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Salojärvi J, Rambani A, Yu Z, Guyot R, Strickler S, Lepelley M, Wang C, Rajaraman S, Rastas P, Zheng C, Muñoz DS, Meidanis J, Paschoal AR, Bawin Y, Krabbenhoft TJ, Wang ZQ, Fleck SJ, Aussel R, Bellanger L, Charpagne A, Fournier C, Kassam M, Lefebvre G, Métairon S, Moine D, Rigoreau M, Stolte J, Hamon P, Couturon E, Tranchant-Dubreuil C, Mukherjee M, Lan T, Engelhardt J, Stadler P, Correia De Lemos SM, Suzuki SI, Sumirat U, Wai CM, Dauchot N, Orozco-Arias S, Garavito A, Kiwuka C, Musoli P, Nalukenge A, Guichoux E, Reinout H, Smit M, Carretero-Paulet L, Filho OG, Braghini MT, Padilha L, Sera GH, Ruttink T, Henry R, Marraccini P, Van de Peer Y, Andrade A, Domingues D, Giuliano G, Mueller L, Pereira LF, Plaisance S, Poncet V, Rombauts S, Sankoff D, Albert VA, Crouzillat D, de Kochko A, Descombes P. The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars. Nat Genet 2024; 56:721-731. [PMID: 38622339 PMCID: PMC11018527 DOI: 10.1038/s41588-024-01695-w] [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: 05/10/2022] [Accepted: 02/23/2024] [Indexed: 04/17/2024]
Abstract
Coffea arabica, an allotetraploid hybrid of Coffea eugenioides and Coffea canephora, is the source of approximately 60% of coffee products worldwide, and its cultivated accessions have undergone several population bottlenecks. We present chromosome-level assemblies of a di-haploid C. arabica accession and modern representatives of its diploid progenitors, C. eugenioides and C. canephora. The three species exhibit largely conserved genome structures between diploid parents and descendant subgenomes, with no obvious global subgenome dominance. We find evidence for a founding polyploidy event 350,000-610,000 years ago, followed by several pre-domestication bottlenecks, resulting in narrow genetic variation. A split between wild accessions and cultivar progenitors occurred ~30.5 thousand years ago, followed by a period of migration between the two populations. Analysis of modern varieties, including lines historically introgressed with C. canephora, highlights their breeding histories and loci that may contribute to pathogen resistance, laying the groundwork for future genomics-based breeding of C. arabica.
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Affiliation(s)
- Jarkko Salojärvi
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland.
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore.
| | - Aditi Rambani
- Boyce Thompson Institute, Cornell University, Ithaca, NY, USA
| | - Zhe Yu
- Department of Mathematics and Statistics, University of Ottawa, Ottawa, Ontario, Canada
| | - Romain Guyot
- Institut de Recherche pour le Développement (IRD), Université de Montpellier, Montpellier, France
- Department of Electronics and Automation, Universidad Autónoma de Manizales, Manizales, Colombia
| | - Susan Strickler
- Boyce Thompson Institute, Cornell University, Ithaca, NY, USA
| | - Maud Lepelley
- Société des Produits Nestlé SA, Nestlé Research, Tours, France
| | - Cui Wang
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland
| | - Sitaram Rajaraman
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland
| | - Pasi Rastas
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Chunfang Zheng
- Department of Mathematics and Statistics, University of Ottawa, Ottawa, Ontario, Canada
| | - Daniella Santos Muñoz
- Department of Mathematics and Statistics, University of Ottawa, Ottawa, Ontario, Canada
| | - João Meidanis
- Institute of Computing, University of Campinas, Campinas, Brazil
| | - Alexandre Rossi Paschoal
- Department of Computer Science, The Federal University of Technology - Paraná (UTFPR), Cornélio Procópio, Brazil
| | - Yves Bawin
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Melle, Belgium
| | | | - Zhen Qin Wang
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, USA
| | - Steven J Fleck
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, USA
| | - Rudy Aussel
- Société des Produits Nestlé SA, Nestlé Research, Tours, France
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université, Marseille, France
| | | | - Aline Charpagne
- Société des Produits Nestlé SA, Nestlé Research, Lausanne, Switzerland
| | - Coralie Fournier
- Société des Produits Nestlé SA, Nestlé Research, Lausanne, Switzerland
| | - Mohamed Kassam
- Société des Produits Nestlé SA, Nestlé Research, Lausanne, Switzerland
| | - Gregory Lefebvre
- Société des Produits Nestlé SA, Nestlé Research, Lausanne, Switzerland
| | - Sylviane Métairon
- Société des Produits Nestlé SA, Nestlé Research, Lausanne, Switzerland
| | - Déborah Moine
- Société des Produits Nestlé SA, Nestlé Research, Lausanne, Switzerland
| | - Michel Rigoreau
- Société des Produits Nestlé SA, Nestlé Research, Tours, France
| | - Jens Stolte
- Société des Produits Nestlé SA, Nestlé Research, Lausanne, Switzerland
| | - Perla Hamon
- Institut de Recherche pour le Développement (IRD), Université de Montpellier, Montpellier, France
| | - Emmanuel Couturon
- Institut de Recherche pour le Développement (IRD), Université de Montpellier, Montpellier, France
| | | | - Minakshi Mukherjee
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, USA
| | - Tianying Lan
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, USA
| | - Jan Engelhardt
- Department of Computer Science, University of Leipzig, Leipzig, Germany
| | - Peter Stadler
- Department of Computer Science, University of Leipzig, Leipzig, Germany
- Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany
| | | | | | - Ucu Sumirat
- Indonesian Coffee and Cocoa Research Institute (ICCRI), Jember, Indonesia
| | - Ching Man Wai
- University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Nicolas Dauchot
- Research Unit in Plant Cellular and Molecular Biology, University of Namur, Namur, Belgium
| | - Simon Orozco-Arias
- Department of Electronics and Automation, Universidad Autónoma de Manizales, Manizales, Colombia
| | - Andrea Garavito
- Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas y Naturales, Universidad de Caldas, Manizales, Colombia
| | - Catherine Kiwuka
- National Agricultural Research Organization (NARO), Entebbe, Uganda
| | - Pascal Musoli
- National Agricultural Research Organization (NARO), Entebbe, Uganda
| | - Anne Nalukenge
- National Agricultural Research Organization (NARO), Entebbe, Uganda
| | - Erwan Guichoux
- Biodiversité Gènes & Communautés, INRA, Bordeaux, France
| | | | - Martin Smit
- Hortus Botanicus Amsterdam, Amsterdam, the Netherlands
| | | | - Oliveiro Guerreiro Filho
- Instituto Agronômico (IAC) Centro de Café 'Alcides Carvalho', Fazenda Santa Elisa, Campinas, Brazil
| | - Masako Toma Braghini
- Instituto Agronômico (IAC) Centro de Café 'Alcides Carvalho', Fazenda Santa Elisa, Campinas, Brazil
| | - Lilian Padilha
- Embrapa Café/Instituto Agronômico (IAC) Centro de Café 'Alcides Carvalho', Fazenda Santa Elisa, Campinas, Brazil
| | | | - Tom Ruttink
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Melle, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Robert Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Queensland, Australia
| | - Pierre Marraccini
- CIRAD - UMR DIADE (IRD-CIRAD-Université de Montpellier) BP 64501, Montpellier, France
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, China
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Alan Andrade
- Embrapa Café/Inovacafé Laboratory of Molecular Genetics Campus da UFLA-MG, Lavras, Brazil
| | - Douglas Domingues
- Group of Genomics and Transcriptomes in Plants, São Paulo State University, UNESP, Rio Claro, Brazil
| | - Giovanni Giuliano
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development, ENEA Casaccia Research Center, Rome, Italy
| | - Lukas Mueller
- Boyce Thompson Institute, Cornell University, Ithaca, NY, USA
| | - Luiz Filipe Pereira
- Embrapa Café/Lab. Biotecnologia, Área de Melhoramento Genético, Londrina, Brazil
| | | | - Valerie Poncet
- Institut de Recherche pour le Développement (IRD), Université de Montpellier, Montpellier, France
| | - Stephane Rombauts
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - David Sankoff
- Department of Mathematics and Statistics, University of Ottawa, Ottawa, Ontario, Canada
| | - Victor A Albert
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, USA.
| | | | - Alexandre de Kochko
- Institut de Recherche pour le Développement (IRD), Université de Montpellier, Montpellier, France.
| | - Patrick Descombes
- Société des Produits Nestlé SA, Nestlé Research, Lausanne, Switzerland.
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de Hoon M, Bonetti A, Plessy C, Ando Y, Hon CC, Ishizu Y, Itoh M, Kato S, Lin D, Maekawa S, Murata M, Nishiyori H, Shin JW, Stolte J, Suzuki AM, Tagami M, Takahashi H, Thongjuea S, Forrest ARR, Hayashizaki Y, Kere J, Carninci P. Deep sequencing of short capped RNAs reveals novel families of noncoding RNAs. Genome Res 2022; 32:gr.276647.122. [PMID: 35961773 PMCID: PMC9528987 DOI: 10.1101/gr.276647.122] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 08/09/2022] [Indexed: 12/03/2022]
Abstract
In eukaryotes, capped RNAs include long transcripts such as messenger RNAs and long noncoding RNAs, as well as shorter transcripts such as spliceosomal RNAs, small nucleolar RNAs, and enhancer RNAs. Long capped transcripts can be profiled using cap analysis gene expression (CAGE) sequencing and other methods. Here, we describe a sequencing library preparation protocol for short capped RNAs, apply it to a differentiation time course of the human cell line THP-1, and systematically compare the landscape of short capped RNAs to that of long capped RNAs. Transcription initiation peaks associated with genes in the sense direction have a strong preference to produce either long or short capped RNAs, with one out of six peaks detected in the short capped RNA libraries only. Gene-associated short capped RNAs have highly specific 3' ends, typically overlapping splice sites. Enhancers also preferentially generate either short or long capped RNAs, with 10% of enhancers observed in the short capped RNA libraries only. Enhancers producing either short or long capped RNAs show enrichment for GWAS-associated disease SNPs. We conclude that deep sequencing of short capped RNAs reveals new families of noncoding RNAs and elucidates the diversity of transcripts generated at known and novel promoters and enhancers.
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Affiliation(s)
- Michiel de Hoon
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Alessandro Bonetti
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Charles Plessy
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Yoshinari Ando
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Chung-Chau Hon
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Yuri Ishizu
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Masayoshi Itoh
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Saitama 351-0198, Japan
| | - Sachi Kato
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Dongyan Lin
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
- Integrated Program in Neuroscience, McGill University, Montreal, Quebec H3A 1A1, Canada
- Mila, Montreal, Quebec H2S 3H1, Canada
| | - Sho Maekawa
- RIKEN Omics Science Center (OSC), Yokohama, Kanagawa 230-0045, Japan
| | - Mitsuyoshi Murata
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Hiromi Nishiyori
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Jay W Shin
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, 138632, Singapore
| | - Jens Stolte
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Ana Maria Suzuki
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Michihira Tagami
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Hazuki Takahashi
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Supat Thongjuea
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Alistair R R Forrest
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Nedlands, Perth, Western Australia 6009, Australia
| | - Yoshihide Hayashizaki
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Saitama 351-0198, Japan
- RIKEN Omics Science Center (OSC), Yokohama, Kanagawa 230-0045, Japan
| | - Juha Kere
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge 14157, Sweden
- Stem Cells and Metabolism Research Program, University of Helsinki and Folkhälsan Research Center, Helsinki 00290, Finland
| | - Piero Carninci
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
- Human Technopole, Milan 20157, Italy
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3
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Rhein P, Desjardins EM, Rong P, Ahwazi D, Bonhoure N, Stolte J, Santos MD, Ovens AJ, Ehrlich AM, Sanchez Garcia JL, Ouyang Q, Yabut JM, Kjolby M, Membrez M, Jessen N, Oakhill JS, Treebak JT, Maire P, Scott JW, Sanders MJ, Descombes P, Chen S, Steinberg GR, Sakamoto K. Compound- and fiber type-selective requirement of AMPKγ3 for insulin-independent glucose uptake in skeletal muscle. Mol Metab 2021; 51:101228. [PMID: 33798773 PMCID: PMC8381060 DOI: 10.1016/j.molmet.2021.101228] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 03/21/2021] [Accepted: 03/26/2021] [Indexed: 12/20/2022] Open
Abstract
Objective The metabolic master-switch AMP-activated protein kinase (AMPK) mediates insulin-independent glucose uptake in muscle and regulates the metabolic activity of brown and beige adipose tissue (BAT). The regulatory AMPKγ3 isoform is uniquely expressed in skeletal muscle and potentially in BAT. Herein, we investigated the role that AMPKγ3 plays in mediating skeletal muscle glucose uptake and whole-body glucose clearance in response to small-molecule activators that act on AMPK via distinct mechanisms. We also assessed whether γ3 plays a role in adipose thermogenesis and browning. Methods Global AMPKγ3 knockout (KO) mice were generated. A systematic whole-body, tissue, and molecular phenotyping linked to glucose homeostasis was performed in γ3 KO and wild-type (WT) mice. Glucose uptake in glycolytic and oxidative skeletal muscle ex vivo as well as blood glucose clearance in response to small molecule AMPK activators that target the nucleotide-binding domain of the γ subunit (AICAR) and allosteric drug and metabolite (ADaM) site located at the interface of the α and β subunit (991, MK-8722) were assessed. Oxygen consumption, thermography, and molecular phenotyping with a β3-adrenergic receptor agonist (CL-316,243) treatment were performed to assess BAT thermogenesis, characteristics, and function. Results Genetic ablation of γ3 did not affect body weight, body composition, physical activity, and parameters associated with glucose homeostasis under chow or high-fat diet. γ3 deficiency had no effect on fiber-type composition, mitochondrial content and components, or insulin-stimulated glucose uptake in skeletal muscle. Glycolytic muscles in γ3 KO mice showed a partial loss of AMPKα2 activity, which was associated with reduced levels of AMPKα2 and β2 subunit isoforms. Notably, γ3 deficiency resulted in a selective loss of AICAR-, but not MK-8722-induced blood glucose-lowering in vivo and glucose uptake specifically in glycolytic muscle ex vivo. We detected γ3 in BAT and found that it preferentially interacts with α2 and β2. We observed no differences in oxygen consumption, thermogenesis, morphology of BAT and inguinal white adipose tissue (iWAT), or markers of BAT activity between WT and γ3 KO mice. Conclusions These results demonstrate that γ3 plays a key role in mediating AICAR- but not ADaM site binding drug-stimulated blood glucose clearance and glucose uptake specifically in glycolytic skeletal muscle. We also showed that γ3 is dispensable for β3-adrenergic receptor agonist-induced thermogenesis and browning of iWAT. Loss of AMPKγ3 reduces glucose uptake in glycolytic skeletal muscle and whole-body glucose clearance with AMP-mimetic drug. γ3 is not required for muscle glucose uptake and whole-body glucose clearance with ADaM site-targeted allosteric activators. γ3 is present and forms a trimeric complex with α2 and β2 in brown adipose tissue. γ3 is dispensable for adipose thermogenesis and browning in response to a β3-adrenergic receptor agonist.
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Affiliation(s)
- Philipp Rhein
- Nestlé Research, Société des Produits Nestlé S.A., EPFL Innovation Park, Lausanne, 1015, Switzerland; School of Life Sciences, EPFL Innovation Park, Lausanne, 1015, Switzerland
| | - Eric M Desjardins
- Centre for Metabolism, Obesity, and Diabetes Research, McMaster University, Hamilton, ON, L8N3Z5, Canada; Department of Medicine and Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, L8N3Z5, Canada
| | - Ping Rong
- MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, School of Medicine, Nanjing University, Nanjing, 210061, China
| | - Danial Ahwazi
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Nicolas Bonhoure
- Nestlé Research, Société des Produits Nestlé S.A., EPFL Innovation Park, Lausanne, 1015, Switzerland
| | - Jens Stolte
- Nestlé Research, Société des Produits Nestlé S.A., EPFL Innovation Park, Lausanne, 1015, Switzerland
| | - Matthieu D Santos
- Université de Paris, Institut Cochin, INSERM, CNRS, 75014, Paris, France
| | - Ashley J Ovens
- Metabolic Signalling Laboratory, St Vincent's Institute of Medical Research, School of Medicine, University of Melbourne, Fitzroy, VIC, 3065, Australia; Mary MacKillop Institute for Health Research, Australian Catholic University, Melbourne, VIC, 3000, Australia
| | - Amy M Ehrlich
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, 2200, Denmark
| | - José L Sanchez Garcia
- Nestlé Research, Société des Produits Nestlé S.A., EPFL Innovation Park, Lausanne, 1015, Switzerland
| | - Qian Ouyang
- MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, School of Medicine, Nanjing University, Nanjing, 210061, China
| | - Julian M Yabut
- Centre for Metabolism, Obesity, and Diabetes Research, McMaster University, Hamilton, ON, L8N3Z5, Canada; Department of Medicine and Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, L8N3Z5, Canada
| | - Mads Kjolby
- Department of Biomedicine, Aarhus University, Aarhus, Denmark; Department of Clinical Pharmacology and Steno Diabetes Center Aarhus, Aarhus University Hospital, Aarhus, Denmark
| | - Mathieu Membrez
- Nestlé Research, Société des Produits Nestlé S.A., EPFL Innovation Park, Lausanne, 1015, Switzerland
| | - Niels Jessen
- Department of Biomedicine, Aarhus University, Aarhus, Denmark; Department of Clinical Pharmacology and Steno Diabetes Center Aarhus, Aarhus University Hospital, Aarhus, Denmark
| | - Jonathan S Oakhill
- Metabolic Signalling Laboratory, St Vincent's Institute of Medical Research, School of Medicine, University of Melbourne, Fitzroy, VIC, 3065, Australia; Mary MacKillop Institute for Health Research, Australian Catholic University, Melbourne, VIC, 3000, Australia
| | - Jonas T Treebak
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Pascal Maire
- Université de Paris, Institut Cochin, INSERM, CNRS, 75014, Paris, France
| | - John W Scott
- Mary MacKillop Institute for Health Research, Australian Catholic University, Melbourne, VIC, 3000, Australia; Protein Chemistry and Metabolism Unit, St Vincent's Institute of Medical Research, Fitzroy, VIC, 3065, Australia; The Florey Institute of Neuroscience and Mental Health, Parkville, VIC, 3052, Australia
| | - Matthew J Sanders
- Nestlé Research, Société des Produits Nestlé S.A., EPFL Innovation Park, Lausanne, 1015, Switzerland
| | - Patrick Descombes
- Nestlé Research, Société des Produits Nestlé S.A., EPFL Innovation Park, Lausanne, 1015, Switzerland
| | - Shuai Chen
- MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, School of Medicine, Nanjing University, Nanjing, 210061, China
| | - Gregory R Steinberg
- Centre for Metabolism, Obesity, and Diabetes Research, McMaster University, Hamilton, ON, L8N3Z5, Canada; Department of Medicine and Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, L8N3Z5, Canada
| | - Kei Sakamoto
- Nestlé Research, Société des Produits Nestlé S.A., EPFL Innovation Park, Lausanne, 1015, Switzerland; Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, 2200, Denmark.
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4
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Havas KM, Milchevskaya V, Radic K, Alladin A, Kafkia E, Garcia M, Stolte J, Klaus B, Rotmensz N, Gibson TJ, Burwinkel B, Schneeweiss A, Pruneri G, Patil KR, Sotillo R, Jechlinger M. Metabolic shifts in residual breast cancer drive tumor recurrence. J Clin Invest 2017; 127:2091-2105. [PMID: 28504653 DOI: 10.1172/jci89914] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 03/16/2017] [Indexed: 12/22/2022] Open
Abstract
Tumor recurrence is the leading cause of breast cancer-related death. Recurrences are largely driven by cancer cells that survive therapeutic intervention. This poorly understood population is referred to as minimal residual disease. Here, using mouse models that faithfully recapitulate human disease together with organoid cultures, we have demonstrated that residual cells acquire a transcriptionally distinct state from normal epithelium and primary tumors. Gene expression changes and functional characterization revealed altered lipid metabolism and elevated ROS as hallmarks of the cells that survive tumor regression. These residual cells exhibited increased oxidative DNA damage, potentiating the acquisition of somatic mutations during hormonal-induced expansion of the mammary cell population. Inhibition of either cellular fatty acid synthesis or fatty acid transport into mitochondria reduced cellular ROS levels and DNA damage, linking these features to lipid metabolism. Direct perturbation of these hallmarks in vivo, either by scavenging ROS or by halting the cyclic mammary cell population expansion, attenuated tumor recurrence. Finally, these observations were mirrored in transcriptomic and histological signatures of residual cancer cells from neoadjuvant-treated breast cancer patients. These results highlight the potential of lipid metabolism and ROS as therapeutic targets for reducing tumor recurrence in breast cancer patients.
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Affiliation(s)
- Kristina M Havas
- EMBL Monterotondo, Adriano Buzzati-Traverso Campus, Monterotondo, Italy.,Istituto Firc di Oncologia Molecolare (IFOM) the Italian Foundation for Cancer Research (FIRC) Institute of Molecular Oncology, Milan, Italy
| | | | | | | | | | | | - Jens Stolte
- EMBL Monterotondo, Adriano Buzzati-Traverso Campus, Monterotondo, Italy
| | | | - Nicole Rotmensz
- Division of Epidemiology and Biostatistics European Institute of Oncology, Milan, Italy
| | | | - Barbara Burwinkel
- Molecular Biology of Breast Cancer, University Women's Clinic, Heidelberg, Germany
| | - Andreas Schneeweiss
- Gynecologic Oncology, National Center for Tumor Diseases, University of Heidelberg, Heidelberg, Germany
| | - Giancarlo Pruneri
- Department of Pathology, Biobank for Translational Medicine Unit, European Institute of Oncology, Milan and University of Milan, School of Medicine, Milan, Italy
| | | | - Rocio Sotillo
- EMBL Monterotondo, Adriano Buzzati-Traverso Campus, Monterotondo, Italy.,Division of Molecular Thoracic Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Translational Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), Heidelberg, Germany
| | - Martin Jechlinger
- EMBL Monterotondo, Adriano Buzzati-Traverso Campus, Monterotondo, Italy.,EMBL Heidelberg, Heidelberg, Germany
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5
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van den Berg F, Tiktak A, Heuvelink GBM, Burgers SLGE, Brus DJ, de Vries F, Stolte J, Kroes JG. Propagation of uncertainties in soil and pesticide properties to pesticide leaching. J Environ Qual 2012; 41:253-261. [PMID: 22218193 DOI: 10.2134/jeq2011.0167] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
In the new Dutch decision tree for the evaluation of pesticide leaching to groundwater, spatially distributed soil data are used by the GeoPEARL model to calculate the 90th percentile of the spatial cumulative distribution function of the leaching concentration in the area of potential usage (SP90). Until now it was not known to what extent uncertainties in soil and pesticide properties propagate to spatially aggregated parameters like the SP90. A study was performed to quantify the uncertainties in soil and pesticide properties and to analyze their contribution to the uncertainty in SP90. First, uncertainties in the soil and pesticide properties were quantified. Next, a regular grid sample of points covering the whole of the agricultural area in the Netherlands was randomly selected. At the grid nodes, realizations from the probability distributions of the uncertain inputs were generated and used as input to a Monte Carlo uncertainty propagation analysis. The analysis showed that the uncertainty concerning the SP90 is 10 times smaller than the uncertainty about the leaching concentration at individual point locations. The parameters that contribute most to the uncertainty about the SP90 are, however, the same as the parameters that contribute most to uncertainty about the leaching concentration at individual point locations (e.g., the transformation half-life in soil and the coefficient of sorption on organic matter). Taking uncertainties in soil and pesticide properties into account further leads to a systematic increase of the predicted SP90. The important implication for pesticide regulation is that the leaching concentration is systematically underestimated when these uncertainties are ignored.
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Affiliation(s)
- F van den Berg
- Environmental Sciences Group, Wageningen Univ. and Research Centre, 6700 AA Wageningen, the Netherlands.
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Mueller C, Schrag M, Crofton A, Stolte J, Muckenthaler MU, Magaki S, Kirsch W. Altered serum iron and copper homeostasis predicts cognitive decline in mild cognitive impairment. J Alzheimers Dis 2012; 29:341-50. [PMID: 22232013 PMCID: PMC3596019 DOI: 10.3233/jad-2011-111841] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [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] [Indexed: 11/15/2022]
Abstract
Alzheimer's disease (AD) brain is marked by severe neuronal death which has been partly attributed to increased oxidative stress. The pathophysiology accounting for this free radical injury is not well-delineated at this point, but one hypothesis is that a derangement in transition metal metabolism contributes to the process. We tested the hypothesis that peripheral derangement of transition metal metabolism is present early in the dementing process. We analyzed non-heme iron and copper levels in serum from subjects with normal cognition, mild cognitive impairment, and early stage senile dementia and followed these subjects over 5 years. An increase in the ratio of serum copper to non-heme iron levels predicted which subjects with mild cognitive impairment would progress to dementia versus those that would remain cognitively stable. This increase did not correlate with changes in expression of iron regulatory protein 2 or selected downstream targets in peripheral lymphocytes. A cDNA-based microarray (IronChip) containing genes relevant to iron and copper metabolism was used to assess transition metal metabolism in circulating lymphocytes from cognitively normal and demented subjects. No gene was identified as being dysregulated more than 2-fold, and verification using quantitative RT-PCR demonstrated no significant changes in expression for ALAS2, FOS, and CTR1. The increased ratio of serum copper to serum iron prior to dementia has potential as a biomarker for cognitive decline and mirrors other changes in serum previously reported by others, but iron and copper metabolism pathways appear to be broadly unaffected in peripheral blood in AD.
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Affiliation(s)
- Claudius Mueller
- Neurosurgery Center for Research, Loma Linda University, Loma Linda, CA, USA
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA
| | - Matthew Schrag
- Neurosurgery Center for Research, Loma Linda University, Loma Linda, CA, USA
- Department of Neurology, Yale University, New Haven, CT, USA
| | - Andrew Crofton
- Neurosurgery Center for Research, Loma Linda University, Loma Linda, CA, USA
- Department of Human Anatomy and Pathology, Loma Linda University, Loma Linda, CA, USA
| | - Jens Stolte
- Molecular Medicine, University of Heidelberg, Heidelberg, Germany
| | | | - Shino Magaki
- Neurosurgery Center for Research, Loma Linda University, Loma Linda, CA, USA
- Department of Pathology, University of California, Los Angeles, CA, USA
| | - Wolff Kirsch
- Neurosurgery Center for Research, Loma Linda University, Loma Linda, CA, USA
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7
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Rodrigues PN, Gomes SS, Neves JV, Gomes-Pereira S, Correia-Neves M, Nunes-Alves C, Stolte J, Sanchez M, Appelberg R, Muckenthaler MU, Gomes MS. Mycobacteria-induced anaemia revisited: A molecular approach reveals the involvement of NRAMP1 and lipocalin-2, but not of hepcidin. Immunobiology 2011; 216:1127-34. [DOI: 10.1016/j.imbio.2011.04.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2010] [Revised: 04/11/2011] [Accepted: 04/13/2011] [Indexed: 01/08/2023]
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Castoldi M, Vujic Spasic M, Altamura S, Elmén J, Lindow M, Kiss J, Stolte J, Sparla R, D'Alessandro LA, Klingmüller U, Fleming RE, Longerich T, Gröne HJ, Benes V, Kauppinen S, Hentze MW, Muckenthaler MU. The liver-specific microRNA miR-122 controls systemic iron homeostasis in mice. J Clin Invest 2011; 121:1386-96. [PMID: 21364282 DOI: 10.1172/jci44883] [Citation(s) in RCA: 186] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2010] [Accepted: 01/05/2011] [Indexed: 12/12/2022] Open
Abstract
Systemic iron homeostasis is mainly controlled by the liver through synthesis of the peptide hormone hepcidin (encoded by Hamp), the key regulator of duodenal iron absorption and macrophage iron release. Here we show that the liver-specific microRNA miR-122 is important for regulating Hamp mRNA expression and tissue iron levels. Efficient and specific depletion of miR-122 by injection of a locked-nucleic-acid-modified (LNA-modified) anti-miR into WT mice caused systemic iron deficiency, characterized by reduced plasma and liver iron levels, mildly impaired hematopoiesis, and increased extramedullary erythropoiesis in the spleen. Moreover, miR-122 inhibition increased the amount of mRNA transcribed by genes that control systemic iron levels, such as hemochromatosis (Hfe), hemojuvelin (Hjv), bone morphogenetic protein receptor type 1A (Bmpr1a), and Hamp. Importantly, miR-122 directly targeted the 3′ untranslated region of 2 mRNAs that encode activators of hepcidin expression, Hfe and Hjv. These data help to explain the increased Hamp mRNA levels and subsequent iron deficiency in mice with reduced miR-122 levels and establish a direct mechanistic link between miR-122 and the regulation of systemic iron metabolism.
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Affiliation(s)
- Mirco Castoldi
- Department of Pediatric Hematology, Oncology, and Immunology, University of Heidelberg, Heidelberg, Germany
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9
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Gavriouchkina D, Fischer S, Ivacevic T, Stolte J, Benes V, Dekens MPS. Thyrotroph embryonic factor regulates light-induced transcription of repair genes in zebrafish embryonic cells. PLoS One 2010; 5:e12542. [PMID: 20830285 PMCID: PMC2935359 DOI: 10.1371/journal.pone.0012542] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2010] [Accepted: 07/27/2010] [Indexed: 11/30/2022] Open
Abstract
Numerous responses are triggered by light in the cell. How the light signal is detected and transduced into a cellular response is still an enigma. Each zebrafish cell has the capacity to directly detect light, making this organism particularly suitable for the study of light dependent transcription. To gain insight into the light signalling mechanism we identified genes that are activated by light exposure at an early embryonic stage, when specialised light sensing organs have not yet formed. We screened over 14,900 genes using micro-array GeneChips, and identified 19 light-induced genes that function primarily in light signalling, stress response, and DNA repair. Here we reveal that PAR Response Elements are present in all promoters of the light-induced genes, and demonstrate a pivotal role for the PAR bZip transcription factor Thyrotroph embryonic factor (Tef) in regulating the majority of light-induced genes. We show that tefβ transcription is directly regulated by light while transcription of tefα is under circadian clock control at later stages of development. These data leads us to propose their involvement in light-induced UV tolerance in the zebrafish embryo.
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Affiliation(s)
- Daria Gavriouchkina
- Genomics Core Unit, European Molecular Biology Laboratory, Heidelberg, Federal Republic of Germany
| | - Sabine Fischer
- Genomics Core Unit, European Molecular Biology Laboratory, Heidelberg, Federal Republic of Germany
| | - Tomi Ivacevic
- Genomics Core Unit, European Molecular Biology Laboratory, Heidelberg, Federal Republic of Germany
| | - Jens Stolte
- Genomics Core Unit, European Molecular Biology Laboratory, Heidelberg, Federal Republic of Germany
| | - Vladimir Benes
- Genomics Core Unit, European Molecular Biology Laboratory, Heidelberg, Federal Republic of Germany
- * E-mail: (MPSD); (VB)
| | - Marcus P. S. Dekens
- Genomics Core Unit, European Molecular Biology Laboratory, Heidelberg, Federal Republic of Germany
- * E-mail: (MPSD); (VB)
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Marro S, Chiabrando D, Messana E, Stolte J, Turco E, Tolosano E, Muckenthaler MU. Heme controls ferroportin1 (FPN1) transcription involving Bach1, Nrf2 and a MARE/ARE sequence motif at position -7007 of the FPN1 promoter. Haematologica 2010; 95:1261-8. [PMID: 20179090 DOI: 10.3324/haematol.2009.020123] [Citation(s) in RCA: 209] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Macrophages of the reticuloendothelial system play a key role in recycling iron from hemoglobin of senescent or damaged erythrocytes. Heme oxygenase 1 degrades the heme moiety and releases inorganic iron that is stored in ferritin or exported to the plasma via the iron export protein ferroportin. In the plasma, iron binds to transferrin and is made available for de novo red cell synthesis. The aim of this study was to gain insight into the regulatory mechanisms that control the transcriptional response of iron export protein ferroportin to hemoglobin in macrophages. DESIGN AND METHODS Iron export protein ferroportin mRNA expression was analyzed in RAW264.7 mouse macrophages in response to hemoglobin, heme, ferric ammonium citrate or protoporphyrin treatment or to siRNA mediated knockdown or overexpression of Btb And Cnc Homology 1 or nuclear accumulation of Nuclear Factor Erythroid 2-like. Iron export protein ferroportin promoter activity was analyzed using reporter constructs that contain specific truncations of the iron export protein ferroportin promoter or mutations in a newly identified MARE/ARE element. RESULTS We show that iron export protein ferroportin is transcriptionally co-regulated with heme oxygenase 1 by heme, a degradation product of hemoglobin. The protoporphyrin ring of heme is sufficient to increase iron export protein ferroportin transcriptional activity while the iron released from the heme moiety controls iron export protein ferroportin translation involving the IRE in the 5'untranslated region. Transcription of iron export protein ferroportin is inhibited by Btb and Cnc Homology 1 and activated by Nuclear Factor Erythroid 2-like involving a MARE/ARE element located at position -7007/-7016 of the iron export protein ferroportin promoter. CONCLUSIONS This finding suggests that heme controls a macrophage iron recycling regulon involving Btb and Cnc Homology 1 and Nuclear Factor Erythroid 2-like to assure the coordinated degradation of heme by heme oxygenase 1, iron storage and detoxification by ferritin, and iron export by iron export protein ferroportin.
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Affiliation(s)
- Samuele Marro
- Department of Pediatric Oncology, University of Heidelberg, Im Neuenheimer Feld 153, 69120 Heidelberg, Germany
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Vujić Spasić M, Kiss J, Herrmann T, Galy B, Martinache S, Stolte J, Gröne HJ, Stremmel W, Hentze MW, Muckenthaler MU. Hfe acts in hepatocytes to prevent hemochromatosis. Cell Metab 2008; 7:173-8. [PMID: 18249176 DOI: 10.1016/j.cmet.2007.11.014] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/28/2007] [Revised: 11/07/2007] [Accepted: 11/29/2007] [Indexed: 10/22/2022]
Abstract
Hereditary hemochromatosis (HH) is a prevalent, potentially fatal disorder of iron metabolism hallmarked by intestinal hyperabsorption of iron, hyperferremia, and hepatic iron overload. In both humans and mice, type I HH is associated with mutations in the broadly expressed HFE/Hfe gene. To identify where Hfe acts to prevent HH, we generated mice with tissue-specific Hfe ablations. This work demonstrates that local Hfe expression in hepatocytes serves to maintain physiological iron homeostasis, answering a long-standing question in medicine and explaining earlier clinical observations.
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Affiliation(s)
- Maja Vujić Spasić
- Department of Pediatric Oncology, Hematology and Immunology, University Hospital of Heidelberg, 69120 Heidelberg, Germany
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12
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Marro S, Barisani D, Chiabrando D, Fagoonee S, Muckenthaler MU, Stolte J, Meneveri R, Haile D, Silengo L, Altruda F, Tolosano E. Lack of haptoglobin affects iron transport across duodenum by modulating ferroportin expression. Gastroenterology 2007; 133:1261-1271. [PMID: 17919498 DOI: 10.1053/j.gastro.2007.07.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2006] [Accepted: 06/28/2007] [Indexed: 12/02/2022]
Abstract
BACKGROUND & AIMS Haptoglobin is an acute phase protein responsible for the recovery of free hemoglobin from plasma. Haptoglobin-null mice were previously shown to have an altered heme-iron distribution, thus reproducing what occurs in humans in cases of congenital or acquired anhaptoglobinemia. Here, we report the analysis of iron homeostasis in haptoglobin-null mice. METHODS Iron absorption was measured in tied-off duodenal segments. Iron stores were evaluated on tissue homogenates and sections. The expression of molecules involved in iron homeostasis was analyzed at the protein and messenger RNA levels both in mice and in murine RAW264.7 macrophages stimulated in vitro with hemoglobin. RESULTS Analysis of intestinal iron transport reveals that haptoglobin-null mice export significantly more iron from the duodenal mucosa to plasma compared with control counterparts. Increased iron export from the duodenum correlates with increased duodenal expression of ferroportin, both at the protein and messenger RNA levels, whereas hepatic hepcidin expression remains unchanged. Up-regulation of the ferroportin transcript, but not of the protein, also occurs in haptoglobin-null spleen macrophages, which accumulate free hemoglobin-derived iron. Finally, we demonstrate that hemoglobin induces ferroportin expression in RAW264.7 cells. CONCLUSIONS Taking together these data, we suggest that haptoglobin, by controlling plasma levels of hemoglobin, participates in the regulation of ferroportin expression, thus contributing to the regulation of iron transfer from duodenal mucosa to plasma.
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Affiliation(s)
- Samuele Marro
- Department of Genetics, Biology and Biochemistry, and Molecular Biotechnology Center, University of Torino, Torino, Italy
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Vujic Spasic M, Kiss J, Herrmann T, Kessler R, Stolte J, Galy B, Rathkolb B, Wolf E, Stremmel W, Hentze MW, Muckenthaler MU. Physiologic systemic iron metabolism in mice deficient for duodenal Hfe. Blood 2007; 109:4511-7. [PMID: 17264297 DOI: 10.1182/blood-2006-07-036186] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Mutations in the Hfe gene result in hereditary hemochromatosis (HH), a disorder characterized by increased duodenal iron absorption and tissue iron overload. Identification of a direct interaction between Hfe and transferrin receptor 1 in duodenal cells led to the hypothesis that the lack of functional Hfe in the duodenum affects TfR1-mediated serosal uptake of iron and misprogramming of the iron absorptive cells. Contrasting this view, Hfe deficiency causes inappropriately low expression of the hepatic iron hormone hepcidin, which causes increased duodenal iron absorption. We specifically ablated Hfe expression in mouse enterocytes using Cre/LoxP technology. Mice with efficient deletion of Hfe in crypt- and villi-enterocytes maintain physiologic iron metabolism with wild-type unsaturated iron binding capacity, hepatic iron levels, and hepcidin mRNA expression. Furthermore, the expression of genes encoding the major intestinal iron transporters is unchanged in duodenal Hfe-deficient mice. Our data demonstrate that intestinal Hfe is dispensable for the physiologic control of systemic iron homeostasis under steady state conditions. These findings exclude a primary role for duodenal Hfe in the pathogenesis of HH and support the model according to which Hfe is required for appropriate expression of the "iron hormone" hepcidin which then controls intestinal iron absorption.
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Affiliation(s)
- Maja Vujic Spasic
- Molecular Medicine Partnership Unit, University of Heidelberg, Germany
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Verga Falzacappa MV, Vujic Spasic M, Kessler R, Stolte J, Hentze MW, Muckenthaler MU. STAT3 mediates hepatic hepcidin expression and its inflammatory stimulation. Blood 2006; 109:353-8. [PMID: 16946298 DOI: 10.1182/blood-2006-07-033969] [Citation(s) in RCA: 403] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Hepcidin is a key iron-regulatory hormone produced by the liver. Inappropriately low hepcidin levels cause iron overload, while increased hepcidin expression plays an important role in the anemia of inflammation (AI) by restricting intestinal iron absorption and macrophage iron release. Its expression is modulated in response to body iron stores, hypoxia, and inflammatory and infectious stimuli involving at least in part cytokines secreted by macrophages. In this study we established and characterized IL6-mediated hepcidin activation in the human liver cell line Huh7. We show that the proximal 165 bp of the hepcidin promoter is critical for hepcidin activation in response to exogenously administered IL6 or to conditioned medium from the monocyte/macrophage cell line THP-1. Importantly, we show that hepcidin activation by these stimuli requires a STAT3 binding motif located at position -64/-72 of the promoter. The same STAT binding site is also required for high basal-level hepcidin mRNA expression under control culture conditions, and siRNA-mediated RNA knockdown of STAT3 strongly reduces hepcidin mRNA expression. These results identify a missing link in the acute-phase activation of hepcidin and establish STAT3 as a key effector of baseline hepcidin expression and during inflammatory conditions.
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15
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Sanchez M, Galy B, Dandekar T, Bengert P, Vainshtein Y, Stolte J, Muckenthaler MU, Hentze MW. Iron regulation and the cell cycle: identification of an iron-responsive element in the 3'-untranslated region of human cell division cycle 14A mRNA by a refined microarray-based screening strategy. J Biol Chem 2006; 281:22865-74. [PMID: 16760464 DOI: 10.1074/jbc.m603876200] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Iron regulatory proteins (IRPs) 1 and 2 post-transcriptionally control mammalian iron homeostasis by binding to iron-responsive elements (IREs), conserved RNA stem-loop structures located in the 5'- or 3'-untranslated regions of genes involved in iron metabolism (e.g. FTH1, FTL, and TFRC). To identify novel IRE-containing mRNAs, we integrated biochemical, biocomputational, and microarray-based experimental approaches. IRP/IRE messenger ribonucleoproteins were immunoselected, and their mRNA composition was analyzed using an IronChip microarray enriched for genes predicted computationally to contain IRE-like motifs. Among different candidates, this report focuses on a novel IRE located in the 3'-untranslated region of the cell division cycle 14A mRNA. We show that this IRE motif efficiently binds both IRP1 and IRP2. Differential splicing of cell division cycle 14A produces IRE- and non-IRE-containing mRNA isoforms. Interestingly, only the expression of the IRE-containing mRNA isoforms is selectively increased by cellular iron deficiency. This work describes a new experimental strategy to explore the IRE/IRP regulatory network and uncovers a previously unrecognized regulatory link between iron metabolism and the cell cycle.
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Affiliation(s)
- Mayka Sanchez
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
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Brandstetter T, Ninci E, Bettendorf H, Perewusnyk G, Stolte J, Herchenbach D, Sellin D, Wagner E, Köchli OR, Bauknecht T. Granulocyte colony-stimulating factor (G-CSF) receptor gene expression of ovarian carcinoma does not correlate with G-CSF caused cell proliferation. Cancer 2001; 91:1372-83. [PMID: 11283939 DOI: 10.1002/1097-0142(20010401)91:7<1372::aid-cncr1141>3.0.co;2-e] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
BACKGROUND Recombinant human granulocyte colony-stimulating factor (rhG-CSF) is a growth factor commonly used to avoid leukopenia after chemotherapy. Endogenous G-CSF is produced by macrophages and granulocytes that infiltrate tumors. It has been reported that rhG-CSF stimulates the proliferation of several cell lines as well as bladder carcinoma cells. Conversely, in some hematopoietic cell lines such as U-937, WEHI-3B, and K-562 no effect or in some cases a differentiation pattern was found. Moreover, the role of rhG-CSF on the proliferation of solid tumors is not well understood. METHODS In this study, 10 ovarian carcinoma biopsies were characterized for the presence of G-CSF and G-CSF receptor by reverse transcription-polymerase chain reaction (RT-PCR) and immunohistochemical analysis. Proliferation was analyzed by ATP viability assays. RESULTS Performing RT-PCR, these biopsies and four ovarian carcinoma cell lines were analyzed for endogenous G-CSF production, which was found in some biopsies and in all cell lines. Despite the presence of the G-CSF receptor in all biopsies and cell lines, no proliferation was found after rhG-CSF incubation of the cell lines or the tumor samples for 3 and for 6 days, respectively. CONCLUSIONS Summarizing the authors' in vitro studies, rhG-CSF does not affect the proliferation of ovarian carcinoma cells in vitro.
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Affiliation(s)
- T Brandstetter
- Department of Biology II, University of Freiburg, Freiburg Germany.
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17
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Affiliation(s)
- H A Struijker-Boudier
- Department of Pharmacology, Cardiovascular Research Institute Maastricht, University of Limburg, The Netherlands
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18
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Muller-Fahlbusch H, Stolte J. [Focal and systemic causes of disease in the stomatognathic system or psychosomatic disease?]. ZWR 1985; 94:954-60. [PMID: 3869402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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