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Kilpiö T, Skarp S, Perjés Á, Swan J, Kaikkonen L, Saarimäki S, Szokodi I, Penninger JM, Szabó Z, Magga J, Kerkelä R. Apelin regulates skeletal muscle adaptation to exercise in a high-intensity interval training model. Am J Physiol Cell Physiol 2024; 326:C1437-C1450. [PMID: 38525542 DOI: 10.1152/ajpcell.00427.2023] [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: 03/18/2024] [Accepted: 03/18/2024] [Indexed: 03/26/2024]
Abstract
Plasma apelin levels are reduced in aging and muscle wasting conditions. We aimed to investigate the significance of apelin signaling in cardiac and skeletal muscle responses to physiological stress. Apelin knockout (KO) and wild-type (WT) mice were subjected to high-intensity interval training (HIIT) by treadmill running. The effects of apelin on energy metabolism were studied in primary mouse skeletal muscle myotubes and cardiomyocytes. Apelin increased mitochondrial ATP production and mitochondrial coupling efficiency in myotubes and promoted the expression of mitochondrial genes both in primary myotubes and cardiomyocytes. HIIT induced mild concentric cardiac hypertrophy in WT mice, whereas eccentric growth was observed in the left ventricles of apelin KO mice. HIIT did not affect myofiber size in skeletal muscles of WT mice but decreased the myofiber size in apelin KO mice. The decrease in myofiber size resulted from a fiber type switch toward smaller slow-twitch type I fibers. The increased proportion of slow-twitch type I fibers in apelin KO mice was associated with upregulation of myosin heavy chain slow isoform expression, accompanied with upregulated expression of genes related to fatty acid transport and downregulated expression of genes related to glucose metabolism. Mechanistically, skeletal muscles of apelin KO mice showed defective induction of insulin-like growth factor-1 signaling in response to HIIT. In conclusion, apelin is required for proper skeletal and cardiac muscle adaptation to high-intensity exercise. Promoting apelinergic signaling may have benefits in aging- or disease-related muscle wasting conditions.NEW & NOTEWORTHY Apelin levels decline with age. This study demonstrates that in trained mice, apelin deficiency results in a switch from fast type II myofibers to slow oxidative type I myofibers. This is associated with a concomitant change in gene expression profile toward fatty acid utilization, indicating an aged-muscle phenotype in exercised apelin-deficient mice. These data are of importance in the design of exercise programs for aging individuals and could offer therapeutic target to maintain muscle mass.
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Affiliation(s)
- Teemu Kilpiö
- Research Unit of Biomedicine and Internal Medicine, Department of Pharmacology and Toxicology, University of Oulu, Oulu, Finland
| | - Sini Skarp
- Research Unit of Biomedicine and Internal Medicine, Department of Pharmacology and Toxicology, University of Oulu, Oulu, Finland
| | - Ábel Perjés
- Research Unit of Biomedicine and Internal Medicine, Department of Pharmacology and Toxicology, University of Oulu, Oulu, Finland
| | - Julia Swan
- Research Unit of Biomedicine and Internal Medicine, Department of Pharmacology and Toxicology, University of Oulu, Oulu, Finland
| | - Leena Kaikkonen
- Research Unit of Biomedicine and Internal Medicine, Department of Pharmacology and Toxicology, University of Oulu, Oulu, Finland
| | - Samu Saarimäki
- Research Unit of Biomedicine and Internal Medicine, Department of Pharmacology and Toxicology, University of Oulu, Oulu, Finland
| | - István Szokodi
- Heart Institute, Medical School, and Szentágothai Research Centre, University of Pécs, Pécs, Hungary
| | - Josef M Penninger
- IMBA, Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna, Austria
- Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Zoltán Szabó
- Research Unit of Biomedicine and Internal Medicine, Department of Pharmacology and Toxicology, University of Oulu, Oulu, Finland
| | - Johanna Magga
- Research Unit of Biomedicine and Internal Medicine, Department of Pharmacology and Toxicology, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Risto Kerkelä
- Research Unit of Biomedicine and Internal Medicine, Department of Pharmacology and Toxicology, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
- Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland
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Lautaoja-Kivipelto JH, Karvinen S, Korhonen TM, O'Connell TM, Tiirola M, Hulmi JJ, Pekkala S. Interaction of the C2C12 myotube contractions and glucose availability on transcriptome and extracellular vesicle microRNAs. Am J Physiol Cell Physiol 2024; 326:C348-C361. [PMID: 38047306 DOI: 10.1152/ajpcell.00401.2023] [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: 08/22/2023] [Revised: 11/26/2023] [Accepted: 11/26/2023] [Indexed: 12/05/2023]
Abstract
Exercise-like electrical pulse stimulation (EL-EPS) of myotubes mimics many key physiological changes induced by in vivo exercise. Besides enabling intracellular research, EL-EPS allows to study secreted factors, including muscle-specific microRNAs (myomiRs) carried in extracellular vesicles (EVs). These factors can participate in contraction-induced intercellular cross talk and may mediate the health benefits of exercise. However, the current knowledge of these responses, especially under variable nutritional conditions, is limited. We investigated the effects of EL-EPS on C2C12 myotube transcriptome in high- and low-glucose conditions by messenger RNA sequencing, while the expression of EV-carried miRNAs was analyzed by small RNA sequencing and RT-qPCR. We show that higher glucose availability augmented contraction-induced transcriptional changes and that the majority of the differentially expressed genes were upregulated. Furthermore, based on the pathway analyses, processes related to contractility and cytokine/inflammatory responses were upregulated. In addition, we report that EL-EPS increased packing of miR-1-3p into EVs independent of glucose availability. Together our findings suggest that in vitro EL-EPS is a usable tool not only to study contraction-induced intracellular mechanisms but also extracellular responses. The distinct transcriptional changes observed under variable nutritional conditions emphasize the importance of careful consideration of media composition in future exercise-mimicking studies.NEW & NOTEWORTHY The present study examined for the first time the effects of exercise-like electrical pulse stimulation administered under distinct nutritional conditions on 1) the transcriptome of the C2C12 myotubes and 2) their media containing extracellular vesicle-carried microRNAs. We report that higher glucose availability augmented transcriptional responses related especially to contractility and cytokine/inflammatory pathways. Agreeing with in vivo studies, we show that the packing of exercise-responsive miR-1-3p was increased in the extracellular vesicles in response to myotube contractions.
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Affiliation(s)
- Juulia H Lautaoja-Kivipelto
- Faculty of Sport and Sciences, Gerontology Research Center, University of Jyväskylä, Jyväskylä, Finland
- Faculty of Medicine, Research Unit of Biomedicine and Internal Medicine, University of Oulu, Oulu, Finland
| | - Sira Karvinen
- Faculty of Sport and Sciences, Gerontology Research Center, University of Jyväskylä, Jyväskylä, Finland
| | - Tia-Marje Korhonen
- Faculty of Sport and Sciences, Gerontology Research Center, University of Jyväskylä, Jyväskylä, Finland
| | - Thomas M O'Connell
- Department of Otolaryngology, Head & Neck Surgery, Indiana University School of Medicine, Indianapolis, Indiana, United States
| | - Marja Tiirola
- Department of Biological and Environmental Science, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - Juha J Hulmi
- Faculty of Sport and Sciences, Gerontology Research Center, University of Jyväskylä, Jyväskylä, Finland
| | - Satu Pekkala
- Faculty of Sport and Sciences, Gerontology Research Center, University of Jyväskylä, Jyväskylä, Finland
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Mäntyselkä S, Kolari K, Baumert P, Ylä-Outinen L, Kuikka L, Lahtonen S, Permi P, Wackerhage H, Kalenius E, Kivelä R, Hulmi JJ. Serine synthesis pathway enzyme PHGDH is critical for muscle cell biomass, anabolic metabolism, and mTORC1 signaling. Am J Physiol Endocrinol Metab 2024; 326:E73-E91. [PMID: 37991454 DOI: 10.1152/ajpendo.00151.2023] [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: 05/16/2023] [Revised: 11/13/2023] [Accepted: 11/16/2023] [Indexed: 11/23/2023]
Abstract
Cells use glycolytic intermediates for anabolism, e.g., via the serine synthesis and pentose phosphate pathways. However, we still understand poorly how these metabolic pathways contribute to skeletal muscle cell biomass generation. The first aim of this study was therefore to identify enzymes that limit protein synthesis, myotube size, and proliferation in skeletal muscle cells. We inhibited key enzymes of glycolysis, the pentose phosphate pathway, and the serine synthesis pathway to evaluate their importance in C2C12 myotube protein synthesis. Based on the results of this first screen, we then focused on the serine synthesis pathway enzyme phosphoglycerate dehydrogenase (PHGDH). We used two different PHGDH inhibitors and mouse C2C12 and human primary muscle cells to study the importance and function of PHGDH. Both myoblasts and myotubes incorporated glucose-derived carbon into proteins, RNA, and lipids, and we showed that PHGDH is essential in these processes. PHGDH inhibition decreased protein synthesis, myotube size, and myoblast proliferation without cytotoxic effects. The decreased protein synthesis in response to PHGDH inhibition appears to occur mainly mechanistic target of rapamycin complex 1 (mTORC1)-dependently, as was evident from experiments with insulin-like growth factor 1 and rapamycin. Further metabolomics analyses revealed that PHGDH inhibition accelerated glycolysis and altered amino acid, nucleotide, and lipid metabolism. Finally, we found that supplementing an antioxidant and redox modulator, N-acetylcysteine, partially rescued the decreased protein synthesis and mTORC1 signaling during PHGDH inhibition. The data suggest that PHGDH activity is critical for skeletal muscle cell biomass generation from glucose and that it regulates protein synthesis and mTORC1 signaling.NEW & NOTEWORTHY The use of glycolytic intermediates for anabolism was demonstrated in both myoblasts and myotubes, which incorporate glucose-derived carbon into proteins, RNA, and lipids. We identify phosphoglycerate dehydrogenase (PHGDH) as a critical enzyme in those processes and also for muscle cell hypertrophy, proliferation, protein synthesis, and mTORC1 signaling. Our results thus suggest that PHGDH in skeletal muscle is more than just a serine-synthesizing enzyme.
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Affiliation(s)
- Sakari Mäntyselkä
- Faculty of Sport and Health Sciences, NeuroMuscular Research Center, University of Jyväskylä, Jyväskylä, Finland
| | - Kalle Kolari
- Faculty of Sport and Health Sciences, NeuroMuscular Research Center, University of Jyväskylä, Jyväskylä, Finland
| | - Philipp Baumert
- Department for Sport and Health Sciences, Technical University of Munich, Munich, Germany
| | - Laura Ylä-Outinen
- Faculty of Sport and Health Sciences, NeuroMuscular Research Center, University of Jyväskylä, Jyväskylä, Finland
| | - Lauri Kuikka
- Central Finland Health Care District Hospital District, Jyväskylä, Finland
| | - Suvi Lahtonen
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Perttu Permi
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
- Department of Chemistry, University of Jyväskylä, Jyväskylä, Finland
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Henning Wackerhage
- Department for Sport and Health Sciences, Technical University of Munich, Munich, Germany
| | - Elina Kalenius
- Department of Chemistry, University of Jyväskylä, Jyväskylä, Finland
| | - Riikka Kivelä
- Faculty of Sport and Health Sciences, NeuroMuscular Research Center, University of Jyväskylä, Jyväskylä, Finland
- Stem Cells and Metabolism Research Program, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Wihuri Research Institute, Helsinki, Finland
| | - Juha J Hulmi
- Faculty of Sport and Health Sciences, NeuroMuscular Research Center, University of Jyväskylä, Jyväskylä, Finland
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Wang MM, Coupland SE, Aittokallio T, Figueiredo CR. Resistance to immune checkpoint therapies by tumour-induced T-cell desertification and exclusion: key mechanisms, prognostication and new therapeutic opportunities. Br J Cancer 2023; 129:1212-1224. [PMID: 37454231 PMCID: PMC10575907 DOI: 10.1038/s41416-023-02361-4] [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] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 06/26/2023] [Accepted: 06/29/2023] [Indexed: 07/18/2023] Open
Abstract
Immune checkpoint therapies (ICT) can reinvigorate the effector functions of anti-tumour T cells, improving cancer patient outcomes. Anti-tumour T cells are initially formed during their first contact (priming) with tumour antigens by antigen-presenting cells (APCs). Unfortunately, many patients are refractory to ICT because their tumours are considered to be 'cold' tumours-i.e., they do not allow the generation of T cells (so-called 'desert' tumours) or the infiltration of existing anti-tumour T cells (T-cell-excluded tumours). Desert tumours disturb antigen processing and priming of T cells by targeting APCs with suppressive tumour factors derived from their genetic instabilities. In contrast, T-cell-excluded tumours are characterised by blocking effective anti-tumour T lymphocytes infiltrating cancer masses by obstacles, such as fibrosis and tumour-cell-induced immunosuppression. This review delves into critical mechanisms by which cancer cells induce T-cell 'desertification' and 'exclusion' in ICT refractory tumours. Filling the gaps in our knowledge regarding these pro-tumoral mechanisms will aid researchers in developing novel class immunotherapies that aim at restoring T-cell generation with more efficient priming by APCs and leukocyte tumour trafficking. Such developments are expected to unleash the clinical benefit of ICT in refractory patients.
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Affiliation(s)
- Mona Meng Wang
- Medical Immune Oncology Research Group (MIORG), Institute of Biomedicine, Faculty of Medicine, University of Turku, Turku, Finland
- Singapore National Eye Centre and Singapore Eye Research Institute, Singapore, Singapore
| | - Sarah E Coupland
- InFLAMES Research Flagship Center, University of Turku, Turku, Finland
- Liverpool Ocular Oncology Research Group (LOORG), Institute of Systems Molecular and Integrative Biology, Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, UK
| | - Tero Aittokallio
- InFLAMES Research Flagship Center, University of Turku, Turku, Finland
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Institute for Cancer Research, Department of Cancer Genetics, Oslo University Hospital, Oslo, Norway
- Oslo Centre for Biostatistics and Epidemiology (OCBE), Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Carlos R Figueiredo
- Medical Immune Oncology Research Group (MIORG), Institute of Biomedicine, Faculty of Medicine, University of Turku, Turku, Finland.
- InFLAMES Research Flagship Center, University of Turku, Turku, Finland.
- Turku Bioscience Centre, University of Turku, Turku, Finland.
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5
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Pajanoja C, Hsin J, Olinger B, Schiffmacher A, Yazejian R, Abrams S, Dapkunas A, Zainul Z, Doyle AD, Martin D, Kerosuo L. Maintenance of pluripotency-like signature in the entire ectoderm leads to neural crest stem cell potential. Nat Commun 2023; 14:5941. [PMID: 37741818 PMCID: PMC10518019 DOI: 10.1038/s41467-023-41384-6] [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: 01/17/2023] [Accepted: 09/01/2023] [Indexed: 09/25/2023] Open
Abstract
The ability of the pluripotent epiblast to contribute progeny to all three germ layers is thought to be lost after gastrulation. The later-forming neural crest (NC) rises from ectoderm and it remains poorly understood how its exceptionally high stem-cell potential to generate mesodermal- and endodermal-like derivatives is obtained. Here, we monitor transcriptional changes from gastrulation to neurulation using single-cell-Multiplex-Spatial-Transcriptomics (scMST) complemented with RNA-sequencing. We show maintenance of pluripotency-like signature (Nanog, Oct4/PouV, Klf4-positive) in undecided pan-ectodermal stem-cells spanning the entire ectoderm late during neurulation with ectodermal patterning completed only at the end of neurulation when the pluripotency-like signature becomes restricted to NC, challenging our understanding of gastrulation. Furthermore, broad ectodermal pluripotency-like signature is found at multiple axial levels unrelated to the NC lineage the cells later commit to, suggesting a general role in stemness enhancement and proposing a mechanism by which the NC acquires its ability to form derivatives beyond "ectodermal-capacity" in chick and mouse embryos.
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Affiliation(s)
- Ceren Pajanoja
- National Institute of Dental and Craniofacial Research, Intramural Research Program, Neural Crest Development and Disease Unit, National Institutes of Health, Bethesda, MD, USA
- Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Jenny Hsin
- National Institute of Dental and Craniofacial Research, Intramural Research Program, Neural Crest Development and Disease Unit, National Institutes of Health, Bethesda, MD, USA
| | - Bradley Olinger
- National Institute of Dental and Craniofacial Research, Intramural Research Program, Neural Crest Development and Disease Unit, National Institutes of Health, Bethesda, MD, USA
| | - Andrew Schiffmacher
- National Institute of Dental and Craniofacial Research, Intramural Research Program, Neural Crest Development and Disease Unit, National Institutes of Health, Bethesda, MD, USA
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD, USA
| | - Rita Yazejian
- National Institute of Dental and Craniofacial Research, Intramural Research Program, Neural Crest Development and Disease Unit, National Institutes of Health, Bethesda, MD, USA
| | - Shaun Abrams
- National Institute of Dental and Craniofacial Research, Intramural Research Program, Neural Crest Development and Disease Unit, National Institutes of Health, Bethesda, MD, USA
| | - Arvydas Dapkunas
- Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Zarin Zainul
- National Institute of Dental and Craniofacial Research, Intramural Research Program, Neural Crest Development and Disease Unit, National Institutes of Health, Bethesda, MD, USA
| | - Andrew D Doyle
- National Institute of Dental and Craniofacial Research, Intramural Research Program, NIDCR Imaging Core, National Institutes of Health, Bethesda, MD, USA
| | - Daniel Martin
- National Institute of Dental and Craniofacial Research, Intramural Research Program, Genomics and Computational Biology Core, National Institutes of Health, Bethesda, MD, USA
| | - Laura Kerosuo
- National Institute of Dental and Craniofacial Research, Intramural Research Program, Neural Crest Development and Disease Unit, National Institutes of Health, Bethesda, MD, USA.
- Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
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Rehan S, Tranter D, Sharp PP, Craven GB, Lowe E, Anderl JL, Muchamuel T, Abrishami V, Kuivanen S, Wenzell NA, Jennings A, Kalyanaraman C, Strandin T, Javanainen M, Vapalahti O, Jacobson MP, McMinn D, Kirk CJ, Huiskonen JT, Taunton J, Paavilainen VO. Signal peptide mimicry primes Sec61 for client-selective inhibition. Nat Chem Biol 2023; 19:1054-1062. [PMID: 37169961 PMCID: PMC10449633 DOI: 10.1038/s41589-023-01326-1] [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: 06/03/2022] [Accepted: 04/06/2023] [Indexed: 05/13/2023]
Abstract
Preventing the biogenesis of disease-relevant proteins is an attractive therapeutic strategy, but attempts to target essential protein biogenesis factors have been hampered by excessive toxicity. Here we describe KZR-8445, a cyclic depsipeptide that targets the Sec61 translocon and selectively disrupts secretory and membrane protein biogenesis in a signal peptide-dependent manner. KZR-8445 potently inhibits the secretion of pro-inflammatory cytokines in primary immune cells and is highly efficacious in a mouse model of rheumatoid arthritis. A cryogenic electron microscopy structure reveals that KZR-8445 occupies the fully opened Se61 lateral gate and blocks access to the lumenal plug domain. KZR-8445 binding stabilizes the lateral gate helices in a manner that traps select signal peptides in the Sec61 channel and prevents their movement into the lipid bilayer. Our results establish a framework for the structure-guided discovery of novel therapeutics that selectively modulate Sec61-mediated protein biogenesis.
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Affiliation(s)
- Shahid Rehan
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Dale Tranter
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Phillip P Sharp
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA
| | - Gregory B Craven
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA
| | - Eric Lowe
- Kezar Life Sciences, South San Francisco, CA, USA
| | | | | | - Vahid Abrishami
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Suvi Kuivanen
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Nicole A Wenzell
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA
| | | | - Chakrapani Kalyanaraman
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of California, San Francisco, CA, USA
| | - Tomas Strandin
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Matti Javanainen
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Olli Vapalahti
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Matthew P Jacobson
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of California, San Francisco, CA, USA
| | | | | | - Juha T Huiskonen
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Jack Taunton
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA.
| | - Ville O Paavilainen
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland.
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7
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Haataja JS, Jacucci G, Parton TG, Schertel L, Vignolini S. Topological invariance in whiteness optimisation. Commun Phys 2023; 6:137. [PMID: 38665411 PMCID: PMC11041678 DOI: 10.1038/s42005-023-01234-9] [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] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 05/09/2023] [Indexed: 04/28/2024]
Abstract
Maximizing the scattering of visible light within disordered nano-structured materials is essential for commercial applications such as brighteners, while also testing our fundamental understanding of light-matter interactions. The progress in the research field has been hindered by the lack of understanding how different structural features contribute to the scattering properties. Here we undertake a systematic investigation of light scattering in correlated disordered structures. We demonstrate that the scattering efficiency of disordered systems is mainly determined by topologically invariant features, such as the filling fraction and correlation length, and residual variations are largely accounted by the surface-averaged mean curvature of the systems. Optimal scattering efficiency can thus be obtained from a broad range of disordered structures, especially when structural anisotropy is included as a parameter. These results suggest that any disordered system can be optimised for whiteness and give comparable performance, which has far-reaching consequences for the industrial use of low-index materials for optical scattering.
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Affiliation(s)
- Johannes S. Haataja
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW UK
- Department of Applied Physics, Aalto University School of Science, P.O. Box 15100, Espoo, FI-02150 Finland
| | - Gianni Jacucci
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW UK
- Laboratoire Kastler Brossel, ENS-PSL Research University, CNRS, Sorbonne Université, Collège de France, Paris, France
| | - Thomas G. Parton
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW UK
| | - Lukas Schertel
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW UK
- Department of Physics, University of Fribourg, Chemin du Musée 3, 1700 Fribourg, Switzerland
| | - Silvia Vignolini
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW UK
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8
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Kansikas M, Vähätalo L, Kantelinen J, Kasela M, Putula J, Døhlen A, Paloviita P, Kärkkäinen E, Lahti N, Arnez P, Kilpinen S, Alcala-Repo B, Pylvänäinen K, Pöyhönen M, Peltomäki P, Järvinen HJ, Seppälä TT, Renkonen-Sinisalo L, Lepistö A, Mecklin JP, Nyström M. Tumor-independent Detection of Inherited Mismatch Repair Deficiency for the Diagnosis of Lynch Syndrome with High Specificity and Sensitivity. Cancer Res Commun 2023; 3:361-370. [PMID: 36875157 PMCID: PMC9979712 DOI: 10.1158/2767-9764.crc-22-0384] [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] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 12/20/2022] [Accepted: 02/07/2023] [Indexed: 06/18/2023]
Abstract
UNLABELLED Lynch syndrome (LS) is the most common hereditary cancer syndrome. Early diagnosis improves prognosis and reduces health care costs, through existing cancer surveillance methods. The problem is finding and diagnosing the cancer predisposing genetic condition. The current workup involves a complex array of tests that combines family cancer history and clinical phenotypes with tumor characteristics and sequencing data, followed by a challenging task to interpret the found variant(s). On the basis of the knowledge that an inherited mismatch repair (MMR) deficiency is a hallmark of LS, we have developed and validated a functional MMR test, DiagMMR, that detects inherited MMR deficiency directly from healthy tissue without need of tumor and variant information. The validation included 119 skin biopsies collected from clinically pathogenic MMR variant carriers (MSH2, MSH6) and controls, and was followed by a small clinical pilot study. The repair reaction was performed on proteins extracted from primary fibroblasts and the interpretation was based on the MMR capability of the sample in relation to cutoff, which distinguishes MMR proficient (non-LS) from MMR deficient (LS) function. The results were compared with the reference standard (germline NGS). The test was shown to have exceptional specificity (100%) with high sensitivity (89%) and accuracy (97%). The ability to efficiently distinguish LS carriers from controls was further shown with a high area under the receiving operating characteristic (AUROC) value (0.97). This test offers an excellent tool for detecting inherited MMR deficiency linked to MSH2 or MSH6 and can be used alone or with conventional tests to recognize genetically predisposed individuals. SIGNIFICANCE Clinical validation of DiagMMR shows high accuracy in distinguishing individuals with hereditary MSH2 or MSH6 MMR deficiency (i.e., LS). The method presented overcomes challenges faced by the complexity of current methods and can be used alone or with conventional tests to improve the ability to recognize genetically predisposed individuals.
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Affiliation(s)
- Minttu Kansikas
- LS CancerDiag Ltd., Helsinki, Finland
- Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Laura Vähätalo
- LS CancerDiag Ltd., Helsinki, Finland
- Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Jukka Kantelinen
- LS CancerDiag Ltd., Helsinki, Finland
- Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Mariann Kasela
- LS CancerDiag Ltd., Helsinki, Finland
- Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Jaana Putula
- LS CancerDiag Ltd., Helsinki, Finland
- Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Anni Døhlen
- LS CancerDiag Ltd., Helsinki, Finland
- Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Pauliina Paloviita
- LS CancerDiag Ltd., Helsinki, Finland
- Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Emmi Kärkkäinen
- LS CancerDiag Ltd., Helsinki, Finland
- Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Niklas Lahti
- LS CancerDiag Ltd., Helsinki, Finland
- Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Philippe Arnez
- LS CancerDiag Ltd., Helsinki, Finland
- Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Sami Kilpinen
- Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | | | - Kirsi Pylvänäinen
- Department of Education and Science, Nova Hospital, Central Finland Health Care District, Jyväskylä, Finland
| | - Minna Pöyhönen
- Department of Genetics, HUSLAB, Helsinki University Hospital Diagnostic Center, Helsinki, Finland
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
- Applied Tumor Genomics, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Päivi Peltomäki
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
| | | | - Toni T. Seppälä
- Department of Surgery, Helsinki University Hospital, Helsinki, Finland
- Applied Tumor Genomics, Research Programs Unit, University of Helsinki, Helsinki, Finland
- Faculty of Medicine and Medical Technology, University of Tampere, Tampere, Finland
- Department of Gastroenterology and Alimentary Tract Surgery, Tampere University Hospital, Tampere, Finland
| | - Laura Renkonen-Sinisalo
- Department of Surgery, Helsinki University Hospital, Helsinki, Finland
- Applied Tumor Genomics, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Anna Lepistö
- Department of Surgery, Helsinki University Hospital, Helsinki, Finland
- Applied Tumor Genomics, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Jukka-Pekka Mecklin
- Department of Education and Science, Nova Hospital, Central Finland Health Care District, Jyväskylä, Finland
- Faculty of Sports and Health Sciences, University of Jyväskylä, Jyväskylä, Finland
| | - Minna Nyström
- Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
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9
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Lindbohm JV, Mars N, Sipilä PN, Singh-Manoux A, Runz H, Livingston G, Seshadri S, Xavier R, Hingorani AD, Ripatti S, Kivimäki M. Immune system-wide Mendelian randomization and triangulation analyses support autoimmunity as a modifiable component in dementia-causing diseases. Nat Aging 2022; 2:956-972. [PMID: 37118290 PMCID: PMC10154235 DOI: 10.1038/s43587-022-00293-x] [Citation(s) in RCA: 10] [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] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 09/05/2022] [Indexed: 04/30/2023]
Abstract
Immune system and blood-brain barrier dysfunction are implicated in the development of Alzheimer's and other dementia-causing diseases, but their causal role remains unknown. We performed Mendelian randomization for 1,827 immune system- and blood-brain barrier-related biomarkers and identified 127 potential causal risk factors for dementia-causing diseases. Pathway analyses linked these biomarkers to amyloid-β, tau and α-synuclein pathways and to autoimmunity-related processes. A phenome-wide analysis using Mendelian randomization-based polygenic risk score in the FinnGen study (n = 339,233) for the biomarkers indicated shared genetic background for dementias and autoimmune diseases. This association was further supported by human leukocyte antigen analyses. In inverse-probability-weighted analyses that simulate randomized controlled drug trials in observational data, anti-inflammatory methotrexate treatment reduced the incidence of Alzheimer's disease in high-risk individuals (hazard ratio compared with no treatment, 0.64, 95% confidence interval 0.49-0.88, P = 0.005). These converging results from different lines of human research suggest that autoimmunity is a modifiable component in dementia-causing diseases.
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Affiliation(s)
- Joni V Lindbohm
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, The Klarman Cell Observatory, Cambridge, MA, USA.
- Department of Epidemiology and Public Health, University College London, London, UK.
- Clinicum, Department of Public Health, University of Helsinki, Helsinki, Finland.
| | - Nina Mars
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, The Klarman Cell Observatory, Cambridge, MA, USA
- Institute for Molecular Medicine Finland, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Pyry N Sipilä
- Clinicum, Department of Public Health, University of Helsinki, Helsinki, Finland
| | - Archana Singh-Manoux
- Department of Epidemiology and Public Health, University College London, London, UK
- Université de Paris, Inserm U1153, Epidemiology of Ageing and Neurodegenerative diseases, Paris, France
| | - Heiko Runz
- Research & Development, Biogen Inc., Cambridge, MA, USA
| | - Gill Livingston
- Division of Psychiatry, University College London, London, UK
- Camden and Islington NHS Foundation Trust, London, UK
| | - Sudha Seshadri
- Glenn Biggs Institute of Alzheimer's and Neurodegenerative Diseases, University of Texas Health Science Center, San Antonio, TX, USA
- Boston University School of Public Health, Boston, MA, USA
- New York University Grossman School of Medicine, New York, NY, USA
- Boston University School of Medicine, Boston, MA, USA
| | - Ramnik Xavier
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, The Klarman Cell Observatory, Cambridge, MA, USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Aroon D Hingorani
- Institute of Cardiovascular Science, University College London, London, UK
- University College London, British Heart Foundation Research Accelerator, London, UK
- Health Data Research UK, London, UK
| | - Samuli Ripatti
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, The Klarman Cell Observatory, Cambridge, MA, USA
- Clinicum, Department of Public Health, University of Helsinki, Helsinki, Finland
- Institute for Molecular Medicine Finland, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Mika Kivimäki
- Department of Epidemiology and Public Health, University College London, London, UK
- Clinicum, Department of Public Health, University of Helsinki, Helsinki, Finland
- Division of Psychiatry, University College London, London, UK
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10
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Parton TG, Parker RM, van de Kerkhof GT, Narkevicius A, Haataja JS, Frka-Petesic B, Vignolini S. Chiral self-assembly of cellulose nanocrystals is driven by crystallite bundles. Nat Commun 2022; 13:2657. [PMID: 35550506 PMCID: PMC9098854 DOI: 10.1038/s41467-022-30226-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [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: 01/11/2022] [Accepted: 04/21/2022] [Indexed: 12/02/2022] Open
Abstract
The transfer of chirality across length-scales is an intriguing and universal natural phenomenon. However, connecting the properties of individual building blocks to the emergent features of their resulting large-scale structure remains a challenge. In this work, we investigate the origins of mesophase chirality in cellulose nanocrystal suspensions, whose self-assembly into chiral photonic films has attracted significant interest. By correlating the ensemble behaviour in suspensions and films with a quantitative morphological analysis of the individual nanoparticles, we reveal an inverse relationship between the cholesteric pitch and the abundance of laterally-bound composite particles. These 'bundles' thus act as colloidal chiral dopants, analogous to those used in molecular liquid crystals, providing the missing link in the hierarchical transfer of chirality from the molecular to the colloidal scale.
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Affiliation(s)
- Thomas G Parton
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Richard M Parker
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Gea T van de Kerkhof
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Aurimas Narkevicius
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Johannes S Haataja
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Bruno Frka-Petesic
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Silvia Vignolini
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
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11
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Zhu Q, Huang S, Gonzalez A, McGrath I, McDonald D, Haiminen N, Armstrong G, Vázquez-Baeza Y, Yu J, Kuczynski J, Sepich-Poore GD, Swafford AD, Das P, Shaffer JP, Lejzerowicz F, Belda-Ferre P, Havulinna AS, Méric G, Niiranen T, Lahti L, Salomaa V, Kim HC, Jain M, Inouye M, Gilbert JA, Knight R. Phylogeny-Aware Analysis of Metagenome Community Ecology Based on Matched Reference Genomes while Bypassing Taxonomy. mSystems 2022; 7:e0016722. [PMID: 35369727 PMCID: PMC9040630 DOI: 10.1128/msystems.00167-22] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [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: 02/19/2022] [Accepted: 02/25/2022] [Indexed: 02/06/2023] Open
Abstract
We introduce the operational genomic unit (OGU) method, a metagenome analysis strategy that directly exploits sequence alignment hits to individual reference genomes as the minimum unit for assessing the diversity of microbial communities and their relevance to environmental factors. This approach is independent of taxonomic classification, granting the possibility of maximal resolution of community composition, and organizes features into an accurate hierarchy using a phylogenomic tree. The outputs are suitable for contemporary analytical protocols for community ecology, differential abundance, and supervised learning while supporting phylogenetic methods, such as UniFrac and phylofactorization, that are seldom applied to shotgun metagenomics despite being prevalent in 16S rRNA gene amplicon studies. As demonstrated in two real-world case studies, the OGU method produces biologically meaningful patterns from microbiome data sets. Such patterns further remain detectable at very low metagenomic sequencing depths. Compared with taxonomic unit-based analyses implemented in currently adopted metagenomics tools, and the analysis of 16S rRNA gene amplicon sequence variants, this method shows superiority in informing biologically relevant insights, including stronger correlation with body environment and host sex on the Human Microbiome Project data set and more accurate prediction of human age by the gut microbiomes of Finnish individuals included in the FINRISK 2002 cohort. We provide Woltka, a bioinformatics tool to implement this method, with full integration with the QIIME 2 package and the Qiita web platform, to facilitate adoption of the OGU method in future metagenomics studies. IMPORTANCE Shotgun metagenomics is a powerful, yet computationally challenging, technique compared to 16S rRNA gene amplicon sequencing for decoding the composition and structure of microbial communities. Current analyses of metagenomic data are primarily based on taxonomic classification, which is limited in feature resolution. To solve these challenges, we introduce operational genomic units (OGUs), which are the individual reference genomes derived from sequence alignment results, without further assigning them taxonomy. The OGU method advances current read-based metagenomics in two dimensions: (i) providing maximal resolution of community composition and (ii) permitting use of phylogeny-aware tools. Our analysis of real-world data sets shows that it is advantageous over currently adopted metagenomic analysis methods and the finest-grained 16S rRNA analysis methods in predicting biological traits. We thus propose the adoption of OGUs as an effective practice in metagenomic studies.
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Affiliation(s)
- Qiyun Zhu
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
- Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, Arizona, USA
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
| | - Shi Huang
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
- Faculty of Dentistry, The University of Hong Kong, Hong Kong SAR, China
| | - Antonio Gonzalez
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
| | - Imran McGrath
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
- Division of Biological Sciences, University of California San Diego, La Jolla, California, USA
| | - Daniel McDonald
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
| | - Niina Haiminen
- IBM T. J. Watson Research Center, Yorktown Heights, New York, USA
| | - George Armstrong
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, California, USA
| | - Yoshiki Vázquez-Baeza
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
| | - Julian Yu
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
- Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, Arizona, USA
| | | | | | - Austin D. Swafford
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
| | - Promi Das
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Justin P. Shaffer
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
| | - Franck Lejzerowicz
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
| | - Pedro Belda-Ferre
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
| | - Aki S. Havulinna
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
- Institute for Molecular Medicine Finland, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Guillaume Méric
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Teemu Niiranen
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
- Department of Internal Medicine, University of Turku, Turku, Finland
- Division of Medicine, Turku University Hospital, Finland
| | - Leo Lahti
- Department of Computing, University of Turku, Turku, Finland
| | - Veikko Salomaa
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Ho-Cheol Kim
- IBM Almaden Research Center, San Jose, California, USA
| | - Mohit Jain
- Department of Medicine, University of California San Diego, La Jolla, California, USA
- Department of Pharmacology, University of California San Diego, La Jolla, California, USA
| | - Michael Inouye
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- Department of Public Health and Primary Care, Cambridge University, Cambridge, United Kingdom
| | - Jack A. Gilbert
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Rob Knight
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
- Department of Bioengineering, University of California San Diego, La Jolla, California, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, California, USA
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12
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Mazac R, Meinilä J, Korkalo L, Järviö N, Jalava M, Tuomisto HL. Incorporation of novel foods in European diets can reduce global warming potential, water use and land use by over 80. Nat Food 2022; 3:286-293. [PMID: 37118200 DOI: 10.1038/s43016-022-00489-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 03/16/2022] [Indexed: 04/30/2023]
Abstract
Global food systems face the challenge of providing healthy and adequate nutrition through sustainable means, which is exacerbated by climate change and increasing protein demand by the world's growing population. Recent advances in novel food production technologies demonstrate potential solutions for improving the sustainability of food systems. Yet, diet-level comparisons are lacking and are needed to fully understand the environmental impacts of incorporating novel foods in diets. Here we estimate the possible reductions in global warming potential, water use and land use by replacing animal-source foods with novel or plant-based foods in European diets. Using a linear programming model, we optimized omnivore, vegan and novel food diets for minimum environmental impacts with nutrition and feasible consumption constraints. Replacing animal-source foods in current diets with novel foods reduced all environmental impacts by over 80% and still met nutrition and feasible consumption constraints.
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Affiliation(s)
- Rachel Mazac
- Department of Agricultural Sciences, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland.
- Helsinki Institute of Sustainability Sciences (HELSUS), University of Helsinki, Helsinki, Finland.
| | - Jelena Meinilä
- Department of Food and Nutrition, University of Helsinki, Helsinki, Finland
| | - Liisa Korkalo
- Helsinki Institute of Sustainability Sciences (HELSUS), University of Helsinki, Helsinki, Finland
- Department of Food and Nutrition, University of Helsinki, Helsinki, Finland
| | - Natasha Järviö
- Department of Agricultural Sciences, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland
- Helsinki Institute of Sustainability Sciences (HELSUS), University of Helsinki, Helsinki, Finland
- Ruralia Institute, Faculty of Agriculture and Forestry, University of Helsinki, Mikkeli, Finland
| | - Mika Jalava
- Department of Built Environment, School of Engineering, Aalto University, Helsinki, Finland
| | - Hanna L Tuomisto
- Department of Agricultural Sciences, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland
- Helsinki Institute of Sustainability Sciences (HELSUS), University of Helsinki, Helsinki, Finland
- Natural Resources Institute Finland, Helsinki, Finland
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13
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Hämäläinen L, Hoppitt W, Rowland HM, Mappes J, Fulford AJ, Sosa S, Thorogood R. Social transmission in the wild can reduce predation pressure on novel prey signals. Nat Commun 2021; 12:3978. [PMID: 34172738 PMCID: PMC8233390 DOI: 10.1038/s41467-021-24154-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [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: 07/19/2020] [Accepted: 05/21/2021] [Indexed: 02/05/2023] Open
Abstract
Social transmission of information is taxonomically widespread and could have profound effects on the ecological and evolutionary dynamics of animal communities. Demonstrating this in the wild, however, has been challenging. Here we show by field experiment that social transmission among predators can shape how selection acts on prey defences. Using artificial prey and a novel approach in statistical analyses of social networks, we find that blue tit (Cyanistes caeruleus) and great tit (Parus major) predators learn about prey defences by watching others. This shifts population preferences rapidly to match changes in prey profitability, and reduces predation pressure from naïve predators. Our results may help resolve how costly prey defences are maintained despite influxes of naïve juvenile predators, and suggest that accounting for social transmission is essential if we are to understand coevolutionary processes.
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Affiliation(s)
- Liisa Hämäläinen
- Department of Zoology, University of Cambridge, Cambridge, UK.
- Department of Biological Sciences, Macquarie University, Sydney, NSW, Australia.
- Department of Biological and Environmental Sciences, University of Jyväskylä, Jyväskylä, Finland.
| | - William Hoppitt
- School of Biological Sciences, Royal Holloway, University of London, Egham, UK
| | - Hannah M Rowland
- Department of Zoology, University of Cambridge, Cambridge, UK
- Max Planck Institute for Chemical Ecology, Jena, Germany
- Institute of Zoology, Zoological Society of London, London, UK
| | - Johanna Mappes
- Department of Biological and Environmental Sciences, University of Jyväskylä, Jyväskylä, Finland
- Research Programme in Organismal and Evolutionary Biology, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | | | - Sebastian Sosa
- Université de Strasbourg, CNRS, IPHC, UMR 7178, Strasbourg, France
| | - Rose Thorogood
- Department of Zoology, University of Cambridge, Cambridge, UK
- Research Programme in Organismal and Evolutionary Biology, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
- HiLIFE Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
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14
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Salosensaari A, Laitinen V, Havulinna AS, Meric G, Cheng S, Perola M, Valsta L, Alfthan G, Inouye M, Watrous JD, Long T, Salido RA, Sanders K, Brennan C, Humphrey GC, Sanders JG, Jain M, Jousilahti P, Salomaa V, Knight R, Lahti L, Niiranen T. Taxonomic signatures of cause-specific mortality risk in human gut microbiome. Nat Commun 2021; 12:2671. [PMID: 33976176 PMCID: PMC8113604 DOI: 10.1038/s41467-021-22962-y] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [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: 07/17/2020] [Accepted: 04/06/2021] [Indexed: 12/26/2022] Open
Abstract
The collection of fecal material and developments in sequencing technologies have enabled standardised and non-invasive gut microbiome profiling. Microbiome composition from several large cohorts have been cross-sectionally linked to various lifestyle factors and diseases. In spite of these advances, prospective associations between microbiome composition and health have remained uncharacterised due to the lack of sufficiently large and representative population cohorts with comprehensive follow-up data. Here, we analyse the long-term association between gut microbiome variation and mortality in a well-phenotyped and representative population cohort from Finland (n = 7211). We report robust taxonomic and functional microbiome signatures related to the Enterobacteriaceae family that are associated with mortality risk during a 15-year follow-up. Our results extend previous cross-sectional studies, and help to establish the basis for examining long-term associations between human gut microbiome composition, incident outcomes, and general health status.
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Affiliation(s)
- Aaro Salosensaari
- Division of Medicine, Turku University Hospital and University of Turku, Turku, Finland
- Department of Computing, University of Turku, Turku, Finland
- Department of Mathematics and Statistics, University of Turku, Turku, Finland
| | - Ville Laitinen
- Department of Computing, University of Turku, Turku, Finland
| | - Aki S Havulinna
- Finnish Institute for Health and Welfare, Helsinki, Finland
- Institute for Molecular Medicine Finland, FIMM-HiLIFE, Helsinki, Finland
| | - Guillaume Meric
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Susan Cheng
- Division of Cardiology, Brigham and Women's Hospital, Boston, MA, USA
- Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Markus Perola
- Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Liisa Valsta
- Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Georg Alfthan
- Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Michael Inouye
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Jeramie D Watrous
- Departments of Medicine and Pharmacology, University of California San Diego, San Diego, CA, USA
| | - Tao Long
- Departments of Medicine and Pharmacology, University of California San Diego, San Diego, CA, USA
| | - Rodolfo A Salido
- Department of Pediatrics, University of California San Diego, San Diego, CA, USA
| | - Karenina Sanders
- Department of Pediatrics, University of California San Diego, San Diego, CA, USA
| | - Caitriona Brennan
- Department of Pediatrics, University of California San Diego, San Diego, CA, USA
| | - Gregory C Humphrey
- Department of Pediatrics, University of California San Diego, San Diego, CA, USA
| | - Jon G Sanders
- Department of Pediatrics, University of California San Diego, San Diego, CA, USA
| | - Mohit Jain
- Departments of Medicine and Pharmacology, University of California San Diego, San Diego, CA, USA
| | | | - Veikko Salomaa
- Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, San Diego, CA, USA
| | - Leo Lahti
- Department of Computing, University of Turku, Turku, Finland.
| | - Teemu Niiranen
- Division of Medicine, Turku University Hospital and University of Turku, Turku, Finland.
- Finnish Institute for Health and Welfare, Helsinki, Finland.
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