneous expression of ICAM-1. EMBO Rep 2023; 24:e55483. [PMID: 36382783 PMCID: PMC9827561 DOI: 10.15252/embr.202255483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 10/25/2022] [Accepted: 10/28/2022] [Indexed: 11/18/2022] Open
Abstract
Upon inflammation, leukocytes leave the circulation by crossing the endothelial monolayer at specific transmigration "hotspot" regions. Although these regions support leukocyte transmigration, their functionality is not clear. We found that endothelial hotspots function to limit vascular leakage during transmigration events. Using the photoconvertible probe mEos4b, we traced back and identified original endothelial transmigration hotspots. Using this method, we show that the heterogeneous distribution of ICAM-1 determines the location of the transmigration hotspot. Interestingly, the loss of ICAM-1 heterogeneity either by CRISPR/Cas9-induced knockout of ICAM-1 or equalizing the distribution of ICAM-1 in all endothelial cells results in the loss of TEM hotspots but not necessarily in reduced TEM events. Functionally, the loss of endothelial hotspots results in increased vascular leakage during TEM. Mechanistically, we demonstrate that the 3 extracellular Ig-like domains of ICAM-1 are crucial for hotspot recognition. However, the intracellular tail of ICAM-1 and the 4th Ig-like dimerization domain are not involved, indicating that intracellular signaling or ICAM-1 dimerization is not required for hotspot recognition. Together, we discovered that hotspots function to limit vascular leakage during inflammation-induced extravasation.
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Affiliation(s)
- Max L B Grönloh
- Molecular Cell Biology Lab, Department of Molecular HematologySanquin Research and Landsteiner LaboratoryAmsterdamThe Netherlands
- Section Molecular Cytology at Swammerdam Institute for Life Sciences, Leeuwenhoek Centre for Advanced MicroscopyUniversity of AmsterdamAmsterdamThe Netherlands
| | - Janine J G Arts
- Molecular Cell Biology Lab, Department of Molecular HematologySanquin Research and Landsteiner LaboratoryAmsterdamThe Netherlands
- Section Molecular Cytology at Swammerdam Institute for Life Sciences, Leeuwenhoek Centre for Advanced MicroscopyUniversity of AmsterdamAmsterdamThe Netherlands
| | - Sebastián Palacios Martínez
- Molecular Cell Biology Lab, Department of Molecular HematologySanquin Research and Landsteiner LaboratoryAmsterdamThe Netherlands
| | - Amerens A van der Veen
- Molecular Cell Biology Lab, Department of Molecular HematologySanquin Research and Landsteiner LaboratoryAmsterdamThe Netherlands
| | - Lanette Kempers
- Molecular Cell Biology Lab, Department of Molecular HematologySanquin Research and Landsteiner LaboratoryAmsterdamThe Netherlands
| | - Abraham C I van Steen
- Molecular Cell Biology Lab, Department of Molecular HematologySanquin Research and Landsteiner LaboratoryAmsterdamThe Netherlands
| | - Joris J T H Roelofs
- Department of Pathology, Amsterdam Cardiovascular SciencesAmsterdam UMC, University of Amsterdam, Location AMCAmsterdamThe Netherlands
| | - Martijn A Nolte
- Molecular Cell Biology Lab, Department of Molecular HematologySanquin Research and Landsteiner LaboratoryAmsterdamThe Netherlands
| | - Joachim Goedhart
- Section Molecular Cytology at Swammerdam Institute for Life Sciences, Leeuwenhoek Centre for Advanced MicroscopyUniversity of AmsterdamAmsterdamThe Netherlands
| | - Jaap D van Buul
- Molecular Cell Biology Lab, Department of Molecular HematologySanquin Research and Landsteiner LaboratoryAmsterdamThe Netherlands
- Section Molecular Cytology at Swammerdam Institute for Life Sciences, Leeuwenhoek Centre for Advanced MicroscopyUniversity of AmsterdamAmsterdamThe Netherlands
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7
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Rovira‐Navarro M, Katz RF, Liao Y, van der Wal W, Nimmo F. The Tides of Enceladus' Porous Core. J Geophys Res Planets 2022; 127:e2021JE007117. [PMID: 35865509 PMCID: PMC9285949 DOI: 10.1029/2021je007117] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 04/01/2022] [Accepted: 04/27/2022] [Indexed: 06/15/2023]
Abstract
The inferred density of Enceladus' core, together with evidence of hydrothermal activity within the moon, suggests that the core is porous. Tidal dissipation in an unconsolidated core has been proposed as the main source of Enceladus' geological activity. However, the tidal response of its core has generally been modeled assuming it behaves viscoelastically rather than poroviscoelastically. In this work, we analyze the poroviscoelastic response to better constrain the distribution of tidal dissipation within Enceladus. A poroviscoelastic body has a different tidal response than a viscoelastic one; pressure within the pores alters the stress field and induces a Darcian porous flow. This flow represents an additional pathway for energy dissipation. Using Biot's theory of poroviscoelasticity, we develop a new framework to obtain the tidal response of a spherically symmetric, self-gravitating moon with porous layers and apply it to Enceladus. We show that the boundary conditions at the interface of the core and overlying ocean play a key role in the tidal response. The ocean hinders the development of a large-amplitude Darcian flow, making negligible the Darcian contribution to the dissipation budget. We therefore infer that Enceladus' core can be the source of its geological activity only if it has a low rigidity and a very low viscosity. A future mission to Enceladus could test this hypothesis by measuring the phase lags of tidally induced changes of gravitational potential and surface displacements.
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Affiliation(s)
- Marc Rovira‐Navarro
- Department of Ocean SystemsNIOZ Royal Netherlands Institute for Sea ResearchYersekeThe Netherlands
- Faculty of Aerospace EngineeringTU DelftDelftThe Netherlands
- Lunar and Planetary LaboratoryUniversity of ArizonaTucsonAZUSA
| | | | - Yang Liao
- Department of Geology and GeophysicsWoods Hole Oceanographic InstitutionWoods HoleMAUSA
| | | | - Francis Nimmo
- Department of Earth and Planetary SciencesUniversity of CaliforniaSanta CruzCAUSA
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8
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Stok JE, Oosenbrug T, ter Haar LR, Gravekamp D, Bromley CP, Zelenay S, Reis e Sousa C, van der Veen AG. RNA sensing via the RIG-I-like receptor LGP2 is essential for the induction of a type I IFN response in ADAR1 deficiency. EMBO J 2022; 41:e109760. [PMID: 35156720 PMCID: PMC8922249 DOI: 10.15252/embj.2021109760] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 01/07/2022] [Accepted: 01/11/2022] [Indexed: 12/12/2022] Open
Abstract
RNA editing by the adenosine deaminase ADAR1 prevents innate immune responses to endogenous RNAs. In ADAR1-deficient cells, unedited self RNAs form base-paired structures that resemble viral RNAs and inadvertently activate the cytosolic RIG-I-like receptor (RLR) MDA5, leading to an antiviral type I interferon (IFN) response. Mutations in ADAR1 cause Aicardi-Goutières Syndrome (AGS), an autoinflammatory syndrome characterized by chronic type I IFN production. Conversely, ADAR1 loss and the consequent type I IFN production restricts tumor growth and potentiates the activity of some chemotherapeutics. Here, we show that another RIG-I-like receptor, LGP2, also has an essential role in the induction of a type I IFN response in ADAR1-deficient human cells. This requires the canonical function of LGP2 as an RNA sensor and facilitator of MDA5-dependent signaling. Furthermore, we show that the sensitivity of tumor cells to ADAR1 loss requires LGP2 expression. Finally, type I IFN induction in tumor cells depleted of ADAR1 and treated with some chemotherapeutics fully depends on LGP2 expression. These findings highlight a central role for LGP2 in self RNA sensing with important clinical implications.
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Affiliation(s)
- Jorn E Stok
- Department of ImmunologyLeiden University Medical CentreLeidenThe Netherlands
| | - Timo Oosenbrug
- Department of ImmunologyLeiden University Medical CentreLeidenThe Netherlands
| | - Laurens R ter Haar
- Department of ImmunologyLeiden University Medical CentreLeidenThe Netherlands
| | - Dennis Gravekamp
- Department of ImmunologyLeiden University Medical CentreLeidenThe Netherlands
| | - Christian P Bromley
- Cancer Research UK Manchester InstituteThe University of ManchesterAlderley ParkUK
| | - Santiago Zelenay
- Cancer Research UK Manchester InstituteThe University of ManchesterAlderley ParkUK
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9
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Jongen HJ, Steeneveld GJ, Beringer J, Christen A, Chrysoulakis N, Fortuniak K, Hong J, Hong JW, Jacobs CMJ, Järvi L, Meier F, Pawlak W, Roth M, Theeuwes NE, Velasco E, Vogt R, Teuling AJ. Urban Water Storage Capacity Inferred From Observed Evapotranspiration Recession. Geophys Res Lett 2022; 49:e2021GL096069. [PMID: 35859568 PMCID: PMC9285425 DOI: 10.1029/2021gl096069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 11/30/2021] [Accepted: 12/19/2021] [Indexed: 06/15/2023]
Abstract
Water storage plays an important role in mitigating heat and flooding in urban areas. Assessment of the water storage capacity of cities remains challenging due to the inherent heterogeneity of the urban surface. Traditionally, effective storage has been estimated from runoff. Here, we present a novel approach to estimate effective water storage capacity from recession rates of observed evaporation during precipitation-free periods. We test this approach for cities at neighborhood scale with eddy-covariance based latent heat flux observations from 14 contrasting sites with different local climate zones, vegetation cover and characteristics, and climates. Based on analysis of 583 drydowns, we find storage capacities to vary between 1.3 and 28.4 mm, corresponding to e-folding timescales of 1.8-20.1 days. This makes the urban storage capacity at least five times smaller than all the observed values for natural ecosystems, reflecting an evaporation regime characterized by extreme water limitation.
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Affiliation(s)
- H. J. Jongen
- Hydrology and Quantitative Water ManagementWageningen UniversityWageningenThe Netherlands
- Meteorology and Air QualityWageningen UniversityWageningenThe Netherlands
| | - G. J. Steeneveld
- Meteorology and Air QualityWageningen UniversityWageningenThe Netherlands
| | - J. Beringer
- School of Agriculture and EnvironmentUniversity of Western AustraliaCrawleyWAAustralia
| | - A. Christen
- Chair of Environmental MeteorologyFaculty of Environment and Natural ResourcesUniversity of FreiburgFreiburgGermany
| | - N. Chrysoulakis
- Foundation for Research and Technology HellasInstitute of Applied and Computational MathematicsThe Remote Sensing LabHeraklionGreece
| | - K. Fortuniak
- Department of Meteorology and ClimatologyFaculty of Geographical SciencesUniversity of ŁódźŁódźPoland
| | - J. Hong
- Department of Atmospheric SciencesYonsei UniversitySeoulSouth Korea
| | - J. W. Hong
- Korea Environment InstituteSejongSouth Korea
| | - C. M. J. Jacobs
- Wageningen Environmental ResearchWageningen University and ResearchWageningenThe Netherlands
- National Institute for Public Health and the Environment (RIVM)BilthovenThe Netherlands
| | - L. Järvi
- Institute for Atmospheric and Earth System Research / PhysicsUniversity of HelsinkiHelsinkiFinland
- Helsinki Institute of Sustainability ScienceUniversity of HelsinkiHesinkiFinland
| | - F. Meier
- Chair of ClimatologyTechnische Universität BerlinBerlinGermany
| | - W. Pawlak
- Department of Meteorology and ClimatologyFaculty of Geographical SciencesUniversity of ŁódźŁódźPoland
| | - M. Roth
- Department of GeographyNational University of SingaporeSingaporeSingapore
| | - N. E. Theeuwes
- Department of MeteorologyUniversity of ReadingReadingUK
- Royal Netherlands Meteorological Institute (KNMI)De BiltThe Netherlands
| | - E. Velasco
- Independent Research ScientistSingaporeSingapore
| | - R. Vogt
- Department of Environmental SciencesUniversity of BaselAtmospheric SciencesBaselSwitzerland
| | - A. J. Teuling
- Hydrology and Quantitative Water ManagementWageningen UniversityWageningenThe Netherlands
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10
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Jilbert T, Gustafsson BG, Veldhuijzen S, Reed DC, van Helmond NAGM, Hermans M, Slomp CP. Iron-Phosphorus Feedbacks Drive Multidecadal Oscillations in Baltic Sea Hypoxia. Geophys Res Lett 2021; 48:e2021GL095908. [PMID: 35860449 PMCID: PMC9285756 DOI: 10.1029/2021gl095908] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 11/16/2021] [Accepted: 11/29/2021] [Indexed: 06/13/2023]
Abstract
Hypoxia has occurred intermittently in the Baltic Sea since the establishment of brackish-water conditions at ∼8,000 years B.P., principally as recurrent hypoxic events during the Holocene Thermal Maximum (HTM) and the Medieval Climate Anomaly (MCA). Sedimentary phosphorus release has been implicated as a key driver of these events, but previous paleoenvironmental reconstructions have lacked the sampling resolution to investigate feedbacks in past iron-phosphorus cycling on short timescales. Here we employ Laser Ablation (LA)-ICP-MS scanning of sediment cores to generate ultra-high resolution geochemical records of past hypoxic events. We show that in-phase multidecadal oscillations in hypoxia intensity and iron-phosphorus cycling occurred throughout these events. Using a box model, we demonstrate that such oscillations were likely driven by instabilities in the dynamics of iron-phosphorus cycling under preindustrial phosphorus loads, and modulated by external climate forcing. Oscillatory behavior could complicate the recovery from hypoxia during future trajectories of external loading reductions.
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Affiliation(s)
- Tom Jilbert
- Aquatic Biogeochemistry Research Unit (ABRU)Ecosystems and Environment Research ProgramFaculty of Biological and Environmental SciencesUniversity of HelsinkiHelsinkiFinland
- Tvärminne Zoological StationUniversity of HelsinkiHankoFinland
- Department of Geosciences and GeographyEnvironmental Geochemistry GroupFaculty of ScienceUniversity of HelsinkiHelsinkiFinland
- Department of Earth Sciences (Geochemistry)Faculty of GeosciencesUtrecht UniversityUtrechtThe Netherlands
| | - Bo G. Gustafsson
- Tvärminne Zoological StationUniversity of HelsinkiHankoFinland
- Baltic Nest InstituteBaltic Sea CentreStockholm UniversityStockholmSweden
| | - Simon Veldhuijzen
- Department of Earth Sciences (Geochemistry)Faculty of GeosciencesUtrecht UniversityUtrechtThe Netherlands
| | - Daniel C. Reed
- Department of Earth Sciences (Geochemistry)Faculty of GeosciencesUtrecht UniversityUtrechtThe Netherlands
- Fisheries & Oceans CanadaBedford Institute of OceanographyDartmouthNSCanada
| | - Niels A. G. M. van Helmond
- Department of Earth Sciences (Geochemistry)Faculty of GeosciencesUtrecht UniversityUtrechtThe Netherlands
| | - Martijn Hermans
- Aquatic Biogeochemistry Research Unit (ABRU)Ecosystems and Environment Research ProgramFaculty of Biological and Environmental SciencesUniversity of HelsinkiHelsinkiFinland
- Department of Geosciences and GeographyEnvironmental Geochemistry GroupFaculty of ScienceUniversity of HelsinkiHelsinkiFinland
- Department of Earth Sciences (Geochemistry)Faculty of GeosciencesUtrecht UniversityUtrechtThe Netherlands
| | - Caroline P. Slomp
- Department of Earth Sciences (Geochemistry)Faculty of GeosciencesUtrecht UniversityUtrechtThe Netherlands
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11
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Bao X, Koorengevel MC, Groot Koerkamp MJA, Homavar A, Weijn A, Crielaard S, Renne MF, Lorent JH, Geerts WJC, Surma MA, Mari M, Holstege FCP, Klose C, de Kroon AIPM. Shortening of membrane lipid acyl chains compensates for phosphatidylcholine deficiency in choline-auxotroph yeast. EMBO J 2021; 40:e107966. [PMID: 34520050 PMCID: PMC8521299 DOI: 10.15252/embj.2021107966] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 07/28/2021] [Accepted: 07/30/2021] [Indexed: 12/21/2022] Open
Abstract
Phosphatidylcholine (PC) is an abundant membrane lipid component in most eukaryotes, including yeast, and has been assigned multiple functions in addition to acting as building block of the lipid bilayer. Here, by isolating S. cerevisiae suppressor mutants that exhibit robust growth in the absence of PC, we show that PC essentiality is subject to cellular evolvability in yeast. The requirement for PC is suppressed by monosomy of chromosome XV or by a point mutation in the ACC1 gene encoding acetyl-CoA carboxylase. Although these two genetic adaptations rewire lipid biosynthesis in different ways, both decrease Acc1 activity, thereby reducing average acyl chain length. Consistently, soraphen A, a specific inhibitor of Acc1, rescues a yeast mutant with deficient PC synthesis. In the aneuploid suppressor, feedback inhibition of Acc1 through acyl-CoA produced by fatty acid synthase (FAS) results from upregulation of lipid synthesis. The results show that budding yeast regulates acyl chain length by fine-tuning the activities of Acc1 and FAS and indicate that PC evolved by benefitting the maintenance of membrane fluidity.
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Affiliation(s)
- Xue Bao
- Membrane Biochemistry & BiophysicsBijvoet Center for Biomolecular Research and Institute of BiomembranesUtrecht UniversityUtrechtThe Netherlands
| | - Martijn C Koorengevel
- Membrane Biochemistry & BiophysicsBijvoet Center for Biomolecular Research and Institute of BiomembranesUtrecht UniversityUtrechtThe Netherlands
| | | | - Amir Homavar
- Membrane Biochemistry & BiophysicsBijvoet Center for Biomolecular Research and Institute of BiomembranesUtrecht UniversityUtrechtThe Netherlands
| | - Amrah Weijn
- Membrane Biochemistry & BiophysicsBijvoet Center for Biomolecular Research and Institute of BiomembranesUtrecht UniversityUtrechtThe Netherlands
| | - Stefan Crielaard
- Membrane Biochemistry & BiophysicsBijvoet Center for Biomolecular Research and Institute of BiomembranesUtrecht UniversityUtrechtThe Netherlands
| | - Mike F Renne
- Membrane Biochemistry & BiophysicsBijvoet Center for Biomolecular Research and Institute of BiomembranesUtrecht UniversityUtrechtThe Netherlands
| | - Joseph H Lorent
- Membrane Biochemistry & BiophysicsBijvoet Center for Biomolecular Research and Institute of BiomembranesUtrecht UniversityUtrechtThe Netherlands
| | - Willie JC Geerts
- Cryo‐Electron MicroscopyBijvoet Center for Biomolecular ResearchUtrecht UniversityUtrechtThe Netherlands
| | | | - Muriel Mari
- Department of Biomedical Sciences of Cells & SystemsUniversity Medical Center GroningenUniversity of GroningenGroningenThe Netherlands
| | | | | | - Anton I P M de Kroon
- Membrane Biochemistry & BiophysicsBijvoet Center for Biomolecular Research and Institute of BiomembranesUtrecht UniversityUtrechtThe Netherlands
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12
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Fleury E, Trnková P, Spruijt K, Herault J, Lebbink F, Heufelder J, Hrbacek J, Horwacik T, Kajdrowicz T, Denker A, Gerard A, Hofverberg P, Mamalui M, Slopsema R, Pignol J, Hoogeman M. Characterization of the HollandPTC proton therapy beamline dedicated to uveal melanoma treatment and an interinstitutional comparison. Med Phys 2021; 48:4506-4522. [PMID: 34091930 PMCID: PMC8457201 DOI: 10.1002/mp.15024] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 05/08/2021] [Accepted: 05/25/2021] [Indexed: 12/30/2022] Open
Abstract
PURPOSE Eye-dedicated proton therapy (PT) facilities are used to treat malignant intraocular lesions, especially uveal melanoma (UM). The first commercial ocular PT beamline from Varian was installed in the Netherlands. In this work, the conceptual design of the new eyeline is presented. In addition, a comprehensive comparison against five PT centers with dedicated ocular beamlines is performed, and the clinical impact of the identified differences is analyzed. MATERIAL/METHODS The HollandPTC eyeline was characterized. Four centers in Europe and one in the United States joined the study. All centers use a cyclotron for proton beam generation and an eye-dedicated nozzle. Differences among the chosen ocular beamlines were in the design of the nozzle, nominal energy, and energy spectrum. The following parameters were collected for all centers: technical characteristics and a set of distal, proximal, and lateral region measurements. The measurements were performed with detectors available in-house at each institution. The institutions followed the International Atomic Energy Agency (IAEA) Technical Report Series (TRS)-398 Code of Practice for absolute dose measurement, and the IAEA TRS-398 Code of Practice, its modified version or International Commission on Radiation Units and Measurements Report No. 78 for spread-out Bragg peak normalization. Energy spreads of the pristine Bragg peaks were obtained with Monte Carlo simulations using Geant4. Seven tumor-specific case scenarios were simulated to evaluate the clinical impact among centers: small, medium, and large UM, located either anteriorly, at the equator, or posteriorly within the eye. Differences in the depth dose distributions were calculated. RESULTS A pristine Bragg peak of HollandPTC eyeline corresponded to the constant energy of 75 MeV (maximal range 3.97 g/cm2 in water) with an energy spread of 1.10 MeV. The pristine Bragg peaks for the five participating centers varied from 62.50 to 104.50 MeV with an energy spread variation between 0.10 and 0.70 MeV. Differences in the average distal fall-offs and lateral penumbrae (LPs) (over the complete set of clinically available beam modulations) among all centers were up to 0.25 g/cm2 , and 0.80 mm, respectively. Average distal fall-offs of the HollandPTC eyeline were 0.20 g/cm2 , and LPs were between 1.50 and 2.15 mm from proximal to distal regions, respectively. Treatment time, around 60 s, was comparable among all centers. The virtual source-to-axis distance of 120 cm at HollandPTC was shorter than for the five participating centers (range: 165-350 cm). Simulated depth dose distributions demonstrated the impact of the different beamline characteristics among institutions. The largest difference was observed for a small UM located at the posterior pole, where a proximal dose between two extreme centers was up to 20%. CONCLUSIONS HollandPTC eyeline specifications are in accordance with five other ocular PT beamlines. Similar clinical concepts can be applied to expect the same high local tumor control. Dosimetrical properties among the six institutions induce most likely differences in ocular radiation-related toxicities. This interinstitutional comparison could support further research on ocular post-PT complications. Finally, the findings reported in this study could be used to define dosimetrical guidelines for ocular PT to unify the concepts among institutions.
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Affiliation(s)
- Emmanuelle Fleury
- Department of RadiotherapyErasmus MC Cancer Institute, University Medical Center RotterdamThe Netherlands
- Holland Proton Therapy CenterDelftThe Netherlands
| | - Petra Trnková
- Department of RadiotherapyErasmus MC Cancer Institute, University Medical Center RotterdamThe Netherlands
- Departement of Radiation OncologyMedical University of ViennaViennaAustria
| | - Kees Spruijt
- Holland Proton Therapy CenterDelftThe Netherlands
| | - Joël Herault
- Departement of Radiation OncologyCentre Antoine LacassagneNiceFrance
| | | | - Jens Heufelder
- Helmholtz‐Zentrum Berlin für Materialien und EnergieBerlinGermany
- Department of OphthalmologyCharité ‐ Universitätsmedizin BerlinBerlinGermany
| | - Jan Hrbacek
- Paul Scherrer Institute Center for Proton TherapyVilligenSwitzerland
| | - Tomasz Horwacik
- Institute of Nuclear PhysicsPolish Academy of SciencesKrakówPoland
| | | | - Andrea Denker
- Helmholtz‐Zentrum Berlin für Materialien und EnergieBerlinGermany
| | - Anaïs Gerard
- Departement of Radiation OncologyCentre Antoine LacassagneNiceFrance
| | - Petter Hofverberg
- Departement of Radiation OncologyCentre Antoine LacassagneNiceFrance
| | - Maria Mamalui
- Department of Radiation OncologyUniversity of FloridaGainesvilleFloridaUSA
| | - Roelf Slopsema
- Department of Radiation OncologyEmory Proton Therapy CenterAtlantaGeorgiaUSA
| | | | - Mischa Hoogeman
- Department of RadiotherapyErasmus MC Cancer Institute, University Medical Center RotterdamThe Netherlands
- Holland Proton Therapy CenterDelftThe Netherlands
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13
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Sellevold R, Vizcaino M. First Application of Artificial Neural Networks to Estimate 21st Century Greenland Ice Sheet Surface Melt. Geophys Res Lett 2021; 48:e2021GL092449. [PMID: 35866045 PMCID: PMC9285918 DOI: 10.1029/2021gl092449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 07/08/2021] [Accepted: 07/26/2021] [Indexed: 06/15/2023]
Abstract
Future Greenland ice sheet (GrIS) melt projections are limited by the lack of explicit melt calculations within most global climate models and the high computational cost of dynamical downscaling with regional climate models (RCMs). Here, we train artificial neural networks (ANNs) to obtain relationships between quantities consistently available from global climate model simulations and annually integrated GrIS surface melt. To this end, we train the ANNs with model output from the Community Earth System Model 2.1 (CESM2), which features an interactive surface melt calculation based on a downscaled surface energy balance. We find that ANNs compare well with an independent CESM2 simulation and RCM simulations forced by a CMIP6 subset. The ANNs estimate a melt increase for 2,081-2,100 ranging from 414 ± 275 Gt y r - 1 (SSP1-2.6) to 1,378 ± 555 Gt y r - 1 (SSP5-8.5) for the full CMIP6 suite. The primary source of uncertainty throughout the 21st century is the spread of climate model sensitivity.
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Affiliation(s)
- Raymond Sellevold
- Geoscience and Remote SensingDelft University of TechnologyDelftThe Netherlands
| | - Miren Vizcaino
- Geoscience and Remote SensingDelft University of TechnologyDelftThe Netherlands
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14
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Muntjewerf L, Sacks WJ, Lofverstrom M, Fyke J, Lipscomb WH, Ernani da Silva C, Vizcaino M, Thayer‐Calder K, Lenaerts JTM, Sellevold R. Description and Demonstration of the Coupled Community Earth System Model v2 - Community Ice Sheet Model v2 (CESM2-CISM2). J Adv Model Earth Syst 2021; 13:e2020MS002356. [PMID: 34434489 PMCID: PMC8365656 DOI: 10.1029/2020ms002356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 05/06/2021] [Accepted: 05/21/2021] [Indexed: 06/13/2023]
Abstract
Earth system/ice-sheet coupling is an area of recent, major Earth System Model (ESM) development. This work occurs at the intersection of glaciology and climate science and is motivated by a need for robust projections of sea-level rise. The Community Ice Sheet Model version 2 (CISM2) is the newest component model of the Community Earth System Model version 2 (CESM2). This study describes the coupling and novel capabilities of the model, including: (1) an advanced energy-balance-based surface mass balance calculation in the land component with downscaling via elevation classes; (2) a closed freshwater budget from ice sheet to the ocean from surface runoff, basal melting, and ice discharge; (3) dynamic land surface types; and (4) dynamic atmospheric topography. The Earth system/ice-sheet coupling is demonstrated in a simulation with an evolving Greenland Ice Sheet (GrIS) under an idealized high CO2 scenario. The model simulates a large expansion of ablation areas (where surface ablation exceeds snow accumulation) and a large increase in surface runoff. This results in an elevated freshwater flux to the ocean, as well as thinning of the ice sheet and area retreat. These GrIS changes result in reduced Greenland surface albedo, changes in the sign and magnitude of sensible and latent heat fluxes, and modified surface roughness and overall ice sheet topography. Representation of these couplings between climate and ice sheets is key for the simulation of ice and climate interactions.
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Affiliation(s)
- Laura Muntjewerf
- Department of Geoscience and Remote SensingDelft University of TechnologyDelftThe Netherlands
| | - William J. Sacks
- Climate and Global Dynamics LaboratoryNational Center for Atmospheric ResearchBoulderCOUSA
| | | | - Jeremy Fyke
- Associated Engineering Group LtdCalgaryABCanada
| | - William H. Lipscomb
- Climate and Global Dynamics LaboratoryNational Center for Atmospheric ResearchBoulderCOUSA
| | | | - Miren Vizcaino
- Department of Geoscience and Remote SensingDelft University of TechnologyDelftThe Netherlands
| | | | - Jan T. M. Lenaerts
- Department of Atmospheric and Oceanic SciencesUniversity of Colorado BoulderBoulderCOUSA
| | - Raymond Sellevold
- Department of Geoscience and Remote SensingDelft University of TechnologyDelftThe Netherlands
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15
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Serlidaki D, van Waarde MAWH, Rohland L, Wentink AS, Dekker SL, Kamphuis MJ, Boertien JM, Brunsting JF, Nillegoda NB, Bukau B, Mayer MP, Kampinga HH, Bergink S. Functional diversity between HSP70 paralogs caused by variable interactions with specific co-chaperones. J Biol Chem 2020; 295:7301-7316. [PMID: 32284329 PMCID: PMC7247296 DOI: 10.1074/jbc.ra119.012449] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 04/08/2020] [Indexed: 12/12/2022] Open
Abstract
Heat shock protein 70 (HSP70) chaperones play a central role in protein quality control and are crucial for many cellular processes, including protein folding, degradation, and disaggregation. Human HSP70s compose a family of 13 members that carry out their functions with the aid of even larger families of co-chaperones. A delicate interplay between HSP70s and co-chaperone recruitment is thought to determine substrate fate, yet it has been generally assumed that all Hsp70 paralogs have similar activities and are largely functionally redundant. However, here we found that when expressed in human cells, two highly homologous HSP70s, HSPA1A and HSPA1L, have opposing effects on cellular handling of various substrates. For example, HSPA1A reduced aggregation of the amyotrophic lateral sclerosis-associated protein variant superoxide dismutase 1 (SOD1)-A4V, whereas HSPA1L enhanced its aggregation. Intriguingly, variations in the substrate-binding domain of these HSP70s did not play a role in this difference. Instead, we observed that substrate fate is determined by differential interactions of the HSP70s with co-chaperones. Whereas most co-chaperones bound equally well to these two HSP70s, Hsp70/Hsp90-organizing protein (HOP) preferentially bound to HSPA1L, and the Hsp110 nucleotide-exchange factor HSPH2 preferred HSPA1A. The role of HSPH2 was especially crucial for the HSPA1A-mediated reduction in SOD1-A4V aggregation. These findings reveal a remarkable functional diversity at the level of the cellular HSP70s and indicate that this diversity is defined by their affinities for specific co-chaperones such as HSPH2.
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Affiliation(s)
- Despina Serlidaki
- Department of Biomedical Sciences of Cells and Systems, University Medical Center Groningen, University of Groningen, 9713 AV Groningen, The Netherlands
| | - Maria A W H van Waarde
- Department of Biomedical Sciences of Cells and Systems, University Medical Center Groningen, University of Groningen, 9713 AV Groningen, The Netherlands
| | - Lukas Rohland
- Center for Molecular Biology of the University of Heidelberg and the German Cancer Research Center, 69120 Heidelberg, Germany
| | - Anne S Wentink
- Center for Molecular Biology of the University of Heidelberg and the German Cancer Research Center, 69120 Heidelberg, Germany
| | - Suzanne L Dekker
- Department of Biomedical Sciences of Cells and Systems, University Medical Center Groningen, University of Groningen, 9713 AV Groningen, The Netherlands
| | - Maarten J Kamphuis
- Department of Biomedical Sciences of Cells and Systems, University Medical Center Groningen, University of Groningen, 9713 AV Groningen, The Netherlands
| | - Jeffrey M Boertien
- Department of Biomedical Sciences of Cells and Systems, University Medical Center Groningen, University of Groningen, 9713 AV Groningen, The Netherlands
| | - Jeanette F Brunsting
- Department of Biomedical Sciences of Cells and Systems, University Medical Center Groningen, University of Groningen, 9713 AV Groningen, The Netherlands
| | - Nadinath B Nillegoda
- Center for Molecular Biology of the University of Heidelberg and the German Cancer Research Center, 69120 Heidelberg, Germany; Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Bernd Bukau
- Center for Molecular Biology of the University of Heidelberg and the German Cancer Research Center, 69120 Heidelberg, Germany
| | - Matthias P Mayer
- Center for Molecular Biology of the University of Heidelberg and the German Cancer Research Center, 69120 Heidelberg, Germany
| | - Harm H Kampinga
- Department of Biomedical Sciences of Cells and Systems, University Medical Center Groningen, University of Groningen, 9713 AV Groningen, The Netherlands.
| | - Steven Bergink
- Department of Biomedical Sciences of Cells and Systems, University Medical Center Groningen, University of Groningen, 9713 AV Groningen, The Netherlands.
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16
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Rontogianni S, Iskit S, van Doorn S, Peeper DS, Altelaar M. Combined EGFR and ROCK Inhibition in Triple-negative Breast Cancer Leads to Cell Death Via Impaired Autophagic Flux. Mol Cell Proteomics 2020; 19:261-277. [PMID: 31772060 PMCID: PMC7000121 DOI: 10.1074/mcp.ra119.001800] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Indexed: 12/12/2022] Open
Abstract
Triple-negative breast cancer (TNBC) is an aggressive subtype of breast cancer with very limited therapeutic options. We have recently shown that the combined inhibition of EGFR and ROCK in TNBC cells results in cell death, however, the underlying mechanisms remain unclear. To investigate this, here we applied a mass spectrometry-based proteomic approach to identify proteins altered on single and combination treatments. Our proteomic data revealed autophagy as the major molecular mechanism implicated in the cells' response to combinatorial treatment. We here show that EGFR inhibition by gefitinib treatment alone induces autophagy, a cellular recycling process that acts as a cytoprotective response for TNBC cells. However, combined inhibition of EGFR and ROCK leads to autophagy blockade and accumulation of autophagic vacuoles. Our data show impaired autophagosome clearance as a likely cause of antitumor activity. We propose that the inhibition of the autophagic flux on combinatorial treatment is attributed to the major cytoskeletal changes induced on ROCK inhibition, given the essential role the cytoskeleton plays throughout the various steps of the autophagy process.
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Affiliation(s)
- Stamatia Rontogianni
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; Netherlands Proteomics Center, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Sedef Iskit
- Division of Molecular Oncology, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Sander van Doorn
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; Netherlands Proteomics Center, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Daniel S Peeper
- Division of Molecular Oncology, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Maarten Altelaar
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; Netherlands Proteomics Center, Padualaan 8, 3584 CH Utrecht, The Netherlands; Mass Spectrometry and Proteomics Facility, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands.
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17
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Abstract
The medical treatment of infectious diseases often requires combination therapies that blend two molecules to enhance drug efficacy. Nature does the same. In a new article, Mrak et al. identify and functionally characterize natural products from Streptomyces rapamycinicus that show synergistic antifungal activity with the well-known immunosuppressant metabolite rapamycin, produced by the same strain. The genomic co-association of the two biosynthetic gene clusters paves the way toward new strategies to discover synergistic pairs of antibiotics through large-scale genome mining.
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Affiliation(s)
- Mohammad Alanjary
- From the Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
| | - Marnix H Medema
- From the Bioinformatics Group, Wageningen University, Wageningen, The Netherlands.
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18
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Halim VA, García-Santisteban I, Warmerdam DO, van den Broek B, Heck AJR, Mohammed S, Medema RH. Doxorubicin-induced DNA Damage Causes Extensive Ubiquitination of Ribosomal Proteins Associated with a Decrease in Protein Translation. Mol Cell Proteomics 2018; 17:2297-2308. [PMID: 29438997 PMCID: PMC6283304 DOI: 10.1074/mcp.ra118.000652] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Indexed: 11/06/2022] Open
Abstract
Protein posttranslational modifications (PTMs) play a central role in the DNA damage response. In particular, protein phosphorylation and ubiquitination have been shown to be essential in the signaling cascade that coordinates break repair with cell cycle progression. Here, we performed whole-cell quantitative proteomics to identify global changes in protein ubiquitination that are induced by DNA double-strand breaks. In total, we quantified more than 9,400 ubiquitin sites and found that the relative abundance of ∼10% of these sites was altered in response to DNA double-strand breaks. Interestingly, a large proportion of ribosomal proteins, including those from the 40S as well as the 60S subunit, were ubiquitinated in response to DNA damage. In parallel, we discovered that DNA damage leads to the inhibition of ribosome function. Taken together, these data uncover the ribosome as a major target of the DNA damage response.
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Affiliation(s)
- Vincentius A Halim
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CH Utrecht, The Netherlands; Netherlands Proteomics Centre, 3584 CH Utrecht, The Netherlands; Division of Cell Biology and Cancer Genomics Center, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Iraia García-Santisteban
- Division of Cell Biology and Cancer Genomics Center, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands; Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Daniel O Warmerdam
- Division of Cell Biology and Cancer Genomics Center, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands; European Research Institute for the Biology of Ageing, University Medical Center Groningen, 9713 AV Groningen, The Netherlands
| | - Bram van den Broek
- Division of Cell Biology and Cancer Genomics Center, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CH Utrecht, The Netherlands; Netherlands Proteomics Centre, 3584 CH Utrecht, The Netherlands
| | - Shabaz Mohammed
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CH Utrecht, The Netherlands; Netherlands Proteomics Centre, 3584 CH Utrecht, The Netherlands; Department of Biochemistry, University of Oxford, OX13TA Oxford, United Kingdom; Chemistry Research Laboratory, Department of Chemistry, University of Oxford, OX13TA Oxford, United Kingdom
| | - René H Medema
- Division of Cell Biology and Cancer Genomics Center, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands.
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