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Muñoz F, Fex M, Moritz T, Mulder H, Cataldo LR. Unique features of β-cell metabolism are lost in type 2 diabetes. Acta Physiol (Oxf) 2024:e14148. [PMID: 38656044 DOI: 10.1111/apha.14148] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 02/28/2024] [Accepted: 04/05/2024] [Indexed: 04/26/2024]
Abstract
Pancreatic β cells play an essential role in the control of systemic glucose homeostasis as they sense blood glucose levels and respond by secreting insulin. Upon stimulating glucose uptake in insulin-sensitive tissues post-prandially, this anabolic hormone restores blood glucose levels to pre-prandial levels. Maintaining physiological glucose levels thus relies on proper β-cell function. To fulfill this highly specialized nutrient sensor role, β cells have evolved a unique genetic program that shapes its distinct cellular metabolism. In this review, the unique genetic and metabolic features of β cells will be outlined, including their alterations in type 2 diabetes (T2D). β cells selectively express a set of genes in a cell type-specific manner; for instance, the glucose activating hexokinase IV enzyme or Glucokinase (GCK), whereas other genes are selectively "disallowed", including lactate dehydrogenase A (LDHA) and monocarboxylate transporter 1 (MCT1). This selective gene program equips β cells with a unique metabolic apparatus to ensure that nutrient metabolism is coupled to appropriate insulin secretion, thereby avoiding hyperglycemia, as well as life-threatening hypoglycemia. Unlike most cell types, β cells exhibit specialized bioenergetic features, including supply-driven rather than demand-driven metabolism and a high basal mitochondrial proton leak respiration. The understanding of these unique genetically programmed metabolic features and their alterations that lead to β-cell dysfunction is crucial for a comprehensive understanding of T2D pathophysiology and the development of innovative therapeutic approaches for T2D patients.
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Affiliation(s)
- Felipe Muñoz
- Clinical Research Center, Department of Clinical Sciences in Malmö, Lund University Diabetes Centre, Lund, Sweden
| | - Malin Fex
- Clinical Research Center, Department of Clinical Sciences in Malmö, Lund University Diabetes Centre, Lund, Sweden
| | - Thomas Moritz
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Hindrik Mulder
- Clinical Research Center, Department of Clinical Sciences in Malmö, Lund University Diabetes Centre, Lund, Sweden
| | - Luis Rodrigo Cataldo
- Clinical Research Center, Department of Clinical Sciences in Malmö, Lund University Diabetes Centre, Lund, Sweden
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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2
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Nandi S, Stenquist A, Papoulia A, Olofsson E, Badano L, Bertolino M, Busto D, Callegari C, Carlström S, Danailov MB, Demekhin PV, Di Fraia M, Eng-Johnsson P, Feifel R, Gallician G, Giannessi L, Gisselbrecht M, Manfredda M, Meyer M, Miron C, Peschel J, Plekan O, Prince KC, Squibb RJ, Zangrando M, Zapata F, Zhong S, Dahlström JM. Generation of entanglement using a short-wavelength seeded free-electron laser. Sci Adv 2024; 10:eado0668. [PMID: 38630815 PMCID: PMC11023495 DOI: 10.1126/sciadv.ado0668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 03/14/2024] [Indexed: 04/19/2024]
Abstract
Quantum entanglement between the degrees of freedom encountered in the classical world is challenging to observe due to the surrounding environment. To elucidate this issue, we investigate the entanglement generated over ultrafast timescales in a bipartite quantum system comprising two massive particles: a free-moving photoelectron, which expands to a mesoscopic length scale, and a light-dressed atomic ion, which represents a hybrid state of light and matter. Although the photoelectron spectra are measured classically, the entanglement allows us to reveal information about the dressed-state dynamics of the ion and the femtosecond extreme ultraviolet pulses delivered by a seeded free-electron laser. The observed generation of entanglement is interpreted using the time-dependent von Neumann entropy. Our results unveil the potential for using short-wavelength coherent light pulses from free-electron lasers to generate entangled photoelectron and ion systems for studying spooky action at a distance.
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Affiliation(s)
- Saikat Nandi
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, 69622, Villeurbanne, France
| | - Axel Stenquist
- Department of Physics, Lund University, 22100 Lund, Sweden
| | | | - Edvin Olofsson
- Department of Physics, Lund University, 22100 Lund, Sweden
| | - Laura Badano
- Elettra-Sincrotrone Trieste, 34149 Basovizza, Trieste, Italy
| | | | - David Busto
- Department of Physics, Lund University, 22100 Lund, Sweden
| | - Carlo Callegari
- Elettra-Sincrotrone Trieste, 34149 Basovizza, Trieste, Italy
| | | | | | - Philipp V. Demekhin
- Institute of Physics and CINSaT, University of Kassel, 34132 Kassel, Germany
| | | | | | - Raimund Feifel
- Department of Physics, University of Gothenburg, 41258 Gothenburg, Sweden
| | | | - Luca Giannessi
- Elettra-Sincrotrone Trieste, 34149 Basovizza, Trieste, Italy
- INFN, Laboratori Nazionali di Frascati, 00044 Frascati, Italy
| | | | | | | | - Catalin Miron
- Université Paris-Saclay, CEA, CNRS, LIDYL, 91191 Gif-sur-Yvette, France
- ELI-NP, “Horia Hulubei” National Institute for Physics and Nuclear Engineering, 077125 Mǎgurele, Romania
| | - Jasper Peschel
- Department of Physics, Lund University, 22100 Lund, Sweden
| | - Oksana Plekan
- Elettra-Sincrotrone Trieste, 34149 Basovizza, Trieste, Italy
| | - Kevin C. Prince
- Elettra-Sincrotrone Trieste, 34149 Basovizza, Trieste, Italy
| | - Richard J. Squibb
- Department of Physics, University of Gothenburg, 41258 Gothenburg, Sweden
| | - Marco Zangrando
- Elettra-Sincrotrone Trieste, 34149 Basovizza, Trieste, Italy
- IOM-CNR, Istituto Officina dei Materiali, 34149 Basovizza, Trieste, Italy
| | - Felipe Zapata
- Department of Physics, Lund University, 22100 Lund, Sweden
| | - Shiyang Zhong
- Department of Physics, Lund University, 22100 Lund, Sweden
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3
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van Osch MJP, Wåhlin A, Scheyhing P, Mossige I, Hirschler L, Eklund A, Mogensen K, Gomolka R, Radbruch A, Qvarlander S, Decker A, Nedergaard M, Mori Y, Eide PK, Deike K, Ringstad G. Human brain clearance imaging: Pathways taken by magnetic resonance imaging contrast agents after administration in cerebrospinal fluid and blood. NMR Biomed 2024:e5159. [PMID: 38634301 DOI: 10.1002/nbm.5159] [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] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 02/26/2024] [Accepted: 03/11/2024] [Indexed: 04/19/2024]
Abstract
Over the last decade, it has become evident that cerebrospinal fluid (CSF) plays a pivotal role in brain solute clearance through perivascular pathways and interactions between the brain and meningeal lymphatic vessels. Whereas most of this fundamental knowledge was gained from rodent models, human brain clearance imaging has provided important insights into the human system and highlighted the existence of important interspecies differences. Current gold standard techniques for human brain clearance imaging involve the injection of gadolinium-based contrast agents and monitoring their distribution and clearance over a period from a few hours up to 2 days. With both intrathecal and intravenous injections being used, which each have their own specific routes of distribution and thus clearance of contrast agent, a clear understanding of the kinetics associated with both approaches, and especially the differences between them, is needed to properly interpret the results. Because it is known that intrathecally injected contrast agent reaches the blood, albeit in small concentrations, and that similarly some of the intravenously injected agent can be detected in CSF, both pathways are connected and will, in theory, reach the same compartments. However, because of clear differences in relative enhancement patterns, both injection approaches will result in varying sensitivities for assessment of different subparts of the brain clearance system. In this opinion review article, the "EU Joint Programme - Neurodegenerative Disease Research (JPND)" consortium on human brain clearance imaging provides an overview of contrast agent pharmacokinetics in vivo following intrathecal and intravenous injections and what typical concentrations and concentration-time curves should be expected. This can be the basis for optimizing and interpreting contrast-enhanced MRI for brain clearance imaging. Furthermore, this can shed light on how molecules may exchange between blood, brain, and CSF.
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Affiliation(s)
- Matthias J P van Osch
- C. J. Gorter MRI Center, Department of Radiology, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Anders Wåhlin
- Department of Radiation Sciences, Radiation Physics, Biomedical Engineering, Umeå University, Umeå, Sweden
- Department of Applied Physics and Electronics, Umeå University, Umeå, Sweden
- Umeå Center for Functional Brain Imaging, Umeå University, Umeå, Sweden
| | - Paul Scheyhing
- Department of Neuroradiology, University Medical Center Bonn, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Ingrid Mossige
- Division of Radiology and Nuclear Medicine, Department of Physics and Computational Radiology, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, The Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Lydiane Hirschler
- C. J. Gorter MRI Center, Department of Radiology, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Anders Eklund
- Department of Radiation Sciences, Radiation Physics, Biomedical Engineering, Umeå University, Umeå, Sweden
- Umeå Center for Functional Brain Imaging, Umeå University, Umeå, Sweden
| | - Klara Mogensen
- Department of Radiation Sciences, Radiation Physics, Biomedical Engineering, Umeå University, Umeå, Sweden
| | - Ryszard Gomolka
- Center for Translational Neuromedicine, University of Copenhagen, Copenhagen, Denmark
| | - Alexander Radbruch
- Department of Neuroradiology, University Medical Center Bonn, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Sara Qvarlander
- Department of Radiation Sciences, Radiation Physics, Biomedical Engineering, Umeå University, Umeå, Sweden
| | - Andreas Decker
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Maiken Nedergaard
- Center for Translational Neuromedicine, University of Copenhagen, Copenhagen, Denmark
- Center for Translational Neuromedicine, University of Rochester Medical Center, Rochester, New York, USA
| | - Yuki Mori
- Center for Translational Neuromedicine, University of Copenhagen, Copenhagen, Denmark
| | - Per Kristian Eide
- Department of Neurosurgery, Oslo University Hospital-Rikshospitalet, Oslo, Norway
- KG Jebsen Centre for Brain Fluid Research, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Katerina Deike
- Department of Neuroradiology, University Medical Center Bonn, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Geir Ringstad
- Department of Radiology, Oslo University Hospital-Rikshospitalet, Oslo, Norway
- Department of Geriatrics and Internal Medicine, Sorlandet Hospital, Arendal, Norway
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Abdel-Fattah WR, Carlsson M, Hu GZ, Singh A, Vergara A, Aslam R, Ronne H, Björklund S. Growth-regulated co-occupancy of Mediator and Lsm3 at intronic ribosomal protein genes. Nucleic Acids Res 2024:gkae266. [PMID: 38613396 DOI: 10.1093/nar/gkae266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 03/22/2024] [Accepted: 04/01/2024] [Indexed: 04/14/2024] Open
Abstract
Mediator is a well-known transcriptional co-regulator and serves as an adaptor between gene-specific regulatory proteins and RNA polymerase II. Studies on the chromatin-bound form of Mediator revealed interactions with additional protein complexes involved in various transcription-related processes, such as the Lsm2-8 complex that is part of the spliceosomal U6 small nuclear ribonucleoprotein complex. Here, we employ Chromatin Immunoprecipitation sequencing (ChIP-seq) of chromatin associated with the Lsm3 protein and the Med1 or Med15 Mediator subunits. We identify 86 genes co-occupied by both Lsm3 and Mediator, of which 73 were intron-containing ribosomal protein genes. In logarithmically growing cells, Mediator primarily binds to their promoter regions but also shows a second, less pronounced occupancy at their 3'-exons. During the late exponential phase, we observe a near-complete transition of Mediator from these promoters to a position in their 3'-ends, overlapping the Lsm3 binding sites ∼250 bp downstream of their last intron-exon boundaries. Using an unbiased RNA sequencing approach, we show that transition of Mediator from promoters to the last exon of these genes correlates to reduction of both their messenger RNA levels and splicing ratios, indicating that the Mediator and Lsm complexes cooperate to control growth-regulated expression of intron-containing ribosomal protein genes at the levels of transcription and splicing.
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Affiliation(s)
- Wael R Abdel-Fattah
- Department of Medical Biochemistry and Biophysics, Umeå University, SE-901 87 Umeå, Sweden
| | - Mattias Carlsson
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Box 7026, SE-750 07 Uppsala, Sweden
| | - Guo-Zhen Hu
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Box 7026, SE-750 07 Uppsala, Sweden
| | - Ajeet Singh
- Department of Medical Biochemistry and Biophysics, Umeå University, SE-901 87 Umeå, Sweden
| | - Alexander Vergara
- Department of Plant Physiology, Umeå University, SE-901 87 Umeå, Sweden
| | - Rameen Aslam
- Department of Medical Biochemistry and Biophysics, Umeå University, SE-901 87 Umeå, Sweden
| | - Hans Ronne
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Box 7026, SE-750 07 Uppsala, Sweden
| | - Stefan Björklund
- Department of Medical Biochemistry and Biophysics, Umeå University, SE-901 87 Umeå, Sweden
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De Vincentis A, Tavaglione F, Namba S, Kanai M, Okada Y, Kamatani Y, Maurotti S, Pedone C, Antonelli Incalzi R, Valenti L, Romeo S, Vespasiani-Gentilucci U. Poor accuracy and sustainability of the first-step FIB4 EASL pathway for stratifying steatotic liver disease risk in the general population. Aliment Pharmacol Ther 2024. [PMID: 38497224 DOI: 10.1111/apt.17953] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 10/15/2023] [Accepted: 03/03/2024] [Indexed: 03/19/2024]
Abstract
BACKGROUND AND AIMS The European Association for the Study of the Liver introduced a clinical pathway (EASL CP) for screening significant/advanced fibrosis in people at risk of steatotic liver disease (SLD). We assessed the performance of the first-step FIB4 EASL CP in the general population across different SLD risk groups (MASLD, Met-ALD and ALD) and various age classes. METHODS We analysed a total of 3372 individuals at risk of SLD from the 2017-2018 National Health and Nutrition Examination Survey (NHANES17-18), projected to 152.3 million U.S. adults, 300,329 from the UK Biobank (UKBB) and 57,644 from the Biobank Japan (BBJ). We assessed liver stiffness measurement (LSM) ≥8 kPa and liver-related events occurring within 3 and 10 years (3/10 year-LREs) as outcomes. We defined MASLD, MetALD, and ALD according to recent international recommendations. RESULTS FIB4 sensitivity for LSM ≥ 8 kPa was low (27.7%), but it ranged approximately 80%-90% for 3-year LREs. Using FIB4, 22%-57% of subjects across the three cohorts were identified as candidates for vibration-controlled transient elastography (VCTE), which was mostly avoidable (positive predictive value of FIB4 ≥ 1.3 for LSM ≥ 8 kPa ranging 9.5%-13% across different SLD categories). Sensitivity for LSM ≥ 8 kPa and LREs increased with increasing alcohol intake (ALD>MetALD>MASLD) and age classes. For individuals aged ≥65 years, using the recommended age-adjusted FIB4 cut-off (≥2) substantially reduced sensitivity for LSM ≥ 8 kPa and LREs. CONCLUSIONS The first-step FIB4 EASL CP is poorly accurate and feasible for individuals at risk of SLD in the general population. It is crucial to enhance the screening strategy with a first-step approach able to reduce unnecessary VCTEs and optimise their yield.
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Affiliation(s)
- Antonio De Vincentis
- Internal Medicine Unit, Department of Internal Medicine and Geriatrics, Campus Bio-Medico University, Rome, Italy
| | - Federica Tavaglione
- Clinical Medicine and Hepatology Unit, Department of Internal Medicine and Geriatrics, Campus Bio-Medico University, Rome, Italy
- Department of Molecular and Clinical Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Shinichi Namba
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
| | - Masahiro Kanai
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Yukinori Okada
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Department of Genome Informatics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan
- Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Japan
| | - Yoichiro Kamatani
- Laboratory of Complex Trait Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Samantha Maurotti
- Clinical Nutrition Unit, Department of Medical and Surgical Science, Magna Graecia University, Catanzaro, Italy
| | - Claudio Pedone
- Unit of Geriatrics, Department of Internal Medicine and Geriatrics, Campus Bio-Medico University, Rome, Italy
| | - Raffaele Antonelli Incalzi
- Internal Medicine Unit, Department of Internal Medicine and Geriatrics, Campus Bio-Medico University, Rome, Italy
| | - Luca Valenti
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milano, Italy
- Translational Medicine, Biological Resource Center, Department of Transfusion Medicine, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milano, Italy
| | - Stefano Romeo
- Department of Molecular and Clinical Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Clinical Nutrition Unit, Department of Medical and Surgical Science, Magna Graecia University, Catanzaro, Italy
- Department of Cardiology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Umberto Vespasiani-Gentilucci
- Clinical Medicine and Hepatology Unit, Department of Internal Medicine and Geriatrics, Campus Bio-Medico University, Rome, Italy
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Salzinger B, Lundwall K, Evans M, Mörtberg J, Wallén H, Jernberg T, Kahan T, Lundman P, Tornvall P, Erlinge D, Lindahl B, Baron T, Rezeli M, Spaak J, Jacobson SH. Associations between inflammatory and angiogenic proteomic biomarkers, and cardiovascular events and mortality in relation to kidney function. Clin Kidney J 2024; 17:sfae050. [PMID: 38524235 PMCID: PMC10959071 DOI: 10.1093/ckj/sfae050] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Indexed: 03/26/2024] Open
Abstract
Background The links between chronic kidney disease (CKD) and the high burden of cardiovascular disease remain unclear. We aimed to explore the association between selected inflammatory and angiogenic biomarkers, kidney function and long-term outcome in patients with an acute coronary syndrome (ACS) and to test the hypothesis that CKD status modifies this association. Methods A total of 1293 ACS patients hospitalized between 2008 and 2015 were followed until 31 December 2017. Plasma was collected on days 1-3 after admission. A total of 13 biomarkers were a priori identified and analysed with two proteomic methods, proximity extension assay or multiple reaction monitoring mass spectrometry. Boxplots and multiple linear regression models were used to study associations between biomarkers and kidney function and adjusted standardized Cox regression with an interaction term for CKD was used to assess whether CKD modified the association between biomarkers and major adverse cardiovascular events and death (MACE+). Results The concentrations of nine biomarkers-endothelial cell-specific molecule-1 (ESM-1), fibroblast growth factor 23 (FGF-23), fractalkine (CX3CL1), interleukin-1 receptor antagonist (IL-1RA), interleukin-18 (IL-18), monocyte chemotactic protein-1 (MCP-1), placenta growth factor (PlGF), transmembrane immunoglobulin 1 (TIM-1) and vascular endothelial growth factor A (VEGFA)-were inversely associated with kidney function. ESM-1, FGF-23 and TIM-1 showed associations with MACE+. Only FGF23 remained independently associated after adjustment for the other biomarkers (hazard ratio per standard deviation increase 1.34; 95% Bonferroni corrected confidence interval 1.19-1.50). None of the biomarkers showed an interaction with CKD. Conclusions The concentrations of 9 of the 13 prespecified inflammatory and angiogenic proteomic biomarkers increased when kidney function declined. Only FGF-23 demonstrated an independent association with MACE+, and this association was not modified by CKD status. These findings further support FGF-23 as an independent prognostic marker in ACS patients with and without CKD.
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Affiliation(s)
- Barbara Salzinger
- Division of Nephrology, Department of Clinical Sciences, Danderyd Hospital, Karolinska Institute, Stockholm, Sweden
| | - Kristina Lundwall
- Division of Cardiovascular Medicine, Department of Clinical Sciences, Danderyd Hospital, Karolinska Institute, Stockholm, Sweden
| | - Marie Evans
- ME Renal Medicine, Department of Clinical Intervention and Technology, Karolinska Institute, Stockholm, Sweden
| | - Josefin Mörtberg
- Division of Nephrology, Department of Internal Medicine, Centre for Clinical Research, County of Vastmanland and Uppsala University, Uppsala, Sweden
| | - Håkan Wallén
- Division of Cardiovascular Medicine, Department of Clinical Sciences, Danderyd Hospital, Karolinska Institute, Stockholm, Sweden
| | - Tomas Jernberg
- Division of Cardiovascular Medicine, Department of Clinical Sciences, Danderyd Hospital, Karolinska Institute, Stockholm, Sweden
| | - Thomas Kahan
- Division of Cardiovascular Medicine, Department of Clinical Sciences, Danderyd Hospital, Karolinska Institute, Stockholm, Sweden
| | - Pia Lundman
- Division of Cardiovascular Medicine, Department of Clinical Sciences, Danderyd Hospital, Karolinska Institute, Stockholm, Sweden
| | - Per Tornvall
- Department of Clinical Science and Education, Sodersjukhuset, Karolinska Institute, Stockholm, Sweden
| | - David Erlinge
- Department of Cardiology, Clinical Sciences, Lund University, Lund, Sweden
| | - Bertil Lindahl
- Department of Medical Sciences, Cardiology, Uppsala Clinical Research Centre, Uppsala University, Uppsala, Sweden
| | - Tomasz Baron
- Department of Medical Sciences, Cardiology, Uppsala Clinical Research Centre, Uppsala University, Uppsala, Sweden
| | - Melinda Rezeli
- Clinical Protein Science & Imaging, Department of Biomedical Engineering, Lund University, Lund, Sweden
| | - Jonas Spaak
- Division of Cardiovascular Medicine, Department of Clinical Sciences, Danderyd Hospital, Karolinska Institute, Stockholm, Sweden
| | - Stefan H Jacobson
- Division of Nephrology, Department of Clinical Sciences, Danderyd Hospital, Karolinska Institute, Stockholm, Sweden
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7
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Sandberg E, Nunes L, Edqvist PH, Mathot L, Chen L, Edgren T, Al Nassralla S, Glimelius B, Landegren U, Sjöblom T. Sensitive and Specific Analyses of Colorectal Cancer Recurrence through Multiplex superRCA Mutation Detection in Blood Plasma. Cancers (Basel) 2024; 16:549. [PMID: 38339300 PMCID: PMC10854605 DOI: 10.3390/cancers16030549] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 01/24/2024] [Accepted: 01/25/2024] [Indexed: 02/12/2024] Open
Abstract
Mutation analysis of circulating tumor DNA (ctDNA) has applications in monitoring of colorectal cancer (CRC) patients for recurrence. Considering the low tumor fraction of ctDNA in cell-free DNA (cfDNA) isolated from blood plasma, the sensitivity of the detection method is important. Here, plasma DNA collected at diagnosis and follow-up from 25 CRC patients was analyzed using a multiplex superRCA mutation detection assay. The assay was also performed on genomic DNA (gDNA) from tumor and normal tissue from 20 of these patients. The lower limit of detection for most sequence variants was in the range of 10-5, while when analyzing cfDNA from plasma with a typical input of 33 ng, the practical detection limit was ~10-4 or 0.01% mutant allele frequency (MAF). In 17 of 19 patients with identified hotspot mutations in tumor gDNA, at least one hotspot mutation could be detected in plasma DNA at the time of diagnosis. The MAF increased at subsequent time points in four of the patients who experienced a clinical relapse. Multiplex superRCA analysis of the remaining six patients did not reveal any hotspot mutations. In conclusion, multiplex superRCA assays proved suitable for monitoring CRC patients by analyzing hotspot mutations in cfDNA, and dynamic changes in MAF were observed in patients with clinical relapse.
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Affiliation(s)
- Emma Sandberg
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, SE-751 85 Uppsala, Sweden; (E.S.); (L.N.); (P.-H.E.); (L.M.); (L.C.); (S.A.N.); (B.G.)
| | - Luís Nunes
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, SE-751 85 Uppsala, Sweden; (E.S.); (L.N.); (P.-H.E.); (L.M.); (L.C.); (S.A.N.); (B.G.)
| | - Per-Henrik Edqvist
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, SE-751 85 Uppsala, Sweden; (E.S.); (L.N.); (P.-H.E.); (L.M.); (L.C.); (S.A.N.); (B.G.)
| | - Lucy Mathot
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, SE-751 85 Uppsala, Sweden; (E.S.); (L.N.); (P.-H.E.); (L.M.); (L.C.); (S.A.N.); (B.G.)
| | - Lei Chen
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, SE-751 85 Uppsala, Sweden; (E.S.); (L.N.); (P.-H.E.); (L.M.); (L.C.); (S.A.N.); (B.G.)
- Rarity Bioscience AB, SE-752 37 Uppsala, Sweden;
| | - Tomas Edgren
- Rarity Bioscience AB, SE-752 37 Uppsala, Sweden;
| | - Shahed Al Nassralla
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, SE-751 85 Uppsala, Sweden; (E.S.); (L.N.); (P.-H.E.); (L.M.); (L.C.); (S.A.N.); (B.G.)
| | - Bengt Glimelius
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, SE-751 85 Uppsala, Sweden; (E.S.); (L.N.); (P.-H.E.); (L.M.); (L.C.); (S.A.N.); (B.G.)
| | - Ulf Landegren
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, SE-751 85 Uppsala, Sweden; (E.S.); (L.N.); (P.-H.E.); (L.M.); (L.C.); (S.A.N.); (B.G.)
| | - Tobias Sjöblom
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, SE-751 85 Uppsala, Sweden; (E.S.); (L.N.); (P.-H.E.); (L.M.); (L.C.); (S.A.N.); (B.G.)
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8
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Jeuken GS, Käll L. Pathway analysis through mutual information. Bioinformatics 2024; 40:btad776. [PMID: 38195928 PMCID: PMC10783954 DOI: 10.1093/bioinformatics/btad776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 12/09/2023] [Accepted: 01/08/2024] [Indexed: 01/11/2024] Open
Abstract
MOTIVATION In pathway analysis, we aim to establish a connection between the activity of a particular biological pathway and a difference in phenotype. There are many available methods to perform pathway analysis, many of them rely on an upstream differential expression analysis, and many model the relations between the abundances of the analytes in a pathway as linear relationships. RESULTS Here, we propose a new method for pathway analysis, MIPath, that relies on information theoretical principles and, therefore, does not model the association between pathway activity and phenotype, resulting in relatively few assumptions. For this, we construct a graph of the data points for each pathway using a nearest-neighbor approach and score the association between the structure of this graph and the phenotype of these same samples using Mutual Information while adjusting for the effects of random chance in each score. The initial nearest neighbor approach evades individual gene-level comparisons, hence making the method scalable and less vulnerable to missing values. These properties make our method particularly useful for single-cell data. We benchmarked our method on several single-cell datasets, comparing it to established and new methods, and found that it produces robust, reproducible, and meaningful scores. AVAILABILITY AND IMPLEMENTATION Source code is available at https://github.com/statisticalbiotechnology/mipath, or through Python Package Index as "mipathway."
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Affiliation(s)
- Gustavo S Jeuken
- Science for Life Laboratory, KTH – Royal Institute of Technology, Stockholm 171 65, Sweden
- Computer Science Department, Vrije Universiteit Amsterdam, Amsterdam 1081 HV, The Netherlands
| | - Lukas Käll
- Science for Life Laboratory, KTH – Royal Institute of Technology, Stockholm 171 65, Sweden
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9
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Mahdavi R, Hashemi-Najafabadi S, Ghiass MA, Adiels CB. Microfluidic design for in-vitro liver zonation-a numerical analysis using COMSOL Multiphysics. Med Biol Eng Comput 2024; 62:121-133. [PMID: 37733153 DOI: 10.1007/s11517-023-02936-6] [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: 05/08/2023] [Accepted: 09/09/2023] [Indexed: 09/22/2023]
Abstract
The liver is one of the most important organs, with a complex physiology. Current in-vitro approaches are not accurate for disease modeling and drug toxicity research. One of those features is liver zonation, where cells display different physiological states due to different levels of oxygen and nutrient supplements. Organ-on-a-chip technology employs microfluidic platforms that enable a controlled environment for in-vitro cell culture. In this study, we propose a microfluidic design embedding a gas channel (of ambient air), creating an oxygen gradient. We numerically simulate different flow rates and cell densities with the COMSOL Multiphysics package considering cell-specific consumption rates of oxygen and glucose. We establish the cell density and flow rate for optimum oxygen and glucose distribution in the cell culture chamber. Furthermore, we show that a physiologically relevant concentration of oxygen and glucose in the chip is reached after 24 h and 30 min, respectively. The proposed microfluidic design and optimal parameters we identify in this paper provide a tool for in-vitro liver zonation studies. However, the microfluidic design is not exclusively for liver cell experiments but is foreseen to be applicable in cell studies where different gas concentration gradients are critical, e.g., studying hypoxia or toxic gas impact.
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Affiliation(s)
- Reza Mahdavi
- Biotechnology Department, Faculty of Chemical Engineering, Tarbiat Modares University, Tehran, P.O. Box 14115-114, Iran
| | - Sameereh Hashemi-Najafabadi
- Biomedical Engineering Department, Faculty of Chemical Engineering, Tarbiat Modares University, Tehran, P.O. Box 14115-114, Iran.
| | - Mohammad Adel Ghiass
- Tissue Engineering Department, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, P.O. Box 14115-114, Iran
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10
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Mohsen Y, Shami A, Edsfeldt A, Sun J, Gonçalves I. Haptoglobin Gene Polymorphism Is Associated With Lower Postoperative Cardiovascular Risk in Carotid Stenosis Patients. J Stroke 2024; 26:125-128. [PMID: 38246719 PMCID: PMC10850447 DOI: 10.5853/jos.2023.03349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 10/25/2023] [Indexed: 01/23/2024] Open
Affiliation(s)
- Yazan Mohsen
- Department of Clinical Sciences Malmö, Lund University, Malmö, Sweden
- Department of Cardiology, Electrophysiology and Rhythmology, Hospital Porz am Rhein, Cologne, Germany
| | - Annelie Shami
- Department of Clinical Sciences Malmö, Lund University, Malmö, Sweden
| | - Andreas Edsfeldt
- Department of Clinical Sciences Malmö, Lund University, Malmö, Sweden
- Department of Cardiology, Skåne University Hospital, Malmö, Sweden
- Wallenberg Center for Molecular Medicine, Lund University, Lund, Sweden
| | - Jiangming Sun
- Department of Clinical Sciences Malmö, Lund University, Malmö, Sweden
| | - Isabel Gonçalves
- Department of Clinical Sciences Malmö, Lund University, Malmö, Sweden
- Department of Cardiology, Skåne University Hospital, Malmö, Sweden
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11
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Kuang C, Chen S, Luo M, Zhang Q, Sun X, Han S, Wang Q, Stanishev V, Darakchieva V, Crispin R, Fahlman M, Zhao D, Wen Q, Jonsson MP. Switchable Broadband Terahertz Absorbers Based on Conducting Polymer-Cellulose Aerogels. Adv Sci (Weinh) 2024; 11:e2305898. [PMID: 37997181 PMCID: PMC10797431 DOI: 10.1002/advs.202305898] [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] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 10/18/2023] [Indexed: 11/25/2023]
Abstract
Terahertz (THz) technologies provide opportunities ranging from calibration targets for satellites and telescopes to communication devices and biomedical imaging systems. A main component will be broadband THz absorbers with switchability. However, optically switchable materials in THz are scarce and their modulation is mostly available at narrow bandwidths. Realizing materials with large and broadband modulation in absorption or transmission forms a critical challenge. This study demonstrates that conducting polymer-cellulose aerogels can provide modulation of broadband THz light with large modulation range from ≈ 13% to 91% absolute transmission, while maintaining specular reflection loss < -30 dB. The exceptional THz modulation is associated with the anomalous optical conductivity peak of conducting polymers, which enhances the absorption in its oxidized state. The study also demonstrates the possibility to reduce the surface hydrophilicity by simple chemical modifications, and shows that broadband absorption of the aerogels at optical frequencies enables de-frosting by solar-induced heating. These low-cost, aqueous solution-processable, sustainable, and bio-friendly aerogels may find use in next-generation intelligent THz devices.
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Affiliation(s)
- Chaoyang Kuang
- Laboratory of Organic Electronics, Department of Science and Technology (ITN)Linköping UniversityNorrköpingSE‐601 74Sweden
| | - Shangzhi Chen
- Laboratory of Organic Electronics, Department of Science and Technology (ITN)Linköping UniversityNorrköpingSE‐601 74Sweden
| | - Min Luo
- School of Electronic Science and Engineering, State Key Laboratory of Electronic Thin Film and Integrated DevicesUniversity of Electronic Science and Technology of ChinaChengduSichuan610 054P. R. China
| | - Qilun Zhang
- Laboratory of Organic Electronics, Department of Science and Technology (ITN)Linköping UniversityNorrköpingSE‐601 74Sweden
- Wallenberg Wood Science CenterLinköping UniversityNorrköpingSE‐601 74Sweden
| | - Xiao Sun
- School of Electronic Science and Engineering, State Key Laboratory of Electronic Thin Film and Integrated DevicesUniversity of Electronic Science and Technology of ChinaChengduSichuan610 054P. R. China
| | - Shaobo Han
- School of Textile Material and EngineeringWuyi University22 DongchengcunJiangmenGuangdong529 020P. R. China
| | - Qingqing Wang
- Laboratory of Organic Electronics, Department of Science and Technology (ITN)Linköping UniversityNorrköpingSE‐601 74Sweden
| | - Vallery Stanishev
- Terahertz Materials Analysis Center (THeMAC) and Center for III‐N Technology, C3NiT‐Janzèn, Department of Physics, Chemistry and Biology (IFM)Linköping UniversityLinköpingSE‐581 83Sweden
- Solid State Physics and NanoLundLund UniversityLundSE‐221 00Sweden
| | - Vanya Darakchieva
- Terahertz Materials Analysis Center (THeMAC) and Center for III‐N Technology, C3NiT‐Janzèn, Department of Physics, Chemistry and Biology (IFM)Linköping UniversityLinköpingSE‐581 83Sweden
- Solid State Physics and NanoLundLund UniversityLundSE‐221 00Sweden
| | - Reverant Crispin
- Laboratory of Organic Electronics, Department of Science and Technology (ITN)Linköping UniversityNorrköpingSE‐601 74Sweden
- Wallenberg Wood Science CenterLinköping UniversityNorrköpingSE‐601 74Sweden
| | - Mats Fahlman
- Laboratory of Organic Electronics, Department of Science and Technology (ITN)Linköping UniversityNorrköpingSE‐601 74Sweden
- Wallenberg Wood Science CenterLinköping UniversityNorrköpingSE‐601 74Sweden
| | - Dan Zhao
- Laboratory of Organic Electronics, Department of Science and Technology (ITN)Linköping UniversityNorrköpingSE‐601 74Sweden
| | - Qiye Wen
- School of Electronic Science and Engineering, State Key Laboratory of Electronic Thin Film and Integrated DevicesUniversity of Electronic Science and Technology of ChinaChengduSichuan610 054P. R. China
- Yangtze Delta Region Institute (Huzhou)University of Electronic Science and Technology of ChinaHuzhouZhejiang313 001P. R. China
| | - Magnus P. Jonsson
- Laboratory of Organic Electronics, Department of Science and Technology (ITN)Linköping UniversityNorrköpingSE‐601 74Sweden
- Wallenberg Wood Science CenterLinköping UniversityNorrköpingSE‐601 74Sweden
- Stellenbosch Institute for Advanced Study (STIAS)Wallenberg Research Center at Stellenbosch UniversityStellenbosch7600South Africa
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12
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Mikryukov V, Dulya O, Zizka A, Bahram M, Hagh-Doust N, Anslan S, Prylutskyi O, Delgado-Baquerizo M, Maestre FT, Nilsson H, Pärn J, Öpik M, Moora M, Zobel M, Espenberg M, Mander Ü, Khalid AN, Corrales A, Agan A, Vasco-Palacios AM, Saitta A, Rinaldi A, Verbeken A, Sulistyo B, Tamgnoue B, Furneaux B, Duarte Ritter C, Nyamukondiwa C, Sharp C, Marín C, Gohar D, Klavina D, Sharmah D, Dai DQ, Nouhra E, Biersma EM, Rähn E, Cameron E, De Crop E, Otsing E, Davydov E, Albornoz F, Brearley F, Buegger F, Zahn G, Bonito G, Hiiesalu I, Barrio I, Heilmann-Clausen J, Ankuda J, Doležal J, Kupagme J, Maciá-Vicente J, Djeugap Fovo J, Geml J, Alatalo J, Alvarez-Manjarrez J, Põldmaa K, Runnel K, Adamson K, Bråthen KA, Pritsch K, Tchan Issifou K, Armolaitis K, Hyde K, Newsham KK, Panksep K, Lateef AA, Hansson L, Lamit L, Saba M, Tuomi M, Gryzenhout M, Bauters M, Piepenbring M, Wijayawardene NN, Yorou N, Kurina O, Mortimer P, Meidl P, Kohout P, Puusepp R, Drenkhan R, Garibay-Orijel R, Godoy R, Alkahtani S, Rahimlou S, Dudov S, Põlme S, Ghosh S, Mundra S, Ahmed T, Netherway T, Henkel T, Roslin T, Nteziryayo V, Fedosov V, Onipchenko V, Yasanthika WAE, Lim Y, Van Nuland M, Soudzilovskaia N, Antonelli A, Kõljalg U, Abarenkov K, Tedersoo L. Connecting the multiple dimensions of global soil fungal diversity. Sci Adv 2023; 9:eadj8016. [PMID: 38019923 PMCID: PMC10686567 DOI: 10.1126/sciadv.adj8016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 10/30/2023] [Indexed: 12/01/2023]
Abstract
How the multiple facets of soil fungal diversity vary worldwide remains virtually unknown, hindering the management of this essential species-rich group. By sequencing high-resolution DNA markers in over 4000 topsoil samples from natural and human-altered ecosystems across all continents, we illustrate the distributions and drivers of different levels of taxonomic and phylogenetic diversity of fungi and their ecological groups. We show the impact of precipitation and temperature interactions on local fungal species richness (alpha diversity) across different climates. Our findings reveal how temperature drives fungal compositional turnover (beta diversity) and phylogenetic diversity, linking them with regional species richness (gamma diversity). We integrate fungi into the principles of global biodiversity distribution and present detailed maps for biodiversity conservation and modeling of global ecological processes.
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Affiliation(s)
- Vladimir Mikryukov
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu 50409, Estonia
| | - Olesya Dulya
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu 50409, Estonia
| | - Alexander Zizka
- Department of Biology, Philipps-University, Marburg 35032, Germany
| | - Mohammad Bahram
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala 75007, Sweden
| | - Niloufar Hagh-Doust
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu 50409, Estonia
| | - Sten Anslan
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu 50409, Estonia
| | - Oleh Prylutskyi
- Department of Mycology and Plant Resistance, School of Biology, V.N. Karazin Kharkiv National University, Kharkiv 61022, Ukraine
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistemico, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), Consejo Superior de Investigaciones Científicas, Sevilla 41012, Spain
| | - Fernando T. Maestre
- Instituto Multidisciplinar para el Estudio del Medio ‘Ramón Margalef’ and Departamento de Ecología, Universidad de Alicante, Alicante 03690, Spain
| | - Henrik Nilsson
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg 40530, Sweden
| | - Jaan Pärn
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu 50409, Estonia
| | - Maarja Öpik
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu 50409, Estonia
| | - Mari Moora
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu 50409, Estonia
| | - Martin Zobel
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu 50409, Estonia
| | - Mikk Espenberg
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu 50409, Estonia
| | - Ülo Mander
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu 50409, Estonia
| | | | - Adriana Corrales
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Universidad del Rosario, Bogotá 111221, Colombia
| | - Ahto Agan
- Institute of Forestry and Engineering, Estonian University of Life Sciences, Tartu 51006, Estonia
| | - Aída-M. Vasco-Palacios
- Grupo de BioMicro y Microbiología Ambiental, Escuela de Microbiologia, Universidad de Antioquia UdeA, Medellin 050010, Colombia
| | - Alessandro Saitta
- Department of Agricultural, Food and Forest Sciences, University of Palermo, Palermo 90128, Italy
| | - Andrea Rinaldi
- Department of Biomedical Sciences, University of Cagliari, Cagliari 09124, Italy
| | | | - Bobby Sulistyo
- Department Biology, Ghent University, Ghent 9000, Belgium
| | - Boris Tamgnoue
- Department of Crop Science, University of Dschang, Dschang, Cameroon
| | - Brendan Furneaux
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä 40014, Finland
| | | | - Casper Nyamukondiwa
- Department of Biological Sciences and Biotechnology, Botswana International University of Science and Technology, Palapye 10071, Botswana
| | - Cathy Sharp
- Natural History Museum of Zimbabwe, Bulawayo, Zimbabwe
| | - César Marín
- Centro de Investigación e Innovación para el Cambio Climático (CiiCC), Universidad SantoTomás, Valdivia, Chile
| | - Daniyal Gohar
- Center of Mycology and Microbiology, University of Tartu, Tartu 50409, Estonia
| | - Darta Klavina
- Latvian State Forest Research Institute Silava, Salaspils 2169, Latvia
| | - Dipon Sharmah
- Department of Botany, Jawaharlal Nehru Rajkeeya Mahavidyalaya, Pondicherry University, Port Blair 744101, India
| | - Dong-Qin Dai
- College of Biological Resource and Food Engineering, Qujing Normal University, Qujing, Yunnan 655011, China
| | - Eduardo Nouhra
- Instituto Multidisciplinario de Biología Vegetal (CONICET), Universidad Nacional de Córdoba, Cordoba 5000, Argentina
| | - Elisabeth Machteld Biersma
- Natural History Museum of Denmark, Copenhagen 1123, Denmark
- British Antarctic Survey, NERC, High Cross, Cambridge CB3 0ET, UK
| | - Elisabeth Rähn
- Institute of Forestry and Engineering, Estonian University of Life Sciences, Tartu 51006, Estonia
| | - Erin Cameron
- Department of Environmental Science, Saint Mary's University, Halifax B3H 3C3, Canada
| | - Eske De Crop
- Department Biology, Ghent University, Ghent 9000, Belgium
| | - Eveli Otsing
- Center of Mycology and Microbiology, University of Tartu, Tartu 50409, Estonia
| | | | - Felipe Albornoz
- Land and Water, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Wembley 6014, Australia
| | - Francis Brearley
- Department of Natural Sciences, Manchester Metropolitan University, Manchester M1 5GD, UK
| | - Franz Buegger
- Helmholtz Zentrum München, Neuherberg 85764, Germany
| | - Geoffrey Zahn
- Biology Department, Utah Valley University, Orem, UT 84058, USA
| | - Gregory Bonito
- Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824-6254, USA
| | - Inga Hiiesalu
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu 50409, Estonia
| | - Isabel Barrio
- Faculty of Natural and Environmental Sciences, Agricultural University of Iceland, Reykjavík 112, Iceland
| | - Jacob Heilmann-Clausen
- Center for Macroecology, Evolution and Climate, University of Copenhagen, Copenhagen 1350, Denmark
| | - Jelena Ankuda
- Vokė branch, Institute of Agriculture, Lithuanian Research Centre for Agriculture and Forestry (LAMMC), Vilnius LT-02232, Lithuania
| | - Jiri Doležal
- Department of Botany, Faculty of Science, University of South Bohemia, České Budějovice 37005, Czech Republic
| | - John Kupagme
- Center of Mycology and Microbiology, University of Tartu, Tartu 50409, Estonia
| | - Jose Maciá-Vicente
- Department of Environmental Sciences, Plant Ecology and Nature Conservation, Wageningen University and Research, Wageningen 6708, Netherlands
| | | | - József Geml
- ELKH-EKKE Lendület Environmental Microbiome Research Group, Eszterházy Károly Catholic University, Eger 3300, Hungary
| | - Juha Alatalo
- Environmental Science Center, Qatar University, Doha, Qatar
| | | | - Kadri Põldmaa
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu 50409, Estonia
- Natural History Museum, University of Tartu, Tartu 51003, Estonia
| | - Kadri Runnel
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu 50409, Estonia
| | - Kalev Adamson
- Institute of Forestry and Engineering, Estonian University of Life Sciences, Tartu 51006, Estonia
| | - Kari-Anne Bråthen
- Department of Arctic and Marine Biology, The Arctic University of Norway, Tromsø 9019, Norway
| | - Karin Pritsch
- Helmholtz Zentrum München, Neuherberg 85764, Germany
| | - Kassim Tchan Issifou
- Research Unit Tropical Mycology and Plants-Soil Fungi Interactions, University of Parakou, Parakou 00229, Benin
| | - Kęstutis Armolaitis
- Department of Silviculture and Ecology, Institute of Forestry, Lithuanian Research Centre for Agriculture and Forestry (LAMMC), Girionys 53101, Lithuania
| | - Kevin Hyde
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand
| | - Kevin K. Newsham
- British Antarctic Survey, NERC, High Cross, Cambridge CB3 0ET, UK
| | - Kristel Panksep
- Chair of Hydrobiology and Fishery, Estonian University of Life Sciences, Tartu 51006, Estonia
| | - Adebola Azeez Lateef
- Department of Plant Biology, Faculty of Life Science, University of Ilorin, Ilorin 240102, Nigeria
- Department of Forest Sciences, University of Helsinki, Helsinki 00014, Finland
| | - Linda Hansson
- Gothenburg Centre for Sustainable Development, Gothenburg 41133, Sweden
| | - Louis Lamit
- Department of Biology, Syracuse University, Syracuse 13244, USA
| | - Malka Saba
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Maria Tuomi
- Department of Arctic and Marine Biology, The Arctic University of Norway, Tromsø 9019, Norway
| | - Marieka Gryzenhout
- Department of Genetics, Faculty of Natural and Agricultural Sciences, University of the Free State, Bloemfontein 9300, South Africa
| | - Marijn Bauters
- Department of Environment, Faculty of Bioscience Engineering, Ghent University, Ghent 9000, Belgium
| | - Meike Piepenbring
- Mycology Working Group, Goethe University Frankfurt am Main, Frankfurt am Main 60438, Germany
| | - Nalin N. Wijayawardene
- College of Biological Resource and Food Engineering, Qujing Normal University, Qujing, China
| | - Nourou Yorou
- Research Unit Tropical Mycology and Plants-Soil Fungi Interactions, University of Parakou, Parakou 00229, Benin
| | - Olavi Kurina
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Tartu 51006, Estonia
| | - Peter Mortimer
- Center For Mountain Futures, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Peter Meidl
- Freie Universität Berlin, Institut für Biologie, Berlin 14195, Germany
| | - Petr Kohout
- Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
| | - Rasmus Puusepp
- Center of Mycology and Microbiology, University of Tartu, Tartu 50409, Estonia
| | - Rein Drenkhan
- Institute of Forestry and Engineering, Estonian University of Life Sciences, Tartu 51006, Estonia
| | - Roberto Garibay-Orijel
- Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
| | - Roberto Godoy
- Instituto Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
| | - Saad Alkahtani
- Department of Zoology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Saleh Rahimlou
- Center of Mycology and Microbiology, University of Tartu, Tartu 50409, Estonia
| | - Sergey Dudov
- Department of Ecology and Plant Geography, Moscow Lomonosov State University, Moscow 119234, Russia
| | - Sergei Põlme
- Center of Mycology and Microbiology, University of Tartu, Tartu 50409, Estonia
- Natural History Museum, University of Tartu, Tartu 51003, Estonia
| | - Soumya Ghosh
- Department of Genetics, Faculty of Natural and Agricultural Sciences, University of the Free State, Bloemfontein 9300, South Africa
| | - Sunil Mundra
- Department of Biology, College of Science, United Arab Emirates University (UAEU), Al Ain, UAE
| | - Talaat Ahmed
- Environmental Science Center, Qatar University, Doha, Qatar
| | - Tarquin Netherway
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala 75007, Sweden
| | - Terry Henkel
- Department of Biological Sciences, California State Polytechnic University, Arcata, CA 95521, USA
| | - Tomas Roslin
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala 75007, Sweden
| | - Vincent Nteziryayo
- Department of Food Science and Technology, University of Burundi, Bujumbura Burundi
| | - Vladimir Fedosov
- Department of Ecology and Plant Geography, Moscow Lomonosov State University, Moscow 119234, Russia
| | - Vladimir Onipchenko
- Department of Ecology and Plant Geography, Moscow Lomonosov State University, Moscow 119234, Russia
| | | | - Young Lim
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul 08826, Korea
| | - Michael Van Nuland
- Society for the Protection of Underground Networks (SPUN), Dover, DE 19901, USA
| | | | | | - Urmas Kõljalg
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu 50409, Estonia
- Natural History Museum, University of Tartu, Tartu 51003, Estonia
| | - Kessy Abarenkov
- Natural History Museum, University of Tartu, Tartu 51003, Estonia
| | - Leho Tedersoo
- Center of Mycology and Microbiology, University of Tartu, Tartu 50409, Estonia
- Department of Zoology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
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13
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Miao R, Jahn M, Shabestary K, Peltier G, Hudson EP. CRISPR interference screens reveal growth-robustness tradeoffs in Synechocystis sp. PCC 6803 across growth conditions. Plant Cell 2023; 35:3937-3956. [PMID: 37494719 PMCID: PMC10615215 DOI: 10.1093/plcell/koad208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 06/01/2023] [Accepted: 07/20/2023] [Indexed: 07/28/2023]
Abstract
Barcoded mutant libraries are a powerful tool for elucidating gene function in microbes, particularly when screened in multiple growth conditions. Here, we screened a pooled CRISPR interference library of the model cyanobacterium Synechocystis sp. PCC 6803 in 11 bioreactor-controlled conditions, spanning multiple light regimes and carbon sources. This gene repression library contained 21,705 individual mutants with high redundancy over all open reading frames and noncoding RNAs. Comparison of the derived gene fitness scores revealed multiple instances of gene repression being beneficial in 1 condition while generally detrimental in others, particularly for genes within light harvesting and conversion, such as antennae components at high light and PSII subunits during photoheterotrophy. Suboptimal regulation of such genes likely represents a tradeoff of reduced growth speed for enhanced robustness to perturbation. The extensive data set assigns condition-specific importance to many previously unannotated genes and suggests additional functions for central metabolic enzymes. Phosphoribulokinase, glyceraldehyde-3-phosphate dehydrogenase, and the small protein CP12 were critical for mixotrophy and photoheterotrophy, which implicates the ternary complex as important for redirecting metabolic flux in these conditions in addition to inactivation of the Calvin cycle in the dark. To predict the potency of sgRNA sequences, we applied machine learning on sgRNA sequences and gene repression data, which showed the importance of C enrichment and T depletion proximal to the PAM site. Fitness data for all genes in all conditions are compiled in an interactive web application.
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Affiliation(s)
- Rui Miao
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH—Royal Institute of Technology, Stockholm, SE-17165,Sweden
| | - Michael Jahn
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH—Royal Institute of Technology, Stockholm, SE-17165,Sweden
- Max Planck Unit for the Science of Pathogens, 10117 Berlin,Germany
| | - Kiyan Shabestary
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH—Royal Institute of Technology, Stockholm, SE-17165,Sweden
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ,UK
| | - Gilles Peltier
- Aix Marseille Univ, CEA, CNRS, Institut de Biosciences et Biotechnologies Aix-Marseille, CEA Cadarache, 13108 Saint Paul-Lez-Durance,France
| | - Elton P Hudson
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH—Royal Institute of Technology, Stockholm, SE-17165,Sweden
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14
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Ollmar S, Fernandez Schrunder A, Birgersson U, Kristoffersson T, Rusu A, Thorsson E, Hedenqvist P, Manell E, Rydén A, Jensen-Waern M, Rodriguez S. A battery-less implantable glucose sensor based on electrical impedance spectroscopy. Sci Rep 2023; 13:18122. [PMID: 37872272 PMCID: PMC10593792 DOI: 10.1038/s41598-023-45154-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [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: 06/19/2023] [Accepted: 10/17/2023] [Indexed: 10/25/2023] Open
Abstract
The ability to perform accurate continuous glucose monitoring without blood sampling has revolutionised the management of diabetes. Newer methods that can allow measurements during longer periods are necessary to substantially improve patients' quality of life. This paper presents an alternative method for glucose monitoring which is based on electrical impedance spectroscopy. A battery-less implantable bioimpedance spectroscope was designed, built, and used in an in vivo study on pigs. After a recovery period of 14 days post surgery, a total of 236 subcutaneous bioimpedance measurements obtained from intravenous glucose tolerance tests, with glucose concentration ranges between 77.4 and 523.8 mg/dL, were analyzed. The results show that glucose concentrations estimated by subcutaneous bioimpedance measurements correlate very well to the blood glucose reference values. The pigs were clinically healthy throughout the study, and the postmortem examinations revealed no signs of adverse effects related to the sensor. The implantation of the sensor requires minor surgery. The implant, being externally powered, could in principle last indefinitely. These encouraging results demonstrate the potential of the bioimpedance method to be used in future continuous glucose monitoring systems.
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Affiliation(s)
- Stig Ollmar
- Department of Clinical Science, Intervention and Technology, Karolinska Institute, Stockholm, Sweden
| | | | - Ulrik Birgersson
- Department of Clinical Science, Intervention and Technology, Karolinska Institute, Stockholm, Sweden
| | | | - Ana Rusu
- School of Electrical Engineering and Computer Science, KTH Royal Institute of Technology, 16440, Kista, Sweden
| | - Elina Thorsson
- Pathology Unit, Department of Biomedical Science and Veterinary Public Health, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Patricia Hedenqvist
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Elin Manell
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Anneli Rydén
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Marianne Jensen-Waern
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Saul Rodriguez
- School of Electrical Engineering and Computer Science, KTH Royal Institute of Technology, 16440, Kista, Sweden.
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15
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Hossain MM, Tovar J, Cloetens L, Nilsson A. Inclusion of Oat Polar Lipids in a Solid Breakfast Improves Glucose Tolerance, Triglyceridemia, and Gut Hormone Responses Postprandially and after a Standardized Second Meal: A Randomized Crossover Study in Healthy Subjects. Nutrients 2023; 15:4389. [PMID: 37892464 PMCID: PMC10609583 DOI: 10.3390/nu15204389] [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: 09/27/2023] [Revised: 10/13/2023] [Accepted: 10/15/2023] [Indexed: 10/29/2023] Open
Abstract
Previously, it has been indicated that oat polar lipids included in a liquid meal may have the potential to beneficially modulate various cardiometabolic variables. The purpose of this study was to evaluate the effects of oat polar lipids in a solid food matrix on acute and second meal glucose tolerance, blood lipids, and concentrations of gut-derived hormones. The oat polar lipids were consumed at breakfast and effects on the biomarkers were investigated in the postprandial period and following a standardized lunch. Twenty young, healthy subjects consumed in total four different breakfast meals in a crossover study design. The breakfasts consisted of 1. White wheat bread (WWB) with an added 7.5 g of oat polar lipids (PLL); 2. WWB with an added 15 g of oat polar lipids (PLH); 3. WWB with and added 16.6 g of rapeseed oil (RSO) as a representative of commonly consumed oils; and 4. WWB consumed alone, included as a reference. All products with added lipids contained equivalent amounts of fat (16.6 g) and available carbohydrates (50 g). Rapeseed oil was added to the oat polar lipid meals to equal 16.6 g of total fat. The standardized lunch was composed of WWB and meatballs and was served 3.5 h after the breakfast. Test variables (blood glucose, serum insulin, triglyceride (TG), free fatty acids (FFA), ghrelin, GLP-1, PYY, and GIP) were measured at fasting and repeatedly during the 5.5 h after ingestion of the breakfast. After breakfast, PLH substantially lowered postprandial glucose and insulin responses (iAUC 0-120 min) compared with RSO and WWB (p < 0.05). Furthermore, a reduced glycaemic response to lunch (210-330 min) was observed following the PLH breakfast compared to all of the other breakfasts served (p < 0.05). Oat polar lipids (PLH) significantly reduced TG and ghrelin and increased circulating gut hormones GLP-1 and PYY compared to RSO (p < 0.05). The results show that exchanging part of the dietary lipids with oat polar lipids has the potential to improve postprandial blood glucose regulation and gut hormones and thus may have a preventive effect against type 2 diabetes.
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Affiliation(s)
- Mohammad Mukul Hossain
- Department of Food Technology, Engineering and Nutrition, Lund University, P.O. Box 124, 221 00 Lund, Sweden; (J.T.); (A.N.)
| | - Juscelino Tovar
- Department of Food Technology, Engineering and Nutrition, Lund University, P.O. Box 124, 221 00 Lund, Sweden; (J.T.); (A.N.)
| | - Lieselotte Cloetens
- Division of Pure and Applied Biochemistry, Lund University, P.O. Box 124, 221 00 Lund, Sweden;
| | - Anne Nilsson
- Department of Food Technology, Engineering and Nutrition, Lund University, P.O. Box 124, 221 00 Lund, Sweden; (J.T.); (A.N.)
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16
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Mastropasqua F, Oksanen M, Soldini C, Alatar S, Arora A, Ballarino R, Molinari M, Agostini F, Poulet A, Watts M, Rabkina I, Becker M, Li D, Anderlid BM, Isaksson J, Lundin Remnelius K, Moslem M, Jacob Y, Falk A, Crosetto N, Bienko M, Santini E, Borgkvist A, Bölte S, Tammimies K. Deficiency of the Heterogeneous Nuclear Ribonucleoprotein U locus leads to delayed hindbrain neurogenesis. Biol Open 2023; 12:bio060113. [PMID: 37815090 PMCID: PMC10581386 DOI: 10.1242/bio.060113] [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: 08/25/2023] [Accepted: 09/04/2023] [Indexed: 10/11/2023] Open
Abstract
Genetic variants affecting Heterogeneous Nuclear Ribonucleoprotein U (HNRNPU) have been identified in several neurodevelopmental disorders (NDDs). HNRNPU is widely expressed in the human brain and shows the highest postnatal expression in the cerebellum. Recent studies have investigated the role of HNRNPU in cerebral cortical development, but the effects of HNRNPU deficiency on cerebellar development remain unknown. Here, we describe the molecular and cellular outcomes of HNRNPU locus deficiency during in vitro neural differentiation of patient-derived and isogenic neuroepithelial stem cells with a hindbrain profile. We demonstrate that HNRNPU deficiency leads to chromatin remodeling of A/B compartments, and transcriptional rewiring, partly by impacting exon inclusion during mRNA processing. Genomic regions affected by the chromatin restructuring and host genes of exon usage differences show a strong enrichment for genes implicated in epilepsies, intellectual disability, and autism. Lastly, we show that at the cellular level HNRNPU downregulation leads to an increased fraction of neural progenitors in the maturing neuronal population. We conclude that the HNRNPU locus is involved in delayed commitment of neural progenitors to differentiate in cell types with hindbrain profile.
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Affiliation(s)
- Francesca Mastropasqua
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institute, Region Stockholm, 17164 Stockholm, Sweden
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Region Stockholm, 17164 Stockholm, Sweden
| | - Marika Oksanen
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institute, Region Stockholm, 17164 Stockholm, Sweden
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Region Stockholm, 17164 Stockholm, Sweden
| | - Cristina Soldini
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institute, Region Stockholm, 17164 Stockholm, Sweden
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Region Stockholm, 17164 Stockholm, Sweden
| | - Shemim Alatar
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institute, Region Stockholm, 17164 Stockholm, Sweden
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Region Stockholm, 17164 Stockholm, Sweden
| | - Abishek Arora
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institute, Region Stockholm, 17164 Stockholm, Sweden
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Region Stockholm, 17164 Stockholm, Sweden
| | - Roberto Ballarino
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 17164 Stockholm, Sweden
- Science for Life Laboratory, Tomtebodavägen 23A, 17165 Solna, Sweden
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17165 Stockholm, Sweden
| | - Maya Molinari
- Department of Neuroscience, Karolinska Institutet, 17176 Solna, Sweden
| | - Federico Agostini
- Science for Life Laboratory, Tomtebodavägen 23A, 17165 Solna, Sweden
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17165 Stockholm, Sweden
| | - Axel Poulet
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
| | - Michelle Watts
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institute, Region Stockholm, 17164 Stockholm, Sweden
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Region Stockholm, 17164 Stockholm, Sweden
| | - Ielyzaveta Rabkina
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institute, Region Stockholm, 17164 Stockholm, Sweden
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Region Stockholm, 17164 Stockholm, Sweden
| | - Martin Becker
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institute, Region Stockholm, 17164 Stockholm, Sweden
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Region Stockholm, 17164 Stockholm, Sweden
| | - Danyang Li
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institute, Region Stockholm, 17164 Stockholm, Sweden
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Region Stockholm, 17164 Stockholm, Sweden
| | - Britt-Marie Anderlid
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 17177 Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, 17164 Stockholm, Sweden
| | - Johan Isaksson
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institute, Region Stockholm, 17164 Stockholm, Sweden
- Department of Medical Sciences, Child and Adolescent Psychiatry Unit, Uppsala University, 75309 Uppsala, Sweden
| | - Karl Lundin Remnelius
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institute, Region Stockholm, 17164 Stockholm, Sweden
| | - Mohsen Moslem
- Department of Neuroscience, Karolinska Institutet, 17176 Solna, Sweden
| | - Yannick Jacob
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
| | - Anna Falk
- Department of Neuroscience, Karolinska Institutet, 17176 Solna, Sweden
- Lund Stem Cell Center, Lund University, 22100 Lund, Sweden
| | - Nicola Crosetto
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 17164 Stockholm, Sweden
- Science for Life Laboratory, Tomtebodavägen 23A, 17165 Solna, Sweden
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157 Milan, Italy
| | - Magda Bienko
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 17164 Stockholm, Sweden
- Science for Life Laboratory, Tomtebodavägen 23A, 17165 Solna, Sweden
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157 Milan, Italy
| | - Emanuela Santini
- Department of Neuroscience, Karolinska Institutet, 17176 Solna, Sweden
| | - Anders Borgkvist
- Department of Neuroscience, Karolinska Institutet, 17176 Solna, Sweden
| | - Sven Bölte
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institute, Region Stockholm, 17164 Stockholm, Sweden
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Region Stockholm, 17164 Stockholm, Sweden
- Curtin Autism Research Group, Curtin School of Allied Health, Curtin University, 6845 Perth, Western Australia
- Child and Adolescent Psychiatry, Stockholm Health Care Services, Region Stockholm, 10431 Stockholm, Sweden
| | - Kristiina Tammimies
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institute, Region Stockholm, 17164 Stockholm, Sweden
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Region Stockholm, 17164 Stockholm, Sweden
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17
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Skantze V, Hjorth T, Wallman M, Brunius C, Dicksved J, Pelve EA, Esberg A, Vitale M, Giacco R, Costabile G, Bergia RE, Jirstrand M, Campbell WW, Riccardi G, Landberg R. Differential Responders to a Mixed Meal Tolerance Test Associated with Type 2 Diabetes Risk Factors and Gut Microbiota-Data from the MEDGI-Carb Randomized Controlled Trial. Nutrients 2023; 15:4369. [PMID: 37892445 PMCID: PMC10609681 DOI: 10.3390/nu15204369] [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: 09/05/2023] [Revised: 10/04/2023] [Accepted: 10/10/2023] [Indexed: 10/29/2023] Open
Abstract
The global prevalence of type 2 diabetes mellitus (T2DM) has surged in recent decades, and the identification of differential glycemic responders can aid tailored treatment for the prevention of prediabetes and T2DM. A mixed meal tolerance test (MMTT) based on regular foods offers the potential to uncover differential responders in dynamical postprandial events. We aimed to fit a simple mathematical model on dynamic postprandial glucose data from repeated MMTTs among participants with elevated T2DM risk to identify response clusters and investigate their association with T2DM risk factors and gut microbiota. Data were used from a 12-week multi-center dietary intervention trial involving high-risk T2DM adults, comparing high- versus low-glycemic index foods within a Mediterranean diet context (MEDGICarb). Model-based analysis of MMTTs from 155 participants (81 females and 74 males) revealed two distinct plasma glucose response clusters that were associated with baseline gut microbiota. Cluster A, inversely associated with HbA1c and waist circumference and directly with insulin sensitivity, exhibited a contrasting profile to cluster B. Findings imply that a standardized breakfast MMTT using regular foods could effectively distinguish non-diabetic individuals at varying risk levels for T2DM using a simple mechanistic model.
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Affiliation(s)
- Viktor Skantze
- Fraunhofer-Chalmers Research Centre for Industrial Mathematics, 412 88 Gothenburg, Sweden (M.J.)
- Department of Life Sciences, Food and Nutrition Science, Chalmers University of Technology, 412 96 Gothenburg, Sweden; (T.H.); (R.L.)
| | - Therese Hjorth
- Department of Life Sciences, Food and Nutrition Science, Chalmers University of Technology, 412 96 Gothenburg, Sweden; (T.H.); (R.L.)
| | - Mikael Wallman
- Fraunhofer-Chalmers Research Centre for Industrial Mathematics, 412 88 Gothenburg, Sweden (M.J.)
| | - Carl Brunius
- Department of Life Sciences, Food and Nutrition Science, Chalmers University of Technology, 412 96 Gothenburg, Sweden; (T.H.); (R.L.)
| | - Johan Dicksved
- Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
| | - Erik A. Pelve
- Department of Animal Nutrition and Management, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden;
| | - Anders Esberg
- Department of Odontology, Umeå University, 901 87 Umeå, Sweden
| | - Marilena Vitale
- Diabetes, Nutrition and Metabolism Unit, Department of Clinical Medicine and Surgery, Federico II University, 80138 Naples, Italy; (M.V.); (R.G.); (G.C.); (G.R.)
| | - Rosalba Giacco
- Diabetes, Nutrition and Metabolism Unit, Department of Clinical Medicine and Surgery, Federico II University, 80138 Naples, Italy; (M.V.); (R.G.); (G.C.); (G.R.)
- Institute of Food Sciences, National Research Council, 83100 Avellino, Italy
| | - Giuseppina Costabile
- Diabetes, Nutrition and Metabolism Unit, Department of Clinical Medicine and Surgery, Federico II University, 80138 Naples, Italy; (M.V.); (R.G.); (G.C.); (G.R.)
| | - Robert E. Bergia
- Department of Nutrition Science, Purdue University, West Lafayette, IN 47907, USA (W.W.C.)
| | - Mats Jirstrand
- Fraunhofer-Chalmers Research Centre for Industrial Mathematics, 412 88 Gothenburg, Sweden (M.J.)
| | - Wayne W. Campbell
- Department of Nutrition Science, Purdue University, West Lafayette, IN 47907, USA (W.W.C.)
| | - Gabriele Riccardi
- Diabetes, Nutrition and Metabolism Unit, Department of Clinical Medicine and Surgery, Federico II University, 80138 Naples, Italy; (M.V.); (R.G.); (G.C.); (G.R.)
| | - Rikard Landberg
- Department of Life Sciences, Food and Nutrition Science, Chalmers University of Technology, 412 96 Gothenburg, Sweden; (T.H.); (R.L.)
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18
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Larsson L, Franzén L, Ståhl PL, Lundeberg J. Semla: a versatile toolkit for spatially resolved transcriptomics analysis and visualization. Bioinformatics 2023; 39:btad626. [PMID: 37846051 PMCID: PMC10597621 DOI: 10.1093/bioinformatics/btad626] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 09/20/2023] [Accepted: 10/13/2023] [Indexed: 10/18/2023] Open
Abstract
SUMMARY Spatially resolved transcriptomics technologies generate gene expression data with retained positional information from a tissue section, often accompanied by a corresponding histological image. Computational tools should make it effortless to incorporate spatial information into data analyses and present analysis results in their histological context. Here, we present semla, an R package for processing, analysis, and visualization of spatially resolved transcriptomics data generated by the Visium platform, that includes interactive web applications for data exploration and tissue annotation. AVAILABILITY AND IMPLEMENTATION The R package semla is available on GitHub (https://github.com/ludvigla/semla), under the MIT License, and deposited on Zenodo (https://doi.org/10.5281/zenodo.8321645). Documentation and tutorials with detailed descriptions of usage can be found at https://ludvigla.github.io/semla/.
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Affiliation(s)
- Ludvig Larsson
- Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Tomtebodavägen 23, 171 65 Solna, Stockholm, Sweden
| | - Lovisa Franzén
- Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Tomtebodavägen 23, 171 65 Solna, Stockholm, Sweden
- Respiratory & Immunology, Neuroscience, Vaccines & Immune Therapies Safety, Clinical Pharmacology & Safety Sciences, BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, 431 83 Mölndal, Gothenburg, Sweden
| | - Patrik L Ståhl
- Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Tomtebodavägen 23, 171 65 Solna, Stockholm, Sweden
| | - Joakim Lundeberg
- Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Tomtebodavägen 23, 171 65 Solna, Stockholm, Sweden
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19
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Armour SL, Frueh A, Chibalina MV, Dou H, Argemi-Muntadas L, Hamilton A, Katzilieris-Petras G, Carmeliet P, Davies B, Moritz T, Eliasson L, Rorsman P, Knudsen JG. Glucose Controls Glucagon Secretion by Regulating Fatty Acid Oxidation in Pancreatic α-Cells. Diabetes 2023; 72:1446-1459. [PMID: 37494670 PMCID: PMC10545563 DOI: 10.2337/db23-0056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 07/16/2023] [Indexed: 07/28/2023]
Abstract
Whole-body glucose homeostasis is coordinated through secretion of glucagon and insulin from pancreatic islets. When glucose is low, glucagon is released from α-cells to stimulate hepatic glucose production. However, the mechanisms that regulate glucagon secretion from pancreatic α-cells remain unclear. Here we show that in α-cells, the interaction between fatty acid oxidation and glucose metabolism controls glucagon secretion. The glucose-dependent inhibition of glucagon secretion relies on pyruvate dehydrogenase and carnitine palmitoyl transferase 1a activity and lowering of mitochondrial fatty acid oxidation by increases in glucose. This results in reduced intracellular ATP and leads to membrane repolarization and inhibition of glucagon secretion. These findings provide a new framework for the metabolic regulation of the α-cell, where regulation of fatty acid oxidation by glucose accounts for the stimulation and inhibition of glucagon secretion. ARTICLE HIGHLIGHTS It has become clear that dysregulation of glucagon secretion and α-cell function plays an important role in the development of diabetes, but we do not know how glucagon secretion is regulated. Here we asked whether glucose inhibits fatty acid oxidation in α-cells to regulate glucagon secretion. We found that fatty acid oxidation is required for the inhibitory effects of glucose on glucagon secretion through reductions in ATP. These findings provide a new framework for the regulation of glucagon secretion by glucose.
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Affiliation(s)
- Sarah L. Armour
- Section for Cell Biology and Physiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Alexander Frueh
- Section for Cell Biology and Physiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Margarita V. Chibalina
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Oxford, U.K
| | - Haiqiang Dou
- Department of Physiology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Lidia Argemi-Muntadas
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Alexander Hamilton
- Section for Cell Biology and Physiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Sciences in Malmö, Islet Cell Exocytosis, Lund University Diabetes Centre, Lund University, Malmö, Sweden
| | - Georgios Katzilieris-Petras
- Section for Cell Biology and Physiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Peter Carmeliet
- Laboratory of Angiogenesis and Vascular Metabolism, Centre for Cancer Biology, Vlaams Instituut voor Biotechnologie (VIB), Department of Oncology, Leuven Cancer Institute, Katholieke Universiteit Leuven, Leuven, Belgium
- Laboratory of Angiogenesis and Vascular Heterogeneity, Department of Biomedicine, Aarhus University, Aarhus, Denmark
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong, People’s Republic of China
| | - Benjamin Davies
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, U.K
| | - Thomas Moritz
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lena Eliasson
- Department of Clinical Sciences in Malmö, Islet Cell Exocytosis, Lund University Diabetes Centre, Lund University, Malmö, Sweden
| | - Patrik Rorsman
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Oxford, U.K
- Department of Physiology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Jakob G. Knudsen
- Section for Cell Biology and Physiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
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20
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Maier N, Grahek SL, Halpern J, Restrepo S, Troncoso F, Shimko J, Torres O, Belkind-Gerson J, Sack DA, Svennerholm AM, Gustafsson B, Sjöstrand B, Carlin N, Bourgeois AL, Porter CK. Efficacy of an Enterotoxigenic Escherichia coli (ETEC) Vaccine on the Incidence and Severity of Traveler's Diarrhea (TD): Evaluation of Alternative Endpoints and a TD Severity Score. Microorganisms 2023; 11:2414. [PMID: 37894071 PMCID: PMC10609384 DOI: 10.3390/microorganisms11102414] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 09/15/2023] [Accepted: 09/20/2023] [Indexed: 10/29/2023] Open
Abstract
The efficacy of an Oral Whole Cell ETEC Vaccine (OEV) against Travelers' Diarrhea (TD) was reexamined using novel outcome and immunologic measures. More specifically, a recently developed disease severity score and alternative clinical endpoints were evaluated as part of an initial validation effort to access the efficacy of a vaccine intervention for the first time in travelers to an ETEC endemic area. A randomized, double-blind, placebo-controlled trial followed travelers to Guatemala or Mexico up to 28 days after arrival in the country following vaccination (two doses two weeks apart) with an ETEC vaccine. Fecal samples were collected upon arrival, departure, and during TD for pathogen identification. Serum was collected in a subset of subjects to determine IgA cholera toxin B subunit (CTB) antibody titers upon their arrival in the country. The ETEC vaccine's efficacy, utilizing a TD severity score and other alternative endpoints, including the relationship between antibody levels and TD risk, was assessed and compared to the per-protocol primary efficacy endpoint. A total of 1435 subjects completed 7-28 days of follow-up and had available data. Vaccine efficacy was higher against more severe (≥5 unformed stools/24 h) ETEC-attributable TD and when accounting for immunologic take (PE ≥ 50%; p < 0.05). The vaccine protected against less severe (3 and 4 unformed stools/24 h) ETEC-attributable TD when accounting for symptom severity or change in activity (PE = 76.3%, p = 0.01). Immunologic take of the vaccine was associated with a reduced risk of infection with ETEC and other enteric pathogens, and with lower TD severity. Clear efficacy was observed among vaccinees with a TD score of ≥4 or ≥5, regardless of immunologic take (PE = 72.0% and 79.0%, respectively, p ≤ 0.03). The vaccine reduced the incidence and severity of ETEC, and this warrants accelerated evaluation of the improved formulation (designated ETVAX), currently undergoing advanced field testing. Subjects with serum IgA titers to CTB had a lower risk of infection with ETEC and Campylobacter jejuni/coli. Furthermore, the TD severity score provided a more robust descriptor of disease severity and should be included as an endpoint in future studies.
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Affiliation(s)
| | - Shannon L. Grahek
- Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA; (S.L.G.); (J.H.); (S.R.); (F.T.); (J.S.); (D.A.S.)
| | - Jane Halpern
- Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA; (S.L.G.); (J.H.); (S.R.); (F.T.); (J.S.); (D.A.S.)
| | - Suzanne Restrepo
- Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA; (S.L.G.); (J.H.); (S.R.); (F.T.); (J.S.); (D.A.S.)
| | - Felipe Troncoso
- Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA; (S.L.G.); (J.H.); (S.R.); (F.T.); (J.S.); (D.A.S.)
| | - Janet Shimko
- Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA; (S.L.G.); (J.H.); (S.R.); (F.T.); (J.S.); (D.A.S.)
| | - Olga Torres
- Laboratorio Diagnostico Molecular, Guatemala City 01009, Guatemala;
| | | | - David A. Sack
- Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA; (S.L.G.); (J.H.); (S.R.); (F.T.); (J.S.); (D.A.S.)
| | - Ann-Mari Svennerholm
- Department of Microbiology and Immunology, University of Gothenburg, 405 30 Gothenburg, Sweden;
| | - Björn Gustafsson
- Scandinavian Biopharma Holding AB, 171 48 Stockholm, Sweden (B.S.); (N.C.)
| | - Björn Sjöstrand
- Scandinavian Biopharma Holding AB, 171 48 Stockholm, Sweden (B.S.); (N.C.)
| | - Nils Carlin
- Scandinavian Biopharma Holding AB, 171 48 Stockholm, Sweden (B.S.); (N.C.)
| | | | - Chad K. Porter
- Naval Medical Research Command, Silver Spring, MD 20910, USA;
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21
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Hörberg J, Reymer A. Decoding the dual recognition mechanism of the glucocorticoid receptor for DNA and RNA: sequence versus shape. Sci Rep 2023; 13:16125. [PMID: 37752333 PMCID: PMC10522765 DOI: 10.1038/s41598-023-43244-1] [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: 03/03/2023] [Accepted: 09/21/2023] [Indexed: 09/28/2023] Open
Abstract
Transcription factors (TFs) regulate eukaryotic transcription through selective DNA-binding, can also specifically interact with RNA, which may present another layer of transcriptional control. The mechanisms of the TFs-DNA recognition are often well-characterised, while the details of TFs-RNA complexation are less understood. Here we investigate the dual recognition mechanism of the glucocorticoid receptor (GR), which interacts with similar affinities with consensus DNA and diverse RNA hairpin motifs but discriminates against uniform dsRNA. Using atomic molecular dynamics simulations, we demonstrate that the GR binding to nucleic acids requires a wide and shallow groove pocket. The protein effectively moulds its binding site within DNA major groove, which enables base-specific interactions. Contrary, the GR binding has little effect on the grooves geometry of RNA systems, most notably in uniform dsRNA. Instead, a hairpin motif in RNA yields a wide and shallow major groove pocket, allowing the protein to anchor itself through nonspecific electrostatic contacts with RNA backbone. Addition of a bulge increases RNA hairpin flexibility, which leads to a greater number of GR-RNA contacts and, thus, higher affinity. Thus, the combination of structural motifs defines the GR-RNA selective binding: a recognition mechanism, which may be shared by other zinc finger TFs.
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Affiliation(s)
- Johanna Hörberg
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30, Göteborg, Sweden
| | - Anna Reymer
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30, Göteborg, Sweden.
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22
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Larsson A, Grespi A, Abbondanza G, Eidhagen J, Gajdek D, Simonov K, Yue X, Lienert U, Hegedüs Z, Jeromin A, Keller TF, Scardamaglia M, Shavorskiy A, Merte LR, Pan J, Lundgren E. The Oxygen Evolution Reaction Drives Passivity Breakdown for Ni-Cr-Mo Alloys. Adv Mater 2023; 35:e2304621. [PMID: 37437599 DOI: 10.1002/adma.202304621] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 06/29/2023] [Accepted: 07/10/2023] [Indexed: 07/14/2023]
Abstract
Corrosion is the main factor limiting the lifetime of metallic materials, and a fundamental understanding of the governing mechanism and surface processes is difficult to achieve since the thin oxide films at the metal-liquid interface governing passivity are notoriously challenging to study. In this work, a combination of synchrotron-based techniques and electrochemical methods is used to investigate the passive film breakdown of a Ni-Cr-Mo alloy, which is used in many industrial applications. This alloy is found to be active toward oxygen evolution reaction (OER), and the OER onset coincides with the loss of passivity and severe metal dissolution. The OER mechanism involves the oxidation of Mo4+ sites in the oxide film to Mo6+ that can be dissolved, which results in passivity breakdown. This is fundamentally different from typical transpassive breakdown of Cr-containing alloys where Cr6+ is postulated to be dissolved at high anodic potentials, which is not observed here. At high current densities, OER also leads to acidification of the solution near the surface, further triggering metal dissolution. The OER plays an important role in the mechanism of passivity breakdown of Ni-Cr-Mo alloys due to their catalytic activity, and this effect needs to be considered when studying the corrosion of catalytically active alloys.
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Affiliation(s)
- Alfred Larsson
- Lund University, Division of Synchrotron Radiation Research, Lund, 221 00, Sweden
| | - Andrea Grespi
- Lund University, Division of Synchrotron Radiation Research, Lund, 221 00, Sweden
| | - Giuseppe Abbondanza
- Lund University, Division of Synchrotron Radiation Research, Lund, 221 00, Sweden
| | - Josefin Eidhagen
- KTH Royal Institute of Technology, Division of Surface and Corrosion Science, Stockholm, 100 44, Sweden
- Alleima (former Sandvik Materials Technology), Sandviken, 811 81, Sweden
| | - Dorotea Gajdek
- Malmö University, Materials Science and Applied Mathematics, Malmö, 205 06, Sweden
| | - Konstantin Simonov
- Swerim AB, Department of Materials and Process Development, Kista, 164 07, Sweden
| | - Xiaoqi Yue
- KTH Royal Institute of Technology, Division of Surface and Corrosion Science, Stockholm, 100 44, Sweden
| | | | | | - Arno Jeromin
- Centre for X-ray and Nano Science (CXNS), Deutsches Elektronen-Synchrotron DESY, 22607, Hamburg, Germany
| | - Thomas F Keller
- Centre for X-ray and Nano Science (CXNS), Deutsches Elektronen-Synchrotron DESY, 22607, Hamburg, Germany
- Department of Physics, University of Hamburg, 22607, Hamburg, Germany
| | | | | | - Lindsay R Merte
- Malmö University, Materials Science and Applied Mathematics, Malmö, 205 06, Sweden
| | - Jinshan Pan
- KTH Royal Institute of Technology, Division of Surface and Corrosion Science, Stockholm, 100 44, Sweden
| | - Edvin Lundgren
- Lund University, Division of Synchrotron Radiation Research, Lund, 221 00, Sweden
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23
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Guan J, Borenäs M, Xiong J, Lai WY, Palmer RH, Hallberg B. IGF1R Contributes to Cell Proliferation in ALK-Mutated Neuroblastoma with Preference for Activating the PI3K-AKT Signaling Pathway. Cancers (Basel) 2023; 15:4252. [PMID: 37686528 PMCID: PMC10563084 DOI: 10.3390/cancers15174252] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 08/15/2023] [Accepted: 08/23/2023] [Indexed: 09/10/2023] Open
Abstract
Aberrant activation of anaplastic lymphoma kinase (ALK) by activating point mutation or amplification drives 5-12% of neuroblastoma (NB). Previous work has identified the involvement of the insulin-like growth factor 1 receptor (IGF1R) receptor tyrosine kinase (RTK) in a wide range of cancers. We show here that many NB cell lines exhibit IGF1R activity, and that IGF1R inhibition led to decreased cell proliferation to varying degrees in ALK-driven NB cells. Furthermore, combined inhibition of ALK and IGF1R resulted in synergistic anti-proliferation effects, in particular in ALK-mutated NB cells. Mechanistically, both ALK and IGF1R contribute significantly to the activation of downstream PI3K-AKT and RAS-MAPK signaling pathways in ALK-mutated NB cells. However, these two RTKs employ a differential repertoire of adaptor proteins to mediate downstream signaling effects. We show here that ALK signaling led to activation of the RAS-MAPK pathway by preferentially phosphorylating the adaptor proteins GAB1, GAB2, and FRS2, while IGF1R signaling preferentially phosphorylated IRS2, promoting activation of the PI3K-AKT pathway. Together, these findings reveal a potentially important role of the IGF1R RTK in ALK-mutated NB and that co-targeting of ALK and IGF1R may be advantageous in clinical treatment of ALK-mutated NB patients.
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Affiliation(s)
- Jikui Guan
- Institute of Pediatric Medicine, Children’s Hospital Affiliated to Zhengzhou University, Zhengzhou 450018, China
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE-40530 Gothenburg, Sweden (R.H.P.); (B.H.)
| | - Marcus Borenäs
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE-40530 Gothenburg, Sweden (R.H.P.); (B.H.)
| | - Junfeng Xiong
- Institute of Pediatric Medicine, Children’s Hospital Affiliated to Zhengzhou University, Zhengzhou 450018, China
- Department of Biochemistry and Molecular Biology, Shanxi Medical University, Taiyuan 030001, China
| | - Wei-Yun Lai
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE-40530 Gothenburg, Sweden (R.H.P.); (B.H.)
| | - Ruth H. Palmer
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE-40530 Gothenburg, Sweden (R.H.P.); (B.H.)
| | - Bengt Hallberg
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE-40530 Gothenburg, Sweden (R.H.P.); (B.H.)
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24
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Doimo M, Chaudhari N, Abrahamsson S, L’Hôte V, Nguyen TH, Berner A, Ndi M, Abrahamsson A, Das R, Aasumets K, Goffart S, Pohjoismäki JLO, López MD, Chorell E, Wanrooij S. Enhanced mitochondrial G-quadruplex formation impedes replication fork progression leading to mtDNA loss in human cells. Nucleic Acids Res 2023; 51:7392-7408. [PMID: 37351621 PMCID: PMC10415151 DOI: 10.1093/nar/gkad535] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 06/09/2023] [Indexed: 06/24/2023] Open
Abstract
Mitochondrial DNA (mtDNA) replication stalling is considered an initial step in the formation of mtDNA deletions that associate with genetic inherited disorders and aging. However, the molecular details of how stalled replication forks lead to mtDNA deletions accumulation are still unclear. Mitochondrial DNA deletion breakpoints preferentially occur at sequence motifs predicted to form G-quadruplexes (G4s), four-stranded nucleic acid structures that can fold in guanine-rich regions. Whether mtDNA G4s form in vivo and their potential implication for mtDNA instability is still under debate. In here, we developed new tools to map G4s in the mtDNA of living cells. We engineered a G4-binding protein targeted to the mitochondrial matrix of a human cell line and established the mtG4-ChIP method, enabling the determination of mtDNA G4s under different cellular conditions. Our results are indicative of transient mtDNA G4 formation in human cells. We demonstrate that mtDNA-specific replication stalling increases formation of G4s, particularly in the major arc. Moreover, elevated levels of G4 block the progression of the mtDNA replication fork and cause mtDNA loss. We conclude that stalling of the mtDNA replisome enhances mtDNA G4 occurrence, and that G4s not resolved in a timely manner can have a negative impact on mtDNA integrity.
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Affiliation(s)
- Mara Doimo
- Department of Medical Biochemistry and Biophysics, Umeå University, 90187 Umeå, Sweden
- Department of Women and Children Health, University of Padova, 35128 Padova, Italy
| | - Namrata Chaudhari
- Department of Medical Biochemistry and Biophysics, Umeå University, 90187 Umeå, Sweden
| | - Sanna Abrahamsson
- Bioinformatics and Data Centre, Sahlgrenska Academy, University of Gothenburg, 41390 Gothenburg, Sweden
| | - Valentin L’Hôte
- Department of Medical Biochemistry and Biophysics, Umeå University, 90187 Umeå, Sweden
| | - Tran V H Nguyen
- Department of Medical Biochemistry and Biophysics, Umeå University, 90187 Umeå, Sweden
| | - Andreas Berner
- Department of Medical Biochemistry and Biophysics, Umeå University, 90187 Umeå, Sweden
| | - Mama Ndi
- Department of Medical Biochemistry and Biophysics, Umeå University, 90187 Umeå, Sweden
| | | | | | - Koit Aasumets
- Department of Environmental and Biological Sciences, University of Eastern Finland, FI-80101 Joensuu, Finland
| | - Steffi Goffart
- Department of Environmental and Biological Sciences, University of Eastern Finland, FI-80101 Joensuu, Finland
| | - Jaakko L O Pohjoismäki
- Department of Environmental and Biological Sciences, University of Eastern Finland, FI-80101 Joensuu, Finland
| | - Marcela Dávila López
- Bioinformatics and Data Centre, Sahlgrenska Academy, University of Gothenburg, 41390 Gothenburg, Sweden
| | - Erik Chorell
- Department of Chemistry, Umeå University, 90187 Umeå, Sweden
| | - Sjoerd Wanrooij
- Department of Medical Biochemistry and Biophysics, Umeå University, 90187 Umeå, Sweden
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25
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Elander PH, Holla S, Sabljić I, Gutierrez-Beltran E, Willems P, Bozhkov PV, Minina EA. Interactome of Arabidopsis ATG5 Suggests Functions beyond Autophagy. Int J Mol Sci 2023; 24:12300. [PMID: 37569688 PMCID: PMC10418956 DOI: 10.3390/ijms241512300] [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: 07/05/2023] [Revised: 07/27/2023] [Accepted: 07/28/2023] [Indexed: 08/13/2023] Open
Abstract
Autophagy is a catabolic pathway capable of degrading cellular components ranging from individual molecules to organelles. Autophagy helps cells cope with stress by removing superfluous or hazardous material. In a previous work, we demonstrated that transcriptional upregulation of two autophagy-related genes, ATG5 and ATG7, in Arabidopsis thaliana positively affected agronomically important traits: biomass, seed yield, tolerance to pathogens and oxidative stress. Although the occurrence of these traits correlated with enhanced autophagic activity, it is possible that autophagy-independent roles of ATG5 and ATG7 also contributed to the phenotypes. In this study, we employed affinity purification and LC-MS/MS to identify the interactome of wild-type ATG5 and its autophagy-inactive substitution mutant, ATG5K128R Here we present the first interactome of plant ATG5, encompassing not only known autophagy regulators but also stress-response factors, components of the ubiquitin-proteasome system, proteins involved in endomembrane trafficking, and potential partners of the nuclear fraction of ATG5. Furthermore, we discovered post-translational modifications, such as phosphorylation and acetylation present on ATG5 complex components that are likely to play regulatory functions. These results strongly indicate that plant ATG5 complex proteins have roles beyond autophagy itself, opening avenues for further investigations on the complex roles of autophagy in plant growth and stress responses.
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Affiliation(s)
- Pernilla H. Elander
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, 750-07 Uppsala, Sweden; (P.H.E.); (S.H.); (I.S.); (P.V.B.)
| | - Sanjana Holla
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, 750-07 Uppsala, Sweden; (P.H.E.); (S.H.); (I.S.); (P.V.B.)
| | - Igor Sabljić
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, 750-07 Uppsala, Sweden; (P.H.E.); (S.H.); (I.S.); (P.V.B.)
| | - Emilio Gutierrez-Beltran
- Instituto de Bioquımica Vegetal y Fotosıntesis, Universidad de Sevilla and Consejo Superior de Investigaciones Cientıficas, 41092 Sevilla, Spain;
- Departamento de Bioquimica Vegetal y Biologia Molecular, Facultad de Biologia, Universidad de Sevilla, 41012 Sevilla, Spain
| | - Patrick Willems
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium;
- Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
| | - Peter V. Bozhkov
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, 750-07 Uppsala, Sweden; (P.H.E.); (S.H.); (I.S.); (P.V.B.)
| | - Elena A. Minina
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, 750-07 Uppsala, Sweden; (P.H.E.); (S.H.); (I.S.); (P.V.B.)
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26
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Akinwekomi A, Akhtar F. Microstructural, Mechanical, and Electrochemical Characterization of CrMoNbTiZr High-Entropy Alloy for Biomedical Application. Materials (Basel) 2023; 16:5320. [PMID: 37570024 PMCID: PMC10420154 DOI: 10.3390/ma16155320] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 07/25/2023] [Accepted: 07/26/2023] [Indexed: 08/13/2023]
Abstract
High-entropy alloys (HEA) with superior biocompatibility, high pitting resistance, minimal debris accumulation, and reduced release of metallic ions into surrounding tissues are potential replacements for traditional metallic bio-implants. A novel equiatomic HEA based on biocompatible metals, CrMoNbTiZr, was consolidated by spark plasma sintering (SPS). The relative sintered density of the alloy was about 97% of the theoretical density, indicating the suitability of the SPS technique to produce relatively dense material. The microstructure of the sintered HEA consisted of a BCC matrix and Laves phase, corresponding to the prediction of the thermodynamic CALPHAD simulation. The HEA exhibited a global Vickers microhardness of 531.5 ± 99.7 HV, while the individual BCC and Laves phases had hardness values of 364.6 ± 99.4 and 641.8 ± 63.0 HV, respectively. Its ultimate compressive and compressive yield strengths were 1235.7 ± 42.8 MPa and 1110.8 ± 78.6 MPa, respectively. The elasticity modulus of 34.9 ± 2.9 GPa of the HEA alloy was well within the range of cortical bone and significantly lower than the values reported for commonly used biomaterials made from Ti-based and Cr-Co-based alloys. In addition, the alloy exhibited good resistance to bio-corrosion in PBS and Hanks solutions. The CrMoNbTiZr HEA exhibited an average COF of 0.43 ± 0.06, characterized mainly by abrasive and adhesive wear mechanisms. The CrMoNbTiZr alloy's mechanical, bio-corrosion, and wear resistance properties developed in this study showed a good propensity for application as a biomaterial.
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Affiliation(s)
- Akeem Akinwekomi
- Division of Materials Science, Luleå University of Technology, 97187 Luleå, Sweden;
- Department of Metallurgical and Materials Engineering, Federal University of Technology Akure, Akure 340252, Ondo State, Nigeria
| | - Farid Akhtar
- Division of Materials Science, Luleå University of Technology, 97187 Luleå, Sweden;
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27
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Armada-Moreira A, Dar AM, Zhao Z, Cea C, Gelinas J, Berggren M, Costa A, Khodagholy D, Stavrinidou E. Plant electrophysiology with conformable organic electronics: Deciphering the propagation of Venus flytrap action potentials. Sci Adv 2023; 9:eadh4443. [PMID: 37494449 PMCID: PMC10371018 DOI: 10.1126/sciadv.adh4443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 06/22/2023] [Indexed: 07/28/2023]
Abstract
Electrical signals in plants are mediators of long-distance signaling and correlate with plant movements and responses to stress. These signals are studied with single surface electrodes that cannot resolve signal propagation and integration, thus impeding their decoding and link to function. Here, we developed a conformable multielectrode array based on organic electronics for large-scale and high-resolution plant electrophysiology. We performed precise spatiotemporal mapping of the action potential (AP) in Venus flytrap and found that the AP actively propagates through the tissue with constant speed and without strong directionality. We also found that spontaneously generated APs can originate from unstimulated hairs and that they correlate with trap movement. Last, we demonstrate that the Venus flytrap circuitry can be activated by cells other than the sensory hairs. Our work reveals key properties of the AP and establishes the capacity of organic bioelectronics for resolving electrical signaling in plants contributing to the mechanistic understanding of long-distance responses in plants.
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Affiliation(s)
- Adam Armada-Moreira
- Laboratory of Organic Electronics, Department of Science and Technology, Linköping University, SE-601 74 Norrköping, Sweden
- Neuronal Dynamics Lab, International School for Advanced Studies, 34136 Trieste TS, Italy
| | - Abdul Manan Dar
- Laboratory of Organic Electronics, Department of Science and Technology, Linköping University, SE-601 74 Norrköping, Sweden
| | - Zifang Zhao
- Department of Electrical Engineering, Columbia University, New York, NY 10027, USA
| | - Claudia Cea
- Department of Electrical Engineering, Columbia University, New York, NY 10027, USA
| | - Jennifer Gelinas
- Department of Neurology, Columbia University Medical Center, New York, NY 10032, USA
| | - Magnus Berggren
- Laboratory of Organic Electronics, Department of Science and Technology, Linköping University, SE-601 74 Norrköping, Sweden
- Wallenberg Wood Science Center, Department of Science and Technology, Linköping University, SE-601 74 Norrköping, Sweden
| | - Alex Costa
- Department of Biosciences, University of Milan, 20133 Milano, Italy
- Institute of Biophysics, National Research Council of Italy (CNR), 20133 Milano, Italy
| | - Dion Khodagholy
- Department of Electrical Engineering, Columbia University, New York, NY 10027, USA
| | - Eleni Stavrinidou
- Laboratory of Organic Electronics, Department of Science and Technology, Linköping University, SE-601 74 Norrköping, Sweden
- Wallenberg Wood Science Center, Department of Science and Technology, Linköping University, SE-601 74 Norrköping, Sweden
- Umeå Plant Science Center, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-901 83 Umeå, Sweden
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28
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Forteza MJ, Berg M, Edsfeldt A, Sun J, Baumgartner R, Kareinen I, Casagrande FB, Hedin U, Zhang S, Vuckovic I, Dzeja PP, Polyzos KA, Gisterå A, Trauelsen M, Schwartz TW, Dib L, Herrmann J, Monaco C, Matic L, Gonçalves I, Ketelhuth DFJ. Pyruvate dehydrogenase kinase regulates vascular inflammation in atherosclerosis and increases cardiovascular risk. Cardiovasc Res 2023; 119:1524-1536. [PMID: 36866436 PMCID: PMC10318388 DOI: 10.1093/cvr/cvad038] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 01/11/2023] [Accepted: 02/01/2023] [Indexed: 03/04/2023] Open
Abstract
AIMS Recent studies have revealed a close connection between cellular metabolism and the chronic inflammatory process of atherosclerosis. While the link between systemic metabolism and atherosclerosis is well established, the implications of altered metabolism in the artery wall are less understood. Pyruvate dehydrogenase kinase (PDK)-dependent inhibition of pyruvate dehydrogenase (PDH) has been identified as a major metabolic step regulating inflammation. Whether the PDK/PDH axis plays a role in vascular inflammation and atherosclerotic cardiovascular disease remains unclear. METHODS AND RESULTS Gene profiling of human atherosclerotic plaques revealed a strong correlation between PDK1 and PDK4 transcript levels and the expression of pro-inflammatory and destabilizing genes. Remarkably, the PDK1 and PDK4 expression correlated with a more vulnerable plaque phenotype, and PDK1 expression was found to predict future major adverse cardiovascular events. Using the small-molecule PDK inhibitor dichloroacetate (DCA) that restores arterial PDH activity, we demonstrated that the PDK/PDH axis is a major immunometabolic pathway, regulating immune cell polarization, plaque development, and fibrous cap formation in Apoe-/- mice. Surprisingly, we discovered that DCA regulates succinate release and mitigates its GPR91-dependent signals promoting NLRP3 inflammasome activation and IL-1β secretion by macrophages in the plaque. CONCLUSIONS We have demonstrated for the first time that the PDK/PDH axis is associated with vascular inflammation in humans and particularly that the PDK1 isozyme is associated with more severe disease and could predict secondary cardiovascular events. Moreover, we demonstrate that targeting the PDK/PDH axis with DCA skews the immune system, inhibits vascular inflammation and atherogenesis, and promotes plaque stability features in Apoe-/- mice. These results point toward a promising treatment to combat atherosclerosis.
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Affiliation(s)
- Maria J Forteza
- Center for Molecular Medicine, Department of Medicine, Solna, Karolinska University Hospital, Karolinska Instutet,BioClinicum, Solnavägen 30, Solna, 17 164, Stockholm, Sweden
| | - Martin Berg
- Center for Molecular Medicine, Department of Medicine, Solna, Karolinska University Hospital, Karolinska Instutet,BioClinicum, Solnavägen 30, Solna, 17 164, Stockholm, Sweden
| | - Andreas Edsfeldt
- Cardiovascular Research Translational Studies, Clinical Research Centre, Clinical Sciences Malmö, Lund University, Jan Waldenströms gata 35, 20 502, Malmö, Sweden
- Department of Cardiology, Skåne University Hospital, Carl-Bertil Laurells gata 9, 21 428, Malmö, Sweden
- Wallenberg Center for Molecular Medicine, Lund University, Jan Waldenströms gata 35, 20 502, Malmö, Sweden
| | - Jangming Sun
- Cardiovascular Research Translational Studies, Clinical Research Centre, Clinical Sciences Malmö, Lund University, Jan Waldenströms gata 35, 20 502, Malmö, Sweden
- Department of Cardiology, Skåne University Hospital, Carl-Bertil Laurells gata 9, 21 428, Malmö, Sweden
| | - Roland Baumgartner
- Center for Molecular Medicine, Department of Medicine, Solna, Karolinska University Hospital, Karolinska Instutet,BioClinicum, Solnavägen 30, Solna, 17 164, Stockholm, Sweden
| | - Ilona Kareinen
- Center for Molecular Medicine, Department of Medicine, Solna, Karolinska University Hospital, Karolinska Instutet,BioClinicum, Solnavägen 30, Solna, 17 164, Stockholm, Sweden
| | - Felipe Beccaria Casagrande
- Center for Molecular Medicine, Department of Medicine, Solna, Karolinska University Hospital, Karolinska Instutet,BioClinicum, Solnavägen 30, Solna, 17 164, Stockholm, Sweden
| | - Ulf Hedin
- Department of Molecular Medicine and Surgery, Karolinska University Hospital, Karolinska Institutet, BioClinicum, Solnavägen 30, Solna, 17 164, Stockholm, Sweden
| | - Song Zhang
- Mayo Clinic Metabolomics Core, Mayo Clinic, 200, First St. SW Rochester, MN 55905, USA
- Department of Cardiovascular Medicine, Mayo Clinic, 200, First St. SW Rochester, MN 55905, USA
| | - Ivan Vuckovic
- Mayo Clinic Metabolomics Core, Mayo Clinic, 200, First St. SW Rochester, MN 55905, USA
| | - Petras P Dzeja
- Department of Cardiovascular Medicine, Mayo Clinic, 200, First St. SW Rochester, MN 55905, USA
| | - Konstantinos A Polyzos
- Center for Molecular Medicine, Department of Medicine, Solna, Karolinska University Hospital, Karolinska Instutet,BioClinicum, Solnavägen 30, Solna, 17 164, Stockholm, Sweden
| | - Anton Gisterå
- Center for Molecular Medicine, Department of Medicine, Solna, Karolinska University Hospital, Karolinska Instutet,BioClinicum, Solnavägen 30, Solna, 17 164, Stockholm, Sweden
| | - Mette Trauelsen
- Section for Metabolic Receptology, Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Blegdamsvej 3A, 2200, Copenhagen, Denmark
| | - Thue W Schwartz
- Section for Metabolic Receptology, Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Blegdamsvej 3A, 2200, Copenhagen, Denmark
| | - Lea Dib
- Kennedy Institute of Rheumatology, University of Oxford, Roosevelt Dr, Headington, Oxford OX3 7FY, UK
| | - Joerg Herrmann
- Department of Cardiovascular Medicine, Mayo Clinic, 200, First St. SW Rochester, MN 55905, USA
| | - Claudia Monaco
- Kennedy Institute of Rheumatology, University of Oxford, Roosevelt Dr, Headington, Oxford OX3 7FY, UK
| | - Ljubica Matic
- Department of Molecular Medicine and Surgery, Karolinska University Hospital, Karolinska Institutet, BioClinicum, Solnavägen 30, Solna, 17 164, Stockholm, Sweden
| | - Isabel Gonçalves
- Cardiovascular Research Translational Studies, Clinical Research Centre, Clinical Sciences Malmö, Lund University, Jan Waldenströms gata 35, 20 502, Malmö, Sweden
- Department of Cardiology, Skåne University Hospital, Carl-Bertil Laurells gata 9, 21 428, Malmö, Sweden
| | - Daniel F J Ketelhuth
- Center for Molecular Medicine, Department of Medicine, Solna, Karolinska University Hospital, Karolinska Instutet,BioClinicum, Solnavägen 30, Solna, 17 164, Stockholm, Sweden
- Department of Cardiovascular and Renal Research, Institute of Molecular Medicine, University of Southern Denmark, J.B. Winsløws vej 21, 5000 Odense, Denmark
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Tavaglione F, Jamialahmadi O, Ljungman C, Romeo S. Reply to: "Fatty liver disease at the basis of cardiac remodelling and increased heart rate: Insights from the UK Biobank". Liver Int 2023; 43:1362-1364. [PMID: 37166135 DOI: 10.1111/liv.15598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 04/19/2023] [Indexed: 05/12/2023]
Affiliation(s)
- Federica Tavaglione
- Department of Molecular and Clinical Medicine, Sahlgrenska Academy, Wallenberg Laboratory, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
- Clinical Medicine and Hepatology Unit, Department of Medicine and Surgery, Campus Bio-Medico University of Rome, Rome, Italy
| | - Oveis Jamialahmadi
- Department of Molecular and Clinical Medicine, Sahlgrenska Academy, Wallenberg Laboratory, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Charlotta Ljungman
- Department of Molecular and Clinical Medicine, Sahlgrenska Academy, Wallenberg Laboratory, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
- Department of Cardiology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Stefano Romeo
- Department of Molecular and Clinical Medicine, Sahlgrenska Academy, Wallenberg Laboratory, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
- Department of Cardiology, Sahlgrenska University Hospital, Gothenburg, Sweden
- Clinical Nutrition Unit, Department of Medical and Surgical Sciences, University Magna Graecia, Catanzaro, Italy
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Yu Chen H, Dina C, Small AM, Shaffer CM, Levinson RT, Helgadóttir A, Capoulade R, Munter HM, Martinsson A, Cairns BJ, Trudsø LC, Hoekstra M, Burr HA, Marsh TW, Damrauer SM, Dufresne L, Le Scouarnec S, Messika-Zeitoun D, Ranatunga DK, Whitmer RA, Bonnefond A, Sveinbjornsson G, Daníelsen R, Arnar DO, Thorgeirsson G, Thorsteinsdottir U, Gudbjartsson DF, Hólm H, Ghouse J, Olesen MS, Christensen AH, Mikkelsen S, Jacobsen RL, Dowsett J, Pedersen OBV, Erikstrup C, Ostrowski SR, O’Donnell CJ, Budoff MJ, Gudnason V, Post WS, Rotter JI, Lathrop M, Bundgaard H, Johansson B, Ljungberg J, Näslund U, Le Tourneau T, Smith JG, Wells QS, Söderberg S, Stefánsson K, Schott JJ, Rader DJ, Clarke R, Engert JC, Thanassoulis G. Dyslipidemia, inflammation, calcification, and adiposity in aortic stenosis: a genome-wide study. Eur Heart J 2023; 44:1927-1939. [PMID: 37038246 PMCID: PMC10232274 DOI: 10.1093/eurheartj/ehad142] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 01/20/2023] [Accepted: 02/21/2023] [Indexed: 04/12/2023] Open
Abstract
AIMS Although highly heritable, the genetic etiology of calcific aortic stenosis (AS) remains incompletely understood. The aim of this study was to discover novel genetic contributors to AS and to integrate functional, expression, and cross-phenotype data to identify mechanisms of AS. METHODS AND RESULTS A genome-wide meta-analysis of 11.6 million variants in 10 cohorts involving 653 867 European ancestry participants (13 765 cases) was performed. Seventeen loci were associated with AS at P ≤ 5 × 10-8, of which 15 replicated in an independent cohort of 90 828 participants (7111 cases), including CELSR2-SORT1, NLRP6, and SMC2. A genetic risk score comprised of the index variants was associated with AS [odds ratio (OR) per standard deviation, 1.31; 95% confidence interval (CI), 1.26-1.35; P = 2.7 × 10-51] and aortic valve calcium (OR per standard deviation, 1.22; 95% CI, 1.08-1.37; P = 1.4 × 10-3), after adjustment for known risk factors. A phenome-wide association study indicated multiple associations with coronary artery disease, apolipoprotein B, and triglycerides. Mendelian randomization supported a causal role for apolipoprotein B-containing lipoprotein particles in AS (OR per g/L of apolipoprotein B, 3.85; 95% CI, 2.90-5.12; P = 2.1 × 10-20) and replicated previous findings of causality for lipoprotein(a) (OR per natural logarithm, 1.20; 95% CI, 1.17-1.23; P = 4.8 × 10-73) and body mass index (OR per kg/m2, 1.07; 95% CI, 1.05-1.9; P = 1.9 × 10-12). Colocalization analyses using the GTEx database identified a role for differential expression of the genes LPA, SORT1, ACTR2, NOTCH4, IL6R, and FADS. CONCLUSION Dyslipidemia, inflammation, calcification, and adiposity play important roles in the etiology of AS, implicating novel treatments and prevention strategies.
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Affiliation(s)
- Hao Yu Chen
- Division of Experimental Medicine, McGill University, 1001 Decarie Blvd., Room EM1.2218, Montreal, Quebec H4A 3J1, Canada
- Preventive and Genomic Cardiology, McGill University Health Centre and Research Institute, 1001 Decarie Blvd., Room D05.5120, Montreal, Quebec H4A 3J1, Canada
| | - Christian Dina
- Nantes Université, CHU Nantes, CNRS, INSERM, l’institut du thorax, 8 Quai Moncousu, Nantes F-44000, France
| | - Aeron M Small
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
| | - Christian M Shaffer
- Vanderbilt Translational and Clinical Cardiovascular Research Center, Vanderbilt University Medical Center, Nashville, USA
| | - Rebecca T Levinson
- Vanderbilt Translational and Clinical Cardiovascular Research Center, Vanderbilt University Medical Center, Nashville, USA
| | | | - Romain Capoulade
- Nantes Université, CHU Nantes, CNRS, INSERM, l’institut du thorax, 8 Quai Moncousu, Nantes F-44000, France
| | | | - Andreas Martinsson
- Department of Cardiology, Clinical Sciences, Lund University, Sweden and Skåne University Hospital, Lund, Sweden
- The Wallenberg Laboratory/Department of Molecular and Clinical Medicine, Institute of Medicine, Gothenburg University and the Department of Cardiology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Benjamin J Cairns
- MRC Population Health Research Unit, Clinical Trial Service Unit and Epidemiological Studies Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Linea C Trudsø
- Laboratory for Molecular Cardiology, Department of Cardiology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Mary Hoekstra
- Division of Experimental Medicine, McGill University, 1001 Decarie Blvd., Room EM1.2218, Montreal, Quebec H4A 3J1, Canada
- Preventive and Genomic Cardiology, McGill University Health Centre and Research Institute, 1001 Decarie Blvd., Room D05.5120, Montreal, Quebec H4A 3J1, Canada
| | - Hannah A Burr
- Division of Experimental Medicine, McGill University, 1001 Decarie Blvd., Room EM1.2218, Montreal, Quebec H4A 3J1, Canada
- Preventive and Genomic Cardiology, McGill University Health Centre and Research Institute, 1001 Decarie Blvd., Room D05.5120, Montreal, Quebec H4A 3J1, Canada
| | - Thomas W Marsh
- Preventive and Genomic Cardiology, McGill University Health Centre and Research Institute, 1001 Decarie Blvd., Room D05.5120, Montreal, Quebec H4A 3J1, Canada
- Department of Human Genetics, McGill University, Montreal, Canada
| | - Scott M Damrauer
- Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
| | - Line Dufresne
- Preventive and Genomic Cardiology, McGill University Health Centre and Research Institute, 1001 Decarie Blvd., Room D05.5120, Montreal, Quebec H4A 3J1, Canada
| | - Solena Le Scouarnec
- Nantes Université, CHU Nantes, CNRS, INSERM, l’institut du thorax, 8 Quai Moncousu, Nantes F-44000, France
| | - David Messika-Zeitoun
- Department of Cardiology, Assistance Publique - Hôpitaux de Paris, Bichat Hospital, Paris, France
- Division of Cardiology, University of Ottawa Heart Institute, Ottawa, Ontario, Canada
| | - Dilrini K Ranatunga
- Division of Research, Kaiser Permanente of Northern California, Oakland, USA
| | - Rachel A Whitmer
- Department of Public Health Sciences, University of California Davis, Davis, USA
| | - Amélie Bonnefond
- University Lille, Inserm, CNRS, CHU Lille, Institut Pasteur de Lille, UMR1283-8199 EGID, Lille, France
- Department of Metabolism, Imperial College London, London, UK
| | | | - Ragnar Daníelsen
- Internal Medicine and Emergency Services, Landspitali—The National University Hospital of Iceland, Reykjavik, Iceland
| | - David O Arnar
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- Internal Medicine and Emergency Services, Landspitali—The National University Hospital of Iceland, Reykjavik, Iceland
- School of Health Sciences, Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Gudmundur Thorgeirsson
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- School of Health Sciences, Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Unnur Thorsteinsdottir
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- School of Health Sciences, Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Daníel F Gudbjartsson
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | - Hilma Hólm
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
| | - Jonas Ghouse
- Laboratory for Molecular Cardiology, Department of Cardiology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Morten Salling Olesen
- Laboratory for Molecular Cardiology, Department of Cardiology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Alex H Christensen
- Laboratory for Molecular Cardiology, Department of Cardiology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
- Department of Cardiology, Herlev-Gentofte Hospital, Copenhagen, Denmark
| | - Susan Mikkelsen
- Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark
| | - Rikke Louise Jacobsen
- Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Joseph Dowsett
- Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | | | - Christian Erikstrup
- Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Sisse R Ostrowski
- Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | | | - Christopher J O’Donnell
- National Heart, Lung, and Blood Institute's and Boston University's Framingham Heart Study, Boston, USA
| | - Matthew J Budoff
- The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, USA
| | | | - Wendy S Post
- Division of Cardiology, Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, USA
| | - Mark Lathrop
- McGill University and Genome Quebec Innovation Centre, Montreal, Canada
- Department of Human Genetics, McGill University, Montreal, Canada
| | - Henning Bundgaard
- Department of Cardiology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Bengt Johansson
- Department of Public Health and Clinical Medicine, Umeå University, Umeå, Sweden
| | - Johan Ljungberg
- Department of Public Health and Clinical Medicine, Umeå University, Umeå, Sweden
| | - Ulf Näslund
- Department of Public Health and Clinical Medicine, Umeå University, Umeå, Sweden
| | - Thierry Le Tourneau
- Nantes Université, CHU Nantes, CNRS, INSERM, l’institut du thorax, 8 Quai Moncousu, Nantes F-44000, France
| | - J Gustav Smith
- Department of Cardiology, Clinical Sciences, Lund University, Sweden and Skåne University Hospital, Lund, Sweden
- Wallenberg Center for Molecular Medicine and Lund University Diabetes Center, Lund, Sweden
- The Wallenberg Laboratory/Department of Molecular and Clinical Medicine, Institute of Medicine, Gothenburg University and the Department of Cardiology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Quinn S Wells
- Vanderbilt Translational and Clinical Cardiovascular Research Center, Vanderbilt University Medical Center, Nashville, USA
| | - Stefan Söderberg
- Department of Public Health and Clinical Medicine, Umeå University, Umeå, Sweden
| | - Kári Stefánsson
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- School of Health Sciences, Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Jean-Jacques Schott
- Nantes Université, CHU Nantes, CNRS, INSERM, l’institut du thorax, 8 Quai Moncousu, Nantes F-44000, France
| | - Daniel J Rader
- Departments of Genetics and Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
| | - Robert Clarke
- MRC Population Health Research Unit, Clinical Trial Service Unit and Epidemiological Studies Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - James C Engert
- Division of Experimental Medicine, McGill University, 1001 Decarie Blvd., Room EM1.2218, Montreal, Quebec H4A 3J1, Canada
- Preventive and Genomic Cardiology, McGill University Health Centre and Research Institute, 1001 Decarie Blvd., Room D05.5120, Montreal, Quebec H4A 3J1, Canada
- Department of Human Genetics, McGill University, Montreal, Canada
| | - George Thanassoulis
- Division of Experimental Medicine, McGill University, 1001 Decarie Blvd., Room EM1.2218, Montreal, Quebec H4A 3J1, Canada
- Preventive and Genomic Cardiology, McGill University Health Centre and Research Institute, 1001 Decarie Blvd., Room D05.5120, Montreal, Quebec H4A 3J1, Canada
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Goetz IK, Pacheco V, Hassila CJ, Jansson U, Schneider JM, Hans M. Convective Flow Redistribution of Oxygen by Laser Melting of a Zr-Based Amorphous Alloy. Materials (Basel) 2023; 16:ma16114113. [PMID: 37297246 DOI: 10.3390/ma16114113] [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] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 05/22/2023] [Accepted: 05/27/2023] [Indexed: 06/12/2023]
Abstract
Oxygen impurities play a crucial role in the glass-forming ability and crystallisation behaviour of metallic glasses. In the present work, single laser tracks were produced on Zr59.3-xCu28.8 Al10.4Nb1.5Ox substrates (x = 0.3, 1.3) to study the redistribution of oxygen in the melt pool under laser melting, which provides the basis for laser powder bed fusion additive manufacturing. Since such substrates are commercially not available, they were fabricated by arc melting and splat quenching. X-ray diffraction revealed that the substrate with 0.3 at.% oxygen was X-ray amorphous, while the substrate with 1.3 at.% oxygen was partially crystalline. Hence, it is evident that the oxygen content affects the crystallisation kinetics. Subsequently, single laser tracks were produced on the surface of these substrates, and the melt pools attained from the laser processing were characterised by atom probe tomography and transmission electron microscopy. Surface oxidation and subsequent convective flow redistribution of oxygen by laser melting were identified as causes of the presence of CuOx and crystalline ZrO nanoparticles in the melt pool. Bands of ZrO likely originate from surface oxides that were moved deeper into the melt pool by convective flow. The findings presented here highlight the influence of oxygen redistribution from the surface into the melt pool during laser processing.
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Affiliation(s)
- Inga K Goetz
- Department of Physics and Astronomy, Materials Physics, Uppsala University, Box 530, SE-75121 Uppsala, Sweden
- Materials Chemistry, RWTH Aachen University, Kopernikusstr. 10, D-52074 Aachen, Germany
| | - Victor Pacheco
- Department of Chemistry-Angström Laboratory, Uppsala University, Box 523, SE-75120 Uppsala, Sweden
| | - Carl J Hassila
- Department of Materials Science and Engineering, Biomedical Engineering, Uppsala University, Box 35, SE-75103 Uppsala, Sweden
| | - Ulf Jansson
- Department of Chemistry-Angström Laboratory, Uppsala University, Box 523, SE-75120 Uppsala, Sweden
| | - Jochen M Schneider
- Materials Chemistry, RWTH Aachen University, Kopernikusstr. 10, D-52074 Aachen, Germany
| | - Marcus Hans
- Materials Chemistry, RWTH Aachen University, Kopernikusstr. 10, D-52074 Aachen, Germany
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Klint E, Richter J, Wårdell K. Combined Use of Frameless Neuronavigation and In Situ Optical Guidance in Brain Tumor Needle Biopsies. Brain Sci 2023; 13:brainsci13050809. [PMID: 37239281 DOI: 10.3390/brainsci13050809] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 05/10/2023] [Accepted: 05/13/2023] [Indexed: 05/28/2023] Open
Abstract
Brain tumor needle biopsies are performed to retrieve tissue samples for neuropathological analysis. Although preoperative images guide the procedure, there are risks of hemorrhage and sampling of non-tumor tissue. This study aimed to develop and evaluate a method for frameless one-insertion needle biopsies with in situ optical guidance and present a processing pipeline for combined postoperative analysis of optical, MRI, and neuropathological data. An optical system for quantified feedback on tissue microcirculation, gray-whiteness, and the presence of a tumor (protoporphyrin IX (PpIX) accumulation) with a one-insertion optical probe was integrated into a needle biopsy kit that was used for frameless neuronavigation. In Python, a pipeline for signal processing, image registration, and coordinate transformation was set up. The Euclidian distances between the pre- and postoperative coordinates were calculated. The proposed workflow was evaluated on static references, a phantom, and three patients with suspected high-grade gliomas. In total, six biopsy samples that overlapped with the region of the highest PpIX peak without increased microcirculation were taken. The samples were confirmed as being tumorous and postoperative imaging was used to define the biopsy locations. A 2.5 ± 1.2 mm difference between the pre- and postoperative coordinates was found. Optical guidance in frameless brain tumor biopsies could offer benefits such as quantified in situ indication of high-grade tumor tissue and indications of increased blood flow along the needle trajectory before the tissue is removed. Additionally, postoperative visualization enables the combined analysis of MRI, optical, and neuropathological data.
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Affiliation(s)
- Elisabeth Klint
- Department of Biomedical Engineering, Linköping University, 581 85 Linköping, Sweden
| | - Johan Richter
- Department of Biomedical Engineering, Linköping University, 581 85 Linköping, Sweden
- Department of Neurosurgery, Linköping University Hospital, 581 85 Linköping, Sweden
| | - Karin Wårdell
- Department of Biomedical Engineering, Linköping University, 581 85 Linköping, Sweden
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España Amórtegui JC, Pekar H, Retrato MDC, Persson M, Karlson B, Bergquist J, Zuberovic-Muratovic A. LC-MS/MS Analysis of Cyanotoxins in Bivalve Mollusks-Method Development, Validation and First Evidence of Occurrence of Nodularin in Mussels ( Mytilus edulis) and Oysters ( Magallana gigas) from the West Coast of Sweden. Toxins (Basel) 2023; 15:toxins15050329. [PMID: 37235362 DOI: 10.3390/toxins15050329] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/09/2023] [Accepted: 05/09/2023] [Indexed: 05/28/2023] Open
Abstract
In this paper, an LC-MS/MS method for the simultaneous identification and quantification of cyanotoxins with hydrophilic and lipophilic properties in edible bivalves is presented. The method includes 17 cyanotoxins comprising 13 microcystins (MCs), nodularin (NOD), anatoxin-a (ATX-a), homoanatoxin (h-ATX) and cylindrospermopsin (CYN). A benefit to the presented method is the possibility for the MS detection of MC-LR-[Dha7] and MC-LR-[Asp3] as separately identified and MS-resolved MRM signals, two congeners which were earlier detected together. The performance of the method was evaluated by in-house validation using spiked mussel samples in the quantification range of 3.12-200 µg/kg. The method was found to be linear over the full calibration range for all included cyanotoxins except CYN for which a quadratic regression was used. The method showed limitations for MC-LF (R2 = 0.94), MC-LA (R2 ≤ 0.98) and MC-LW (R2 ≤ 0.98). The recoveries for ATX-a, h-ATX, CYN, NOD, MC-LF and MC-LW were lower than desired (<70%), but stable. Despite the given limitations, the validation results showed that the method was specific and robust for the investigated parameters. The results demonstrate the suitability of the method to be applied as a reliable monitoring tool for the presented group of cyanotoxins, as well as highlight the compromises that need to be included if multi-toxin methods are to be used for the analysis of cyanotoxins with a broader range of chemical properties. Furthermore, the method was used to analyze 13 samples of mussels (Mytilus edulis) and oysters (Magallana gigas) collected in the 2020-2022 summers along the coast of Bohuslän (Sweden). A complementary qualitative analysis for the presence of cyanotoxins in phytoplankton samples collected from marine waters around southern Sweden was performed with the method. Nodularin was identified in all samples and quantified in bivalve samples in the range of 7-397 µg/kg. Toxins produced by cyanobacteria are not included in the European Union regulatory monitoring of bivalves; thus, the results presented in this study can be useful in providing the basis for future work including cyanotoxins within the frame of regulatory monitoring to increase seafood safety.
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Affiliation(s)
- Julio César España Amórtegui
- Science Department, Swedish Food Agency, Box 622, SE-751 26 Uppsala, Sweden
- Chemistry Department, Science Faculty, Universidad Nacional de Colombia, Cr. 45 N° 26-85, Bogotá P.O. Box 111321, Colombia
| | - Heidi Pekar
- Science Department, Swedish Food Agency, Box 622, SE-751 26 Uppsala, Sweden
- Stockholm Water and Waste Company, Bryggerivägen 10, SE-106 36 Stockholm, Sweden
| | - Mark Dennis Chico Retrato
- Department of Chemistry, Biomedical Center, Analytical Chemistry and Neurochemistry, Uppsala University, Box 599, SE-751 24 Uppsala, Sweden
| | - Malin Persson
- Science Department, Swedish Food Agency, Box 622, SE-751 26 Uppsala, Sweden
| | - Bengt Karlson
- Research and Development, Oceanography, Swedish Meteorological and Hydrological Institute, Sven Källfelts Gata 15, SE-426 71 Västra Frölunda, Sweden
| | - Jonas Bergquist
- Department of Chemistry, Biomedical Center, Analytical Chemistry and Neurochemistry, Uppsala University, Box 599, SE-751 24 Uppsala, Sweden
| | - Aida Zuberovic-Muratovic
- Science Department, Swedish Food Agency, Box 622, SE-751 26 Uppsala, Sweden
- Department of Chemistry, Biomedical Center, Analytical Chemistry and Neurochemistry, Uppsala University, Box 599, SE-751 24 Uppsala, Sweden
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Lebrigand K, Bergenstråhle J, Thrane K, Mollbrink A, Meletis K, Barbry P, Waldmann R, Lundeberg J. The spatial landscape of gene expression isoforms in tissue sections. Nucleic Acids Res 2023; 51:e47. [PMID: 36928528 PMCID: PMC10164556 DOI: 10.1093/nar/gkad169] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 02/06/2023] [Accepted: 02/23/2023] [Indexed: 03/18/2023] Open
Abstract
In situ capturing technologies add tissue context to gene expression data, with the potential of providing a greater understanding of complex biological systems. However, splicing variants and full-length sequence heterogeneity cannot be characterized at spatial resolution with current transcriptome profiling methods. To that end, we introduce spatial isoform transcriptomics (SiT), an explorative method for characterizing spatial isoform variation and sequence heterogeneity using long-read sequencing. We show in mouse brain how SiT can be used to profile isoform expression and sequence heterogeneity in different areas of the tissue. SiT reveals regional isoform switching of Plp1 gene between different layers of the olfactory bulb, and the use of external single-cell data allows the nomination of cell types expressing each isoform. Furthermore, SiT identifies differential isoform usage for several major genes implicated in brain function (Snap25, Bin1, Gnas) that are independently validated by in situ sequencing. SiT also provides for the first time an in-depth A-to-I RNA editing map of the adult mouse brain. Data exploration can be performed through an online resource (https://www.isomics.eu), where isoform expression and RNA editing can be visualized in a spatial context.
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Affiliation(s)
- Kevin Lebrigand
- Université Côte d’Azur, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, F06560 Sophia Antipolis, France
| | - Joseph Bergenstråhle
- Department of Gene Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Science for Life Laboratory, Solna, Sweden
| | - Kim Thrane
- Department of Gene Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Science for Life Laboratory, Solna, Sweden
| | - Annelie Mollbrink
- Department of Gene Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Science for Life Laboratory, Solna, Sweden
| | | | - Pascal Barbry
- Université Côte d’Azur, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, F06560 Sophia Antipolis, France
| | - Rainer Waldmann
- Université Côte d’Azur, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, F06560 Sophia Antipolis, France
| | - Joakim Lundeberg
- Department of Gene Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Science for Life Laboratory, Solna, Sweden
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35
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Nordin T, Blomstedt P, Hemm S, Wårdell K. How Sample Size Impacts Probabilistic Stimulation Maps in Deep Brain Stimulation. Brain Sci 2023; 13:brainsci13050756. [PMID: 37239228 DOI: 10.3390/brainsci13050756] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 04/25/2023] [Accepted: 04/28/2023] [Indexed: 05/28/2023] Open
Abstract
Probabilistic stimulation maps of deep brain stimulation (DBS) effect based on voxel-wise statistics (p-maps) have increased in literature over the last decade. These p-maps require correction for Type-1 errors due to multiple testing based on the same data. Some analyses do not reach overall significance, and this study aims to evaluate the impact of sample size on p-map computation. A dataset of 61 essential tremor patients treated with DBS was used for the investigation. Each patient contributed with four stimulation settings, one for each contact. From the dataset, 5 to 61 patients were randomly sampled with replacement for computation of p-maps and extraction of high- and low-improvement volumes. For each sample size, the process was iterated 20 times with new samples generating in total 1140 maps. The overall p-value corrected for multiple comparisons, significance volumes, and dice coefficients (DC) of the volumes within each sample size were evaluated. With less than 30 patients (120 simulations) in the sample, the variation in overall significance was larger and the median significance volumes increased with sample size. Above 120 simulations, the trends stabilize but present some variations in cluster location, with a highest median DC of 0.73 for n = 57. The variation in location was mainly related to the region between the high- and low-improvement clusters. In conclusion, p-maps created with small sample sizes should be evaluated with caution, and above 120 simulations in single-center studies are probably required for stable results.
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Affiliation(s)
- Teresa Nordin
- Department of Biomedical Engineering, Linköping University, 58185 Linköping, Sweden
| | - Patric Blomstedt
- Department of Clinical Science, Neuroscience, Umeå University, 90185 Umeå, Sweden
| | - Simone Hemm
- Department of Biomedical Engineering, Linköping University, 58185 Linköping, Sweden
- Institute for Medical Engineering and Medical Informatics, School of Life Sciences, University of Applied Sciences and Arts Northwestern Switzerland, 4132 Muttenz, Switzerland
| | - Karin Wårdell
- Department of Biomedical Engineering, Linköping University, 58185 Linköping, Sweden
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Järemo H, Semenas J, Bergström SH, Lundholm M, Thysell E, Widmark A, Crnalic S, Ylitalo EB, Bergh A, Brattsand M, Wikström P. Investigating microRNA Profiles in Prostate Cancer Bone Metastases and Functional Effects of microRNA-23c and microRNA-4328. Cancers (Basel) 2023; 15:cancers15092437. [PMID: 37173903 PMCID: PMC10177411 DOI: 10.3390/cancers15092437] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/30/2023] [Accepted: 04/17/2023] [Indexed: 05/15/2023] Open
Abstract
MicroRNAs (miRNAs) are aberrantly expressed in prostate cancer (PC), but comprehensive knowledge about their levels and function in metastatic PC is lacking. Here, we explored the differential expression of miRNA profiles during PC progression to bone metastasis, and further focused on the downregulation of miRNA-23c and -4328 and their impact on PC growth in experimental models. Using microarray screening, the levels of 1510 miRNAs were compared between bone metastases (n = 14), localized PC (n = 7) and benign prostate tissue (n = 7). Differentially expressed miRNAs (n = 4 increased and n = 75 decreased, p < 0.05) were identified, of which miRNA-1, -23c, -143-3p, -143-5p, -145-3p, -205-5p, -221-3p, -222-3p and -4328 showed consistent downregulation during disease progression (benign > localized PC > bone metastases). The downregulation of miRNA-23c and -4328 was confirmed by reverse transcription and quantitative polymerase chain reaction analysis of 67 metastasis, 12 localized PC and 12 benign prostate tissue samples. The stable overexpression of miRNA-23c and -4328 in the 22Rv1 and PC-3 cell lines resulted in reduced PC cell growth in vitro, and in the secretion of high levels of miRNA-23c (but not -4328) in extracellular vesicles. However, no tumor suppressive effects were observed from miRNA-23c overexpression in PC-3 cells subcutaneously grown in mice. In conclusion, bone metastases display a profound reduction of miRNA levels compared to localized PC and benign disease. The downregulation of those miRNAs, including miRNA-23c and -4328, may lead to a loss of tumor suppressive effects and provide biomarker and therapeutic possibilities that deserve to be further explored.
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Affiliation(s)
- Helena Järemo
- Department of Medical Biosciences, Pathology, Umeå University, 901 87 Umeå, Sweden
| | - Julius Semenas
- Department of Medical Biosciences, Pathology, Umeå University, 901 87 Umeå, Sweden
| | | | - Marie Lundholm
- Department of Medical Biosciences, Pathology, Umeå University, 901 87 Umeå, Sweden
| | - Elin Thysell
- Department of Medical Biosciences, Pathology, Umeå University, 901 87 Umeå, Sweden
| | - Anders Widmark
- Department of Radiation Sciences, Oncology, Umeå University, 901 87 Umeå, Sweden
| | - Sead Crnalic
- Department of Surgical and Perioperative Sciences, Orthopedics, Umeå University, 901 87 Umeå, Sweden
| | | | - Anders Bergh
- Department of Medical Biosciences, Pathology, Umeå University, 901 87 Umeå, Sweden
| | - Maria Brattsand
- Department of Medical Biosciences, Pathology, Umeå University, 901 87 Umeå, Sweden
| | - Pernilla Wikström
- Department of Medical Biosciences, Pathology, Umeå University, 901 87 Umeå, Sweden
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Stenum TS, Kumar AD, Sandbaumhüter FA, Kjellin J, Jerlström-Hultqvist J, Andrén PE, Koskiniemi S, Jansson ET, Holmqvist E. RNA interactome capture in Escherichia coli globally identifies RNA-binding proteins. Nucleic Acids Res 2023; 51:4572-4587. [PMID: 36987847 DOI: 10.1093/nar/gkad216] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 03/03/2023] [Accepted: 03/16/2023] [Indexed: 03/30/2023] Open
Abstract
RNA-binding proteins (RPBs) are deeply involved in fundamental cellular processes in bacteria and are vital for their survival. Despite this, few studies have so far been dedicated to direct and global identification of bacterial RBPs. We have adapted the RNA interactome capture (RIC) technique, originally developed for eukaryotic systems, to globally identify RBPs in bacteria. RIC takes advantage of the base pairing potential of poly(A) tails to pull-down RNA-protein complexes. Overexpressing poly(A) polymerase I in Escherichia coli drastically increased transcriptome-wide RNA polyadenylation, enabling pull-down of crosslinked RNA-protein complexes using immobilized oligo(dT) as bait. With this approach, we identified 169 putative RBPs, roughly half of which are already annotated as RNA-binding. We experimentally verified the RNA-binding ability of a number of uncharacterized RBPs, including YhgF, which is exceptionally well conserved not only in bacteria, but also in archaea and eukaryotes. We identified YhgF RNA targets in vivo using CLIP-seq, verified specific binding in vitro, and reveal a putative role for YhgF in regulation of gene expression. Our findings present a simple and robust strategy for RBP identification in bacteria, provide a resource of new bacterial RBPs, and lay the foundation for further studies of the highly conserved RBP YhgF.
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Affiliation(s)
- Thomas Søndergaard Stenum
- Microbiology and Immunology, Department of Cell and Molecular Biology, Biomedical Centre, Uppsala University, Box 596, 75124 Uppsala, Sweden
| | - Ankith D Kumar
- Microbiology and Immunology, Department of Cell and Molecular Biology, Biomedical Centre, Uppsala University, Box 596, 75124 Uppsala, Sweden
| | - Friederike A Sandbaumhüter
- Medical Mass Spectrometry, Department of Pharmaceutical Biosciences, Biomedical Centre, Uppsala University, Box 591, 75124 Uppsala, Sweden
| | - Jonas Kjellin
- Microbiology and Immunology, Department of Cell and Molecular Biology, Biomedical Centre, Uppsala University, Box 596, 75124 Uppsala, Sweden
| | - Jon Jerlström-Hultqvist
- Microbiology and Immunology, Department of Cell and Molecular Biology, Biomedical Centre, Uppsala University, Box 596, 75124 Uppsala, Sweden
| | - Per E Andrén
- Medical Mass Spectrometry, Department of Pharmaceutical Biosciences, Biomedical Centre, Uppsala University, Box 591, 75124 Uppsala, Sweden
- Science for Life Laboratory, Spatial Mass Spectrometry, Biomedical Centre, Uppsala University, Box 591, 75124 Uppsala, Sweden
| | - Sanna Koskiniemi
- Microbiology and Immunology, Department of Cell and Molecular Biology, Biomedical Centre, Uppsala University, Box 596, 75124 Uppsala, Sweden
| | - Erik T Jansson
- Medical Mass Spectrometry, Department of Pharmaceutical Biosciences, Biomedical Centre, Uppsala University, Box 591, 75124 Uppsala, Sweden
| | - Erik Holmqvist
- Microbiology and Immunology, Department of Cell and Molecular Biology, Biomedical Centre, Uppsala University, Box 596, 75124 Uppsala, Sweden
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Manting CL, Gulyas B, Ullén F, Lundqvist D. Steady-state responses to concurrent melodies: source distribution, top-down, and bottom-up attention. Cereb Cortex 2023; 33:3053-3066. [PMID: 35858223 PMCID: PMC10016039 DOI: 10.1093/cercor/bhac260] [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: 11/22/2021] [Revised: 06/03/2022] [Accepted: 06/03/2022] [Indexed: 11/13/2022] Open
Abstract
Humans can direct attentional resources to a single sound occurring simultaneously among others to extract the most behaviourally relevant information present. To investigate this cognitive phenomenon in a precise manner, we used frequency-tagging to separate neural auditory steady-state responses (ASSRs) that can be traced back to each auditory stimulus, from the neural mix elicited by multiple simultaneous sounds. Using a mixture of 2 frequency-tagged melody streams, we instructed participants to selectively attend to one stream or the other while following the development of the pitch contour. Bottom-up attention towards either stream was also manipulated with salient changes in pitch. Distributed source analyses of magnetoencephalography measurements showed that the effect of ASSR enhancement from top-down driven attention was strongest at the left frontal cortex, while that of bottom-up driven attention was dominant at the right temporal cortex. Furthermore, the degree of ASSR suppression from simultaneous stimuli varied across cortical lobes and hemisphere. The ASSR source distribution changes from temporal-dominance during single-stream perception, to proportionally more activity in the frontal and centro-parietal cortical regions when listening to simultaneous streams. These findings are a step forward to studying cognition in more complex and naturalistic soundscapes using frequency-tagging.
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Affiliation(s)
| | - Balazs Gulyas
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm 17177, Sweden
- Cognitive Neuroimaging Centre (CoNiC), Lee Kong Chien School of Medicine, Nanyang Technological University, Singapore 636921, Singapore
| | - Fredrik Ullén
- Department of Neuroscience, Karolinska Institutet, Stockholm 17177, Sweden
- Department of Cognitive Neuropsychology, Max Planck Institute for Empirical Aesthetics, Frankfurt 60322, Germany
| | - Daniel Lundqvist
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm 17177, Sweden
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Walker CH, Ware A, Šimura J, Ljung K, Wilson Z, Bennett T. Cytokinin signaling regulates two-stage inflorescence arrest in Arabidopsis. Plant Physiol 2023; 191:479-495. [PMID: 36331332 PMCID: PMC9806609 DOI: 10.1093/plphys/kiac514] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 10/20/2022] [Indexed: 05/19/2023]
Abstract
To maximize reproductive success, flowering plants must correctly time entry and exit from the reproductive phase. While much is known about mechanisms that regulate initiation of flowering, end-of-flowering remains largely uncharacterized. End-of-flowering in Arabidopsis (Arabidopsis thaliana) consists of quasi-synchronous arrest of inflorescences, but it is unclear how arrest is correctly timed with respect to environmental stimuli and reproductive success. Here, we showed that Arabidopsis inflorescence arrest is a complex developmental phenomenon, which includes the arrest of the inflorescence meristem (IM), coupled with a separable "floral arrest" of all unopened floral primordia; these events occur well before visible inflorescence arrest. We showed that global inflorescence removal delays both IM and floral arrest, but that local fruit removal only delays floral arrest, emphasizing their separability. We tested whether cytokinin regulates inflorescence arrest, and found that cytokinin signaling dynamics mirror IM activity, while cytokinin treatment can delay both IM and floral arrest. We further showed that gain-of-function cytokinin receptor mutants can delay IM and floral arrest; conversely, loss-of-function mutants prevented the extension of flowering in response to inflorescence removal. Collectively, our data suggest that the dilution of cytokinin among an increasing number of sink organs leads to end-of-flowering in Arabidopsis by triggering IM and floral arrest.
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Affiliation(s)
- Catriona H Walker
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Alexander Ware
- School of Biosciences, University of Nottingham, Loughborough, UK
| | - Jan Šimura
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Karin Ljung
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Zoe Wilson
- School of Biosciences, University of Nottingham, Loughborough, UK
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Nocerino E, Witteveen C, Kobayashi S, Forslund OK, Matsubara N, Zubayer A, Mazza F, Kawaguchi S, Hoshikawa A, Umegaki I, Sugiyama J, Yoshimura K, Sassa Y, von Rohr FO, Månsson M. Nuclear and magnetic spin structure of the antiferromagnetic triangular lattice compound LiCrTe 2 investigated by [Formula: see text]SR, neutron and X-ray diffraction. Sci Rep 2022; 12:21657. [PMID: 36522382 PMCID: PMC9755140 DOI: 10.1038/s41598-022-25921-9] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 12/07/2022] [Indexed: 12/23/2022] Open
Abstract
Two-dimensional (2D) triangular lattice antiferromagnets (2D-TLA) often manifest intriguing physical and technological properties, due to the strong interplay between lattice geometry and electronic properties. The recently synthesized 2-dimensional transition metal dichalcogenide LiCrTe[Formula: see text], being a 2D-TLA, enriched the range of materials which can present such properties. In this work, muon spin rotation ([Formula: see text]SR) and neutron powder diffraction (NPD) have been utilized to reveal the true magnetic nature and ground state of LiCrTe[Formula: see text]. From high-resolution NPD the magnetic spin order at base-temperature is not, as previously suggested, helical, but rather collinear antiferromagnetic (AFM) with ferromagnetic (FM) spin coupling within the ab-plane and AFM coupling along the c-axis. The value if the ordered magnetic Cr moment is established as [Formula: see text]. From detailed [Formula: see text]SR measurements we observe an AFM ordering temperature [Formula: see text] K. This value is remarkably higher than the one previously reported by magnetic bulk measurements. From [Formula: see text]SR we are able to extract the magnetic order parameter, whose critical exponent allows us to categorize LiCrTe[Formula: see text] in the 3D Heisenberg AFM universality class. Finally, by combining our magnetic studies with high-resolution synchrotron X-ray diffraction (XRD), we find a clear coupling between the nuclear and magnetic spin lattices. This suggests the possibility for a strong magnon-phonon coupling, similar to what has been previously observed in the closely related compound LiCrO[Formula: see text].
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Affiliation(s)
- E. Nocerino
- KTH Royal Institute of Technology, Department of Applied Physics, Alba Nova University Center, 114 21 Stockholm, Sweden
| | - C. Witteveen
- Department of Quantum Matter Physics, University of Geneva, 24 Quai Ernest-Ansermet, 1211 Geneva 4, Switzerland
- Department of Physics, University of Zürich, Winterthurerstr. 190, 8057 Zurich, Switzerland
| | - S. Kobayashi
- Japan Synchrotron Radiation Research Institute (JASRI), 1-1-1 Kouto, Sayo, 679-5198 Japan
| | - O. K. Forslund
- Department of Physics, Chalmers University of Technology, 412 96 Göteborg, Sweden
| | - N. Matsubara
- KTH Royal Institute of Technology, Department of Applied Physics, Alba Nova University Center, 114 21 Stockholm, Sweden
| | - A. Zubayer
- Department of Physics, Chemistry and Biology (IFM), Linköping University, 581 83 Linköping, Sweden
| | - F. Mazza
- Insitute of Solid State Physics, TU Wien, Wiedner Haupstraße 8-10, 1040 Vienna, Austria
| | - S. Kawaguchi
- Japan Synchrotron Radiation Research Institute (JASRI), 1-1-1 Kouto, Sayo, 679-5198 Japan
| | - A. Hoshikawa
- Frontier Research Center for Applied Atomic Sciences, Ibaraki University, 162-1 Shirakata, Tokai, Ibaraki 319-1106 Japan
| | - I. Umegaki
- Muon Science Laboratory, Institute of Materials Structure Science, KEK, Tokai, Ibaraki 319-1106 Japan
| | - J. Sugiyama
- Neutron Science and Technology Center, Comprehensive Research Organization for Science and Society (CROSS), Tokai, Ibaraki 319-1106 Japan
- Advanced Science Research Center, Japan Atomic Energy Agency, Tokai, Ibaraki 319-1195 Japan
| | - K. Yoshimura
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, 606-8502 Japan
| | - Y. Sassa
- Department of Physics, Chalmers University of Technology, 412 96 Göteborg, Sweden
| | - F. O. von Rohr
- Department of Quantum Matter Physics, University of Geneva, 24 Quai Ernest-Ansermet, 1211 Geneva 4, Switzerland
| | - M. Månsson
- KTH Royal Institute of Technology, Department of Applied Physics, Alba Nova University Center, 114 21 Stockholm, Sweden
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Eriksson JW, Eliasson B, Bennet L, Sundström J. Registry-based randomised clinical trials: a remedy for evidence-based diabetes care? Diabetologia 2022; 65:1575-1586. [PMID: 35902386 PMCID: PMC9334551 DOI: 10.1007/s00125-022-05762-x] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 06/21/2022] [Indexed: 11/28/2022]
Abstract
This narrative review describes a new approach to navigation in a challenging landscape of clinical drug development in diabetes. Successful outcome studies in recent years have led to new indications and guidelines in type 2 diabetes, yet the number of clinical trials in diabetes is now declining. This is due to many environmental factors acting in concert, including the prioritisation of funding for other diseases, high costs of large randomised clinical trials, increase in regulatory requirements and limited entry of novel candidate drugs. There is a need for novel and cost-effective paradigms of clinical development to meet these and other challenges. The concept of registry-based randomised clinical trials (RRCTs) is an attractive option. In this review we focus on type 2 diabetes and the prevention of cardiovascular and microvascular comorbidities and mortality, using the Swedish SMARTEST trial as an example of an RRCT. We also give some examples from other disease areas. The RRCT concept is a novel, cost-effective and scientifically sound approach for conducting large-scale diabetes trials in a real-world setting.
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Affiliation(s)
- Jan W Eriksson
- Department of Medical Sciences, Clinical Diabetes and Metabolism, Uppsala University, Uppsala, Sweden.
| | - Björn Eliasson
- Department of Medicine, Sahlgrenska University Hospital, Gothenburg, Sweden
- Swedish National Diabetes Register, Västra Götalandsregionen, Gothenburg, Sweden
| | - Louise Bennet
- Department of Clinical Sciences in Malmö, Lund University, Lund, Sweden
- Clinical Trials Unit, Skåne University Hospital in Lund, Lund, Sweden
| | - Johan Sundström
- Department of Medical Sciences, Clinical Epidemiology, Uppsala University, Uppsala, Sweden
- The George Institute for Global Health, University of New South Wales, Sydney, NSW, Australia
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Marco Salas S, Yuan X, Sylven C, Nilsson M, Wählby C, Partel G. De novo spatiotemporal modelling of cell-type signatures in the developmental human heart using graph convolutional neural networks. PLoS Comput Biol 2022; 18:e1010366. [PMID: 35960757 PMCID: PMC9401155 DOI: 10.1371/journal.pcbi.1010366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 08/24/2022] [Accepted: 07/06/2022] [Indexed: 11/21/2022] Open
Abstract
With the emergence of high throughput single cell techniques, the understanding of the molecular and cellular diversity of mammalian organs have rapidly increased. In order to understand the spatial organization of this diversity, single cell data is often integrated with spatial data to create probabilistic cell maps. However, targeted cell typing approaches relying on existing single cell data achieve incomplete and biased maps that could mask the true diversity present in a tissue slide. Here we applied a de novo technique to spatially resolve and characterize cellular diversity of in situ sequencing data during human heart development. We obtained and made accessible well defined spatial cell-type maps of fetal hearts from 4.5 to 9 post conception weeks, not biased by probabilistic cell typing approaches. With our analysis, we could characterize previously unreported molecular diversity within cardiomyocytes and epicardial cells and identified their characteristic expression signatures, comparing them with specific subpopulations found in single cell RNA sequencing datasets. We further characterized the differentiation trajectories of epicardial cells, identifying a clear spatial component on it. All in all, our study provides a novel technique for conducting de novo spatial-temporal analyses in developmental tissue samples and a useful resource for online exploration of cell-type differentiation during heart development at sub-cellular image resolution. With the boom of spatially-resolved transcriptomics methods, a set of big opportunities appear for researchers to understand better developmental processes without relying on existing single cell RNA sequencing datasets. In context, we applied spage2vec, a graph convolutional neural network model, to explore the cellular diversity present during the human heart development from week 4.5 to week 9. We showed that this type of approaches, which do not rely on cellular segmentation, can be used to identify molecular signatures better than existing cell typing tools that can be used to explore the spatial component of processes such as cellular differentiation. Among the signatures identified, we focused on exploring the molecular diversity within cardiomyocytes and we described the differentiation process of epicardial cells in the context of space. All the molecular signatures detected and their gene expression profiles were also integrated in a useful online tool that can be used by the community for further exploration.
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Affiliation(s)
- Sergio Marco Salas
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
| | - Xiao Yuan
- Department of Information Technology and Science for Life Laboratory Uppsala University, Uppsala, Sweden
| | - Christer Sylven
- Department of Medicine, Karolinska Institutet, Huddinge, Stockholm, Sweden
| | - Mats Nilsson
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
- * E-mail: (MN); (CW); (GP)
| | - Carolina Wählby
- Department of Information Technology and Science for Life Laboratory Uppsala University, Uppsala, Sweden
- * E-mail: (MN); (CW); (GP)
| | - Gabriele Partel
- Department of Information Technology and Science for Life Laboratory Uppsala University, Uppsala, Sweden
- Laboratory of Multi-omic Integrative Bioinformatics, Department of Human Genetics, KU Leuven, Leuven, Belgium
- VIB-KU Leuven Center for Brain & Disease Research, Laboratory of Computational Biology, Department of Human Genetics, Leuven, Belgium
- * E-mail: (MN); (CW); (GP)
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Pol T, Hijazi Z, Lindbäck J, Oldgren J, Alexander JH, Connolly SJ, Eikelboom JW, Ezekowitz MD, Granger CB, Lopes RD, Yusuf S, Siegbahn A, Wallentin L. Using multimarker screening to identify biomarkers associated with cardiovascular death in patients with atrial fibrillation. Cardiovasc Res 2022; 118:2112-2123. [PMID: 34358298 PMCID: PMC9302885 DOI: 10.1093/cvr/cvab262] [Citation(s) in RCA: 6] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 08/04/2021] [Indexed: 12/14/2022] Open
Abstract
AIMS Atrial fibrillation (AF) is associated with higher mortality. Biomarkers may improve the understanding of key pathophysiologic processes in AF that lead to death. Using a new multiplex analytic technique, we explored the association between 268 biomarkers and cardiovascular (CV) death in anticoagulated patients with AF. METHODS AND RESULTS A case-cohort design with 1.8- to 1.9-year follow-up. The identification cohort included 517 cases and 4057 randomly selected patients from ARISTOTLE. The validation cohort included 277 cases and 1042 randomly selected controls from RE-LY. Plasma collected at randomization was analysed with conventional immunoassays and the OLINK proximity extension assay panels: CVDII, CVDIII, and Inflammation. Association between biomarkers and CV death was evaluated using Random Survival Forest, Boruta, and adjusted Cox-regression analyses. The biomarkers most strongly and consistently associated with CV death were as follows (hazard ratio for inter-quartile comparison [95% CI]): N-terminal pro-B-type natriuretic peptide [NT-proBNP; 1.63 (1.37-1.93)], cardiac troponin T [cTnT-hs; 1.60 (1.35-1.88)], interleukin-6 [IL-6; 1.29 (1.13-1.47)], growth differentiation factor-15 [GDF-15; 1.30 (1.10-1.53)], fibroblast growth factor 23 [FGF-23; 1.21 (1.10-1.33)], urokinase receptor [uPAR; 1.38 (1.16-1.64)], trefoil factor 3 [TFF3; 1.27 (1.10-1.46)], tumour necrosis factor receptor 1 [TNFR1; 1.21 (1.01-1.45)], TNF-related apoptosis-inducing ligand receptor 2 [TRAILR2; 1.18 (1.04-1.34)], and cathepsin L1 [CTSL1; 1.22 (1.07-1.39)]. CONCLUSION In this comprehensive screening of 268 biomarkers in anticoagulated patients with AF, the underlying mechanisms most strongly associated with CV death were cardiorenal dysfunction (NT-proBNP, cTnT-hs, CTSL1, TFF3), oxidative stress (GDF-15), inflammation (IL-6, GDF-15), calcium balance, vascular and renal dysfunction (FGF-23), fibrinolysis (suPAR), and apoptosis (TNFR1, TRAILR2). These findings provide novel insights into pathophysiologic aspects associated with CV death in AF. CLINICALTRIALS.GOV IDENTIFIER NCT00412984 and NCT00262600.
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Affiliation(s)
- Tymon Pol
- Corresponding author. Tel: +46 18 611 9507, fax: +46 18 51 5570, E-mail:
| | - Ziad Hijazi
- Department of Medical Sciences, Cardiology, Uppsala University, Uppsala Science Park, SE-752 37 Uppsala, Sweden
- Uppsala Clinical Research Center, Uppsala University, Uppsala, Sweden
| | - Johan Lindbäck
- Uppsala Clinical Research Center, Uppsala University, Uppsala, Sweden
| | - Jonas Oldgren
- Department of Medical Sciences, Cardiology, Uppsala University, Uppsala Science Park, SE-752 37 Uppsala, Sweden
- Uppsala Clinical Research Center, Uppsala University, Uppsala, Sweden
| | | | | | | | - Michael D Ezekowitz
- Thomas Jefferson University, Philadelphia, PA, USA
- Cardiovascular Medicine, Lankenau Institute for Medical Research, Wynnewood, PA, USA
| | | | - Renato D Lopes
- Duke Clinical Research Institute, Duke Health, Durham, NC, USA
| | - Salim Yusuf
- Population Health Research Institute, Hamilton, Canada
| | - Agneta Siegbahn
- Uppsala Clinical Research Center, Uppsala University, Uppsala, Sweden
- Department of Medical Sciences, Clinical Chemistry, Uppsala University, Uppsala, Sweden
| | - Lars Wallentin
- Department of Medical Sciences, Cardiology, Uppsala University, Uppsala Science Park, SE-752 37 Uppsala, Sweden
- Uppsala Clinical Research Center, Uppsala University, Uppsala, Sweden
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Christiansen C, Tomlinson M, Eliot M, Nilsson E, Costeira R, Xia Y, Villicaña S, Mompeo O, Wells P, Castillo-Fernandez J, Potier L, Vohl MC, Tchernof A, Moustafa JES, Menni C, Steves CJ, Kelsey K, Ling C, Grundberg E, Small KS, Bell JT. Adipose methylome integrative-omic analyses reveal genetic and dietary metabolic health drivers and insulin resistance classifiers. Genome Med 2022; 14:75. [PMID: 35843982 PMCID: PMC9290282 DOI: 10.1186/s13073-022-01077-z] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 06/21/2022] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND There is considerable evidence for the importance of the DNA methylome in metabolic health, for example, a robust methylation signature has been associated with body mass index (BMI). However, visceral fat (VF) mass accumulation is a greater risk factor for metabolic disease than BMI alone. In this study, we dissect the subcutaneous adipose tissue (SAT) methylome signature relevant to metabolic health by focusing on VF as the major risk factor of metabolic disease. We integrate results with genetic, blood methylation, SAT gene expression, blood metabolomic, dietary intake and metabolic phenotype data to assess and quantify genetic and environmental drivers of the identified signals, as well as their potential functional roles. METHODS Epigenome-wide association analyses were carried out to determine visceral fat mass-associated differentially methylated positions (VF-DMPs) in SAT samples from 538 TwinsUK participants. Validation and replication were performed in 333 individuals from 3 independent cohorts. To assess functional impacts of the VF-DMPs, the association between VF and gene expression was determined at the genes annotated to the VF-DMPs and an association analysis was carried out to determine whether methylation at the VF-DMPs is associated with gene expression. Further epigenetic analyses were carried out to compare methylation levels at the VF-DMPs as the response variables and a range of different metabolic health phenotypes including android:gynoid fat ratio (AGR), lipids, blood metabolomic profiles, insulin resistance, T2D and dietary intake variables. The results from all analyses were integrated to identify signals that exhibit altered SAT function and have strong relevance to metabolic health. RESULTS We identified 1181 CpG positions in 788 genes to be differentially methylated with VF (VF-DMPs) with significant enrichment in the insulin signalling pathway. Follow-up cross-omic analysis of VF-DMPs integrating genetics, gene expression, metabolomics, diet, and metabolic traits highlighted VF-DMPs located in 9 genes with strong relevance to metabolic disease mechanisms, with replication of signals in FASN, SREBF1, TAGLN2, PC and CFAP410. PC methylation showed evidence for mediating effects of diet on VF. FASN DNA methylation exhibited putative causal effects on VF that were also strongly associated with insulin resistance and methylation levels in FASN better classified insulin resistance (AUC=0.91) than BMI or VF alone. CONCLUSIONS Our findings help characterise the adiposity-associated methylation signature of SAT, with insights for metabolic disease risk.
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Affiliation(s)
- Colette Christiansen
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK.
| | - Max Tomlinson
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
- Department of Medical & Molecular Genetics, King's College London, London, UK
| | - Melissa Eliot
- Department of Epidemiology, Brown University School of Public Health, Providence, R.I., USA
| | - Emma Nilsson
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Scania University Hospital, Malmö, Sweden
| | - Ricardo Costeira
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Yujing Xia
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Sergio Villicaña
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Olatz Mompeo
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Philippa Wells
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | | | - Louis Potier
- Diabetology Department, Bichat Hospital, AP-HP, Université de Paris, Paris, France
| | - Marie-Claude Vohl
- Institute of Nutrition and Functional Foods (INAF), Université Laval, Québec, QC, Canada
| | - Andre Tchernof
- Québec Heart and Lung Institute, Université Laval, Québec, QC, Canada
| | | | - Cristina Menni
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Claire J Steves
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Karl Kelsey
- Department of Epidemiology, Brown University School of Public Health, Providence, R.I., USA
| | - Charlotte Ling
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Scania University Hospital, Malmö, Sweden
| | - Elin Grundberg
- Genomic Medicine Center, Children's Mercy Research Institute, Children's Mercy Kansas City, Kansas City, MO, 64108, USA
| | - Kerrin S Small
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Jordana T Bell
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK.
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Wang Y, Li X, Chen X, Siewers V. CRISPR/Cas9-mediated point mutations improve α-amylase secretion in Saccharomyces cerevisiae. FEMS Yeast Res 2022; 22:6626025. [PMID: 35776981 PMCID: PMC9290899 DOI: 10.1093/femsyr/foac033] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 06/28/2022] [Indexed: 11/12/2022] Open
Abstract
The rapid expansion of the application of pharmaceutical proteins and industrial enzymes requires robust microbial workhorses for high protein production. The budding yeast Saccharomyces cerevisiae is an attractive cell factory due to its ability to perform eukaryotic post-translational modifications and to secrete proteins. Many strategies have been used to engineer yeast platform strains for higher protein secretion capacity. Herein, we investigated a line of strains that have previously been selected after UV random mutagenesis for improved α-amylase secretion. A total of 42 amino acid altering point mutations identified in this strain line were reintroduced into the parental strain AAC to study their individual effects on protein secretion. These point mutations included missense mutations (amino acid substitution), nonsense mutations (stop codon generation), and frameshift mutations. For comparison, single gene deletions for the corresponding target genes were also performed in this study. A total of 11 point mutations and seven gene deletions were found to effectively improve α-amylase secretion. These targets were involved in several bioprocesses, including cellular stresses, protein degradation, transportation, mRNA processing and export, DNA replication, and repair, which indicates that the improved protein secretion capacity in the evolved strains is the result of the interaction of multiple intracellular processes. Our findings will contribute to the construction of novel cell factories for recombinant protein secretion.
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Affiliation(s)
- Yanyan Wang
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE-41296 Gothenburg, Sweden
| | - Xiaowei Li
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE-41296 Gothenburg, Sweden
| | - Xin Chen
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE-41296 Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Kemivägen 10, SE-41296 Gothenburg, Sweden
| | - Verena Siewers
- Corresponding author. Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE-41296 Gothenburg, Sweden. Tel: +46 (0)317723853; E-mail:
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Lagomarsino LP, Frankel L, Uribe-Convers S, Antonelli A, Muchhala N. Increased resolution in the face of conflict: phylogenomics of the Neotropical bellflowers (Campanulaceae: Lobelioideae), a rapid plant radiation. Ann Bot 2022; 129:723-736. [PMID: 35363863 PMCID: PMC9113290 DOI: 10.1093/aob/mcac046] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Accepted: 03/24/2022] [Indexed: 06/12/2023]
Abstract
BACKGROUND AND AIMS The centropogonid clade (Lobelioideae: Campanulaceae) is an Andean-centred rapid radiation characterized by repeated convergent evolution of morphological traits, including fruit type and pollination syndromes. While previous studies have resolved relationships of lineages with fleshy fruits into subclades, relationships among capsular species remain unresolved. This lack of resolution has impeded reclassification of non-monophyletic genera, whose current taxonomy relies heavily on traits that have undergone convergent evolution. METHODS Targeted sequence capture using a probe-set recently developed for the centropogonid clade was used to obtain phylogenomic data from DNA extracted from both silica-dried and herbarium leaf tissue. These data were used to infer relationships among species using concatenated and partitioned species tree methods, and to quantify gene tree discordance. KEY RESULTS While silica-dried leaf tissue resulted in longer assembled sequence data, the inclusion of herbarium samples improved taxonomic representation. Relationships among baccate lineages are similar to those inferred in previous studies, although they differ for lineages within and among capsular clades. We improve the phylogenetic resolution of Siphocampylus, which forms ten groups of closely related species which we informally name. Two subclades of Siphocampylus and two individual species are rogue taxa whose placement differs widely across analyses. Gene tree discordance (including cytonuclear discordance) is rampant. CONCLUSIONS This first phylogenomic study of the centropogonid clade considerably improves our understanding of relationships in this rapid radiation. Differences across analyses and the possibility of additional lineage discoveries still hamper a solid and stable reclassification. Rapid morphological innovation corresponds with a high degree of phylogenomic complexity, including cytonuclear discordance, nuclear gene tree conflict and well-supported differences between analyses based on different nuclear loci. Together, these results point to a potential role of hemiplasy underlying repeated convergent evolution. This hallmark of rapid radiations is probably present in many other species-rich Andean plant radiations.
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Affiliation(s)
- Laura P Lagomarsino
- Shirley C. Tucker Herbarium, Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
- Department of Biology, University of Missouri-St. Louis, St. Louis, MO, USA
| | - Lauren Frankel
- Department of Botany, University of Wisconsin-Madison, Madison, WI, USA
| | - Simon Uribe-Convers
- Department of Biology, University of Missouri-St. Louis, St. Louis, MO, USA
- Invitae Corporation, San Francisco, CA, USA
| | - Alexandre Antonelli
- Royal Botanic Gardens, Kew, TW9 3AE, UK
- Gothenburg Global Biodiversity Centre, Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, 405 30, Sweden
- Department of Plant Science, University of Oxford, Oxford, UK
| | - Nathan Muchhala
- Department of Biology, University of Missouri-St. Louis, St. Louis, MO, USA
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Persson S, Shashkova S, Österberg L, Cvijovic M. Modelling of glucose repression signalling in yeast Saccharomyces cerevisiae. FEMS Yeast Res 2022; 22:foac012. [PMID: 35238938 PMCID: PMC8916112 DOI: 10.1093/femsyr/foac012] [Citation(s) in RCA: 2] [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: 12/10/2021] [Revised: 02/11/2022] [Accepted: 03/01/2022] [Indexed: 11/13/2022] Open
Abstract
Saccharomyces cerevisiae has a sophisticated signalling system that plays a crucial role in cellular adaptation to changing environments. The SNF1 pathway regulates energy homeostasis upon glucose derepression; hence, it plays an important role in various processes, such as metabolism, cell cycle and autophagy. To unravel its behaviour, SNF1 signalling has been extensively studied. However, the pathway components are strongly interconnected and inconstant; therefore, elucidating its dynamic behaviour based on experimental data only is challenging. To tackle this complexity, systems biology approaches have been successfully employed. This review summarizes the progress, advantages and disadvantages of the available mathematical modelling frameworks covering Boolean, dynamic kinetic, single-cell models, which have been used to study processes and phenomena ranging from crosstalks to sources of cell-to-cell variability in the context of SNF1 signalling. Based on the lessons from existing models, we further discuss how to develop a consensus dynamic mechanistic model of the entire SNF1 pathway that can provide novel insights into the dynamics of nutrient signalling.
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Affiliation(s)
- Sebastian Persson
- Department of Mathematical Sciences, Chalmers University of Technology, Chalmers tvärgata 3, 412 96 Gothnburg, Sweden
- Department of Mathematical Sciences, University of Gothenburg, Chalmers tvärgata 3, 412 96 Gothnburg, Sweden
| | - Sviatlana Shashkova
- Department of Mathematical Sciences, Chalmers University of Technology, Chalmers tvärgata 3, 412 96 Gothnburg, Sweden
- Department of Mathematical Sciences, University of Gothenburg, Chalmers tvärgata 3, 412 96 Gothnburg, Sweden
| | - Linnea Österberg
- Department of Mathematical Sciences, Chalmers University of Technology, Chalmers tvärgata 3, 412 96 Gothnburg, Sweden
- Department of Mathematical Sciences, University of Gothenburg, Chalmers tvärgata 3, 412 96 Gothnburg, Sweden
- Department of Biology and Biological Engineering, Chalmers University of Technology, Chalmers tvärgata 3, 412 96 Gothnburg, Sweden
| | - Marija Cvijovic
- Department of Mathematical Sciences, Chalmers University of Technology, Chalmers tvärgata 3, 412 96 Gothnburg, Sweden
- Department of Mathematical Sciences, University of Gothenburg, Chalmers tvärgata 3, 412 96 Gothnburg, Sweden
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Lauber C, Gerl MJ, Klose C, Ottosson F, Melander O, Simons K. Lipidomic risk scores are independent of polygenic risk scores and can predict incidence of diabetes and cardiovascular disease in a large population cohort. PLoS Biol 2022; 20:e3001561. [PMID: 35239643 PMCID: PMC8893343 DOI: 10.1371/journal.pbio.3001561] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 01/31/2022] [Indexed: 12/22/2022] Open
Abstract
Type 2 diabetes (T2D) and cardiovascular disease (CVD) represent significant disease burdens for most societies and susceptibility to these diseases is strongly influenced by diet and lifestyle. Physiological changes associated with T2D or CVD, such has high blood pressure and cholesterol and glucose levels in the blood, are often apparent prior to disease incidence. Here we integrated genetics, lipidomics, and standard clinical diagnostics to assess future T2D and CVD risk for 4,067 participants from a large prospective population-based cohort, the Malmö Diet and Cancer-Cardiovascular Cohort. By training Ridge regression-based machine learning models on the measurements obtained at baseline when the individuals were healthy, we computed several risk scores for T2D and CVD incidence during up to 23 years of follow-up. We used these scores to stratify the participants into risk groups and found that a lipidomics risk score based on the quantification of 184 plasma lipid concentrations resulted in a 168% and 84% increase of the incidence rate in the highest risk group and a 77% and 53% decrease of the incidence rate in lowest risk group for T2D and CVD, respectively, compared to the average case rates of 13.8% and 22.0%. Notably, lipidomic risk correlated only marginally with polygenic risk, indicating that the lipidome and genetic variants may constitute largely independent risk factors for T2D and CVD. Risk stratification was further improved by adding standard clinical variables to the model, resulting in a case rate of 51.0% and 53.3% in the highest risk group for T2D and CVD, respectively. The participants in the highest risk group showed significantly altered lipidome compositions affecting 167 and 157 lipid species for T2D and CVD, respectively. Our results demonstrated that a subset of individuals at high risk for developing T2D or CVD can be identified years before disease incidence. The lipidomic risk, which is derived from only one single mass spectrometric measurement that is cheap and fast, is informative and could extend traditional risk assessment based on clinical assays.
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Affiliation(s)
- Chris Lauber
- Lipotype GmbH, Dresden, Germany
- TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Hanover Medical School and the Helmholtz Centre for Infection Research, Institute for Experimental Virology, Hanover, Germany
| | | | | | - Filip Ottosson
- Department of Clinical Sciences, Lund University, Malmö, Sweden
| | - Olle Melander
- Department of Clinical Sciences, Lund University, Malmö, Sweden
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Fawad A, Bergmann A, Schulte J, Butt ZA, Nilsson PM, Bennet L, Orho-Melander M, Melander O. Plasma Proneurotensin and Prediction of Cause-Specific Mortality in a Middle-aged Cohort During Long-term Follow-up. J Clin Endocrinol Metab 2022; 107:e1204-e1211. [PMID: 34665860 PMCID: PMC8852211 DOI: 10.1210/clinem/dgab755] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Indexed: 11/19/2022]
Abstract
CONTEXT Neurotensin is associated with cardiometabolic diseases but its role with mortality risk in humans is unknown. OBJECTIVE This work aims to examine the prediction of proneurotensin (Pro-NT) with respect to total and cause-specific mortality in a middle-aged cohort. METHODS In the population-based middle-aged cohort (n = 4632; mean age, 57 years) of the Malmö Diet and Cancer Study, Pro-NT was assessed and total as well as cause-specific mortality was studied. Main cause of death was based on the International Classification of Diseases. RESULTS During a mean follow-up of 20 ± 3 years, 950 men and 956 women died. There was significantly increased mortality risk in individuals belonging to the highest quartile (Q) of Pro-NT (Q4, Pro-NT ≥ 149 pmol/L) compared with Qs 1 to 3 (Pro-NT < 149 pmol/L), hazard ratio (HR), 95% CI of 1.29 (1.17-1.42; P < .001). Data were adjusted for sex and age. No significant interaction was observed between Pro-NT and sex on mortality risk. Individuals within Q4 vs Qs 1 to 3 had an HR of 1.41 (95% CI, 1.18-1.68; P < .001) for death due to cardiovascular disease (n = 595/4632); 2.53 (95% CI, 1.37-4.67; P = .003), due to digestive tract disease (n = 42/4632), 1.62 (95% CI, 1.04-2.52; P = .032) due to mental and behavioral disease (n = 90/4632); and 1.91 (95% CI, 1.15-3.19; P = .013) due to unspecific causes (n = 64/4632). There was no significant relationship between Pro-NT and deaths due to cancer, infections, neurological, or other causes. Adjustment for cardiovascular risk factors only marginally changed these results. CONCLUSION The relationship between Pro-NT and total mortality risk was mainly driven by cardiovascular mortality, but high Pro-NT also predicts death from digestive, mental, and behavioral disease and deaths attributed to unspecific causes.
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Affiliation(s)
- Ayesha Fawad
- Lund University, Department of Clinical Sciences, SE 20502 Malmö, Sweden
- Correspondence: Ayesha Fawad, MD, Department of Clinical Sciences, Malmoe, CRC, Jan Waldenstroems gata 35, Bldg 91, Level 12, Skane University Hospital, SE 214 28 Malmö, Sweden.
| | | | | | - Zahra A Butt
- University of Southern Denmark, Faculty of Health Sciences, 5000 Odense, Denmark
| | - Peter M Nilsson
- Lund University, Department of Clinical Sciences, SE 20502 Malmö, Sweden
| | - Louise Bennet
- Lund University, Department of Clinical Sciences, SE 20502 Malmö, Sweden
| | | | - Olle Melander
- Lund University, Department of Clinical Sciences, SE 20502 Malmö, Sweden
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Gustafsson ALS, Gussarova G, Borgen L, Ikeda H, Antonelli A, Marie-Orleach L, Rieseberg LH, Brochmann C. Rapid evolution of post-zygotic reproductive isolation is widespread in Arctic plant lineages. Ann Bot 2022; 129:171-184. [PMID: 34643673 PMCID: PMC8796670 DOI: 10.1093/aob/mcab128] [Citation(s) in RCA: 2] [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] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 10/05/2021] [Indexed: 05/03/2023]
Abstract
BACKGROUND AND AIMS The Arctic tundra, with its extreme temperatures and short growing season, is evolutionarily young and harbours one of the most species-poor floras on Earth. Arctic species often show little phenotypic and genetic divergence across circumpolar ranges. However, strong intraspecific post-zygotic reproductive isolation (RI) in terms of hybrid sterility has frequently evolved within selfing Arctic species of the genus Draba. Here we assess whether incipient biological species are common in the Arctic flora. METHODS We conducted an extensive crossing experiment including six species representing four phylogenetically distant families collected across the circumpolar Arctic. We crossed conspecific parental populations representing different spatial scales, raised 740 F1 hybrids to maturity and measured fertility under laboratory conditions. We examined genetic divergence between populations for two of these species (Cardamine bellidifolia and Ranunculus pygmaeus). KEY RESULTS In five of the six species, we find extensive reduction in pollen fertility and seed set in F1 hybrids; 219 (46 %) of the 477 F1 hybrids generated between parents separated by ≥427 km had <20 % pollen fertility. Isolation with migration (IM) and *BEAST analyses of sequences of eight nuclear genes in C. bellidifolia suggests that reproductively isolated populations of this species diverged during, or even after, the last glaciation. Likewise, Arctic populations of R. pygmaeus were genetically very similar despite exhibiting strongly reduced fertility in crosses, suggesting that RI evolved recently also in this species. CONCLUSION We show that post-zygotic RI has developed multiple times within taxonomically recognized Arctic species belonging to several distantly related lineages, and that RI may have developed over just a few millennia. Rapid and widespread evolution of incipient biological species in the Arctic flora might be associated with frequent bottlenecks due to glacial cycles, and/or selfing mating systems, which are common in the harsh Arctic environment where pollinators are scarce.
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Affiliation(s)
| | - Galina Gussarova
- Natural History Museum, University of Oslo, Oslo, Norway
- Botany Department, Faculty of Biology and Soil Science, St Petersburg, Russia
- Tromsø University Museum, University of Tromsø, Tromsø, Norway
| | - Liv Borgen
- Natural History Museum, University of Oslo, Oslo, Norway
| | - Hajime Ikeda
- Institute of Plant Science and Resources, Okayama University, Okayama, Japan
| | - Alexandre Antonelli
- Royal Botanic Gardens, Kew, Richmond, UK
- Gothenburg Global Biodiversity Centre, Department of Biological and Environmental Sciences, University of Gothenburg, Sweden
- Department of Plant Sciences, University of Oxford, Oxford, UK
| | - Lucas Marie-Orleach
- Natural History Museum, University of Oslo, Oslo, Norway
- ECOBIO—Écosystèmes, Biodiversité, Évolution, Rennes, France
| | - Loren H Rieseberg
- Botany Department, University of British Columbia, Vancouver, Canada
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