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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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Raharimalala N, Rombauts S, McCarthy A, Garavito A, Orozco-Arias S, Bellanger L, Morales-Correa AY, Froger S, Michaux S, Berry V, Metairon S, Fournier C, Lepelley M, Mueller L, Couturon E, Hamon P, Rakotomalala JJ, Descombes P, Guyot R, Crouzillat D. The absence of the caffeine synthase gene is involved in the naturally decaffeinated status of Coffea humblotiana, a wild species from Comoro archipelago. Sci Rep 2021; 11:8119. [PMID: 33854089 PMCID: PMC8046976 DOI: 10.1038/s41598-021-87419-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 03/23/2021] [Indexed: 02/02/2023] Open
Abstract
Caffeine is the most consumed alkaloid stimulant in the world. It is synthesized through the activity of three known N-methyltransferase proteins. Here we are reporting on the 422-Mb chromosome-level assembly of the Coffea humblotiana genome, a wild and endangered, naturally caffeine-free, species from the Comoro archipelago. We predicted 32,874 genes and anchored 88.7% of the sequence onto the 11 chromosomes. Comparative analyses with the African Robusta coffee genome (C. canephora) revealed an extensive genome conservation, despite an estimated 11 million years of divergence and a broad diversity of genome sizes within the Coffea genus. In this genome, the absence of caffeine is likely due to the absence of the caffeine synthase gene which converts theobromine into caffeine through an illegitimate recombination mechanism. These findings pave the way for further characterization of caffeine-free species in the Coffea genus and will guide research towards naturally-decaffeinated coffee drinks for consumers.
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Affiliation(s)
- Nathalie Raharimalala
- grid.433118.c0000 0001 2302 6762Centre National de Recherche Appliquée au Développement Rural, BP 1444, 101 Ambatobe, Antananarivo Madagascar
| | - Stephane Rombauts
- grid.5342.00000 0001 2069 7798Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium ,grid.11486.3a0000000104788040VIB Center for Plant Systems Biology, 9052 Gent, Belgium
| | - Andrew McCarthy
- grid.418923.50000 0004 0638 528XEuropean Molecular Biology Laboratory, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France
| | - Andréa Garavito
- grid.7779.e0000 0001 2290 6370Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas y Naturales, Universidad de Caldas, Manizales, Colombia ,Centro de Bioinformática y biología computacional de Colombia – BIOS, Ecoparque los Yarumos, Manizales, Caldas, Colombia
| | - Simon Orozco-Arias
- grid.7779.e0000 0001 2290 6370Department of Systems and Informatics, Universidad de Caldas, Manizales, Colombia ,grid.441739.c0000 0004 0486 2919Universidad Autónoma de Manizales, Manizales, Colombia
| | - Laurence Bellanger
- Nestle Research-Plant Science Research Unit, BP 49716, 37097 Tours Cedex 2, France
| | - Alexa Yadira Morales-Correa
- grid.7779.e0000 0001 2290 6370Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas y Naturales, Universidad de Caldas, Manizales, Colombia
| | - Solène Froger
- Nestle Research-Plant Science Research Unit, BP 49716, 37097 Tours Cedex 2, France
| | - Stéphane Michaux
- Nestle Research-Plant Science Research Unit, BP 49716, 37097 Tours Cedex 2, France
| | - Victoria Berry
- Nestle Research-Plant Science Research Unit, BP 49716, 37097 Tours Cedex 2, France
| | - Sylviane Metairon
- grid.419905.00000 0001 0066 4948Nestle Research, Société des Produits Nestlé SA, 1015 Lausanne, Switzerland
| | - Coralie Fournier
- grid.419905.00000 0001 0066 4948Nestle Research, Société des Produits Nestlé SA, 1015 Lausanne, Switzerland ,grid.8591.50000 0001 2322 4988Present Address: University of Geneva, CMU-Décanat, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland
| | - Maud Lepelley
- Nestle Research-Plant Science Research Unit, BP 49716, 37097 Tours Cedex 2, France
| | - Lukas Mueller
- grid.5386.8000000041936877XBoyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY 14853 USA
| | - Emmanuel Couturon
- grid.121334.60000 0001 2097 0141Institut de Recherche pour le Développement, UMR DIADE, Université de Montpellier, Montpellier, France
| | - Perla Hamon
- grid.121334.60000 0001 2097 0141Institut de Recherche pour le Développement, UMR DIADE, Université de Montpellier, Montpellier, France
| | - Jean-Jacques Rakotomalala
- grid.433118.c0000 0001 2302 6762Centre National de Recherche Appliquée au Développement Rural, BP 1444, 101 Ambatobe, Antananarivo Madagascar
| | - Patrick Descombes
- grid.419905.00000 0001 0066 4948Nestle Research, Société des Produits Nestlé SA, 1015 Lausanne, Switzerland
| | - Romain Guyot
- grid.441739.c0000 0004 0486 2919Universidad Autónoma de Manizales, Manizales, Colombia ,grid.121334.60000 0001 2097 0141Institut de Recherche pour le Développement, UMR DIADE, Université de Montpellier, Montpellier, France
| | - Dominique Crouzillat
- Nestle Research-Plant Science Research Unit, BP 49716, 37097 Tours Cedex 2, France
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Merot‐L'anthoene V, Tournebize R, Darracq O, Rattina V, Lepelley M, Bellanger L, Tranchant‐Dubreuil C, Coulée M, Pégard M, Metairon S, Fournier C, Stoffelen P, Janssens SB, Kiwuka C, Musoli P, Sumirat U, Legnaté H, Kambale J, Ferreira da Costa Neto J, Revel C, de Kochko A, Descombes P, Crouzillat D, Poncet V. Development and evaluation of a genome-wide Coffee 8.5K SNP array and its application for high-density genetic mapping and for investigating the origin of Coffea arabica L. Plant Biotechnol J 2019; 17:1418-1430. [PMID: 30582651 PMCID: PMC6576098 DOI: 10.1111/pbi.13066] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 12/10/2018] [Indexed: 06/09/2023]
Abstract
Coffee species such as Coffea canephora P. (Robusta) and C. arabica L. (Arabica) are important cash crops in tropical regions around the world. C. arabica is an allotetraploid (2n = 4x = 44) originating from a hybridization event of the two diploid species C. canephora and C. eugenioides (2n = 2x = 22). Interestingly, these progenitor species harbour a greater level of genetic variability and are an important source of genes to broaden the narrow Arabica genetic base. Here, we describe the development, evaluation and use of a single-nucleotide polymorphism (SNP) array for coffee trees. A total of 8580 unique and informative SNPs were selected from C. canephora and C. arabica sequencing data, with 40% of the SNP located in annotated genes. In particular, this array contains 227 markers associated to 149 genes and traits of agronomic importance. Among these, 7065 SNPs (~82.3%) were scorable and evenly distributed over the genome with a mean distance of 54.4 Kb between markers. With this array, we improved the Robusta high-density genetic map by adding 1307 SNP markers, whereas 945 SNPs were found segregating in the Arabica mapping progeny. A panel of C. canephora accessions was successfully discriminated and over 70% of the SNP markers were transferable across the three species. Furthermore, the canephora-derived subgenome of C. arabica was shown to be more closely related to C. canephora accessions from northern Uganda than to other current populations. These validated SNP markers and high-density genetic maps will be useful to molecular genetics and for innovative approaches in coffee breeding.
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Drouin P, Chevreuil L, Bellanger L. Développement de méthodes innovantes utilisant un capteur de mouvement pour la détection de troubles de la marche. Rev Epidemiol Sante Publique 2019. [DOI: 10.1016/j.respe.2019.03.046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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Gallais F, Gay-Andrieu F, Picot V, Magassouba N, Mély S, Peyrefitte CN, Bellanger L. Validation sur le terrain du nouveau test de diagnostic rapide Ebola eZYSCREEN®. ACTA ACUST UNITED AC 2017; 110:38-48. [DOI: 10.1007/s13149-016-0540-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 10/13/2016] [Indexed: 11/25/2022]
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Boucher M, Geffroy F, Prévéral S, Bellanger L, Selingue E, Adryanczyk-Perrier G, Péan M, Lefèvre CT, Pignol D, Ginet N, Mériaux S. Genetically tailored magnetosomes used as MRI probe for molecular imaging of brain tumor. Biomaterials 2016; 121:167-178. [PMID: 28088078 DOI: 10.1016/j.biomaterials.2016.12.013] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 12/12/2016] [Accepted: 12/16/2016] [Indexed: 12/20/2022]
Abstract
We investigate here the potential of single step production of genetically engineered magnetosomes, bacterial biogenic iron-oxide nanoparticles embedded in a lipid vesicle, as a new tailorable magnetic resonance molecular imaging probe. We demonstrate in vitro the specific binding and the significant internalization into U87 cells of magnetosomes decorated with RGD peptide. After injection at the tail vein of glioblastoma-bearing mice, we evidence in the first 2 h the rapid accumulation of both unlabeled and functionalized magnetosomes inside the tumor by Enhanced Permeability and Retention effects. 24 h after the injection, a specific enhancement of the tumor contrast is observed on MR images only for RGD-labeled magnetosomes. Post mortem acquisition of histological data confirms MRI results with more magnetosomes found into the tumor treated with functionalized magnetosomes. This work establishes the first proof-of-concept of a successful bio-integrated production of molecular imaging probe for MRI.
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Affiliation(s)
- M Boucher
- UNIRS, CEA/DRF/I(2)BM/NeuroSpin, CEA Saclay, Gif-sur-Yvette, France
| | - F Geffroy
- UNIRS, CEA/DRF/I(2)BM/NeuroSpin, CEA Saclay, Gif-sur-Yvette, France
| | - S Prévéral
- LBC, CEA/DRF/BIAM, CEA Cadarache, Saint-Paul-lez-Durance, France; UMR 7265, Centre National de Recherche Scientifique, Saint-Paul-lez-Durance, France; Aix Marseille Université, Saint-Paul-lez-Durance, France
| | - L Bellanger
- LI2D, CEA/DRF/IBITEC-S/SPI, CEA Marcoule, Bagnols-sur-Cèze, France
| | - E Selingue
- UNIRS, CEA/DRF/I(2)BM/NeuroSpin, CEA Saclay, Gif-sur-Yvette, France
| | - G Adryanczyk-Perrier
- LBC, CEA/DRF/BIAM, CEA Cadarache, Saint-Paul-lez-Durance, France; UMR 7265, Centre National de Recherche Scientifique, Saint-Paul-lez-Durance, France; Aix Marseille Université, Saint-Paul-lez-Durance, France
| | - M Péan
- LBC, CEA/DRF/BIAM, CEA Cadarache, Saint-Paul-lez-Durance, France; UMR 7265, Centre National de Recherche Scientifique, Saint-Paul-lez-Durance, France; Aix Marseille Université, Saint-Paul-lez-Durance, France
| | - C T Lefèvre
- LBC, CEA/DRF/BIAM, CEA Cadarache, Saint-Paul-lez-Durance, France; UMR 7265, Centre National de Recherche Scientifique, Saint-Paul-lez-Durance, France; Aix Marseille Université, Saint-Paul-lez-Durance, France
| | - D Pignol
- LBC, CEA/DRF/BIAM, CEA Cadarache, Saint-Paul-lez-Durance, France; UMR 7265, Centre National de Recherche Scientifique, Saint-Paul-lez-Durance, France; Aix Marseille Université, Saint-Paul-lez-Durance, France
| | - N Ginet
- LBC, CEA/DRF/BIAM, CEA Cadarache, Saint-Paul-lez-Durance, France; UMR 7265, Centre National de Recherche Scientifique, Saint-Paul-lez-Durance, France; Aix Marseille Université, Saint-Paul-lez-Durance, France; Aix Marseille Université, CNRS, Laboratoire de Chimie Bactérienne, Marseille, France
| | - S Mériaux
- UNIRS, CEA/DRF/I(2)BM/NeuroSpin, CEA Saclay, Gif-sur-Yvette, France.
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Bjerner J, Lebedin Y, Bellanger L, Kuroki M, Shively JE, Varaas T, Nustad K, Hammarström S, Børmer OP. Protein epitopes in carcinoembryonic antigen. Report of the ISOBM TD8 workshop. Tumour Biol 2002; 23:249-62. [PMID: 12499780 DOI: 10.1159/000067255] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [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: 11/19/2022] Open
Abstract
To characterize antigenic sites in carcinoembryonic antigen (CEA) further and to investigate whether there are differences between colon tumor CEA and meconium CEA (NCA-2) that can be detected by anti-CEA monoclonal antibodies (MAb), 19 new anti-CEA MAb were analyzed with respect to specificity, epitope reactivity and affinity. Their reactivities were compared with 10 anti-CEA MAb with known CEA-domain binding specificity that have previously been classified into five nonoverlapping epitope groups, GOLD 1-5. Cross-inhibition assays with antigen-coated microtiter plates and immunoradiometric assays were performed in almost all combinations of MAbs, using conventionally purified CEA (domain structure: N-A1B1-A2B2-A3B3-C) from liver metastasis of colorectal carcinomas, recombinant CEA, meconium CEA (NCA-2), truncated forms of CEA and NCA (CEACAM6) as the antigens. The affinity of the MAbs for CEA was also determined. The new MAbs were generally of high affinity and suitable for immunoassays. Three new MAbs were assigned to GOLD epitope group 5 (N-domain binding), 3 MAbs to group 4 (A1B1 domain), 1 to group 3 (A3B3 domain), 3 to group 2 (A2B2 domain) and 3 to group 1 (also the A3B3 domain). Three MAbs formed a separate group related to group 4, they were classified as GOLD 4' (A1B1 domain binding). The remaining 3 MAbs appear to represent new subspecificities with some relationship to GOLD groups 1, 2 or 4, respectively. Five MAbs, all belonging to epitope group 1 and 3, reacted strongly with tumor CEA but only weakly or not at all with meconium CEA, demonstrating that the two products of the CEA gene differ from each other, probably due to different posttranslational modifications.
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Affiliation(s)
- J Bjerner
- Central Laboratory, Norwegian Radium Hospital, Oslo, Norway.
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Nap M, van Wel T, Andrés C, Bellanger L, Bodenmüller H, Bonfrer H, Brundell J, Einarsson R, Erlandsson A, Johansson A, Leca JF, Meier T, Seguin P, Sjödin A, Stigbrand T, Sundström BE, van Dalen A, Wiebelhaus E, Wiklund B, Hilgers J. Immunohistochemical profiles of 30 monoclonal antibodies against cytokeratins 8, 18 and 19. Second report of the TD5 workshop. Tumour Biol 2001; 22:4-10. [PMID: 11054021 DOI: 10.1159/000030149] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [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: 11/19/2022] Open
Abstract
In the first report of the TD5 workshop (TD5-1), the epitope specificities of 30 different monoclonal antibodies against cytokeratins 8, 18 and 19 were determined. This second report presents the immunohistochemical profiles of these antibodies using human appendix and normal skin for evaluation. Each antibody was tested by one or two different laboratories recruited from the Dutch Working Group on Immunohistochemistry and Cytochemistry. Eight different laboratories participated. The histological specimens were pretreated by the participants in three different ways for immunohistochemistry: microwave antigen retrieval in citrate buffer, enzymatic digestion to restore epitope exposure, no specific treatment (untreated paraffin-embedded samples), and tested blindly without knowledge of cytokeratin or epitope specificity of the antibodies at three different concentrations of 50, 10 and 1 microg/ml. Most of the tested antibodies (29/30) were useful in at least one pretreatment method, with microwave antigen retrieval being the most sensitive approach. For some antibodies, very high backgrounds were observed. Furthermore, it can be concluded that 11 MAbs performed well using all three staining protocols, including untreated paraffin-embedded sections. Interestingly, all the antibodies with documented selected specificity towards cytokeratin 8 (i.e. 178, 191, 199, 202 and 206) are reactive with an immunodominant region corresponding to amino acids 340-365 on cytokeratin 8, which evidently is well-suited as target for immunohistochemical interactions. Similarly, three antibodies with the same capacity to react with untreated samples had specificity against cytokeratin 19 (i.e. 179, 197 and 204) in the corresponding region in this filament, i.e. amino acids 311-335, or the KS 19.1 epitope. None of the six antibodies against the other major cytokeratin 19 epitope (BM 19.21) were found useful for immunohistochemistry on untreated samples. The overall conclusions from the present investigation are that all cytokeratin-8-specific antibodies with defined epitope specificities were very useful. Only one of the major two epitopes on cytokeratin 19 seems to be available for efficient immunohistochemistry. Cytokeratin 18 exposes some epitopes outside the immunodominant region reactive with the antibodies 190, 203 and 205 which can be used for untreated samples. The implications of these findings are of significance both for diagnostic histopathology and for the biology of tumor marker epitope expression in tissues.
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Affiliation(s)
- M Nap
- Department of Clinical Pathology, Atrium Medical Center, Herleen, The Netherlands
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9
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Stenman UH, Paus E, Allard WJ, Andersson I, Andrès C, Barnett TR, Becker C, Belenky A, Bellanger L, Pellegrino CM, Børmer OP, Davis G, Dowell B, Grauer LS, Jette DC, Karlsson B, Kreutz FT, van der Kwast TM, Lauren L, Leinimaa M, Leinonen J, Lilja H, Linton HJ, Nap M, Hilgers J. Summary report of the TD-3 workshop: characterization of 83 antibodies against prostate-specific antigen. Tumour Biol 2000; 20 Suppl 1:1-12. [PMID: 10628402 DOI: 10.1159/000056523] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.3] [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: 11/19/2022] Open
Abstract
Twelve research groups participated in the ISOBM TD-3 Workshop in which the reactivity and specificity of 83 antibodies against prostate-specific antigen (PSA) were investigated. Using a variety of techniques including cross-inhibition assays, Western blotting, BIAcore, immunoradiometric assays and immunohistochemistry, the antibodies were categorized into six major groups which formed the basis for mapping onto two- and three-dimensional (2-D and 3-D) models of PSA. The overall findings of the TD-3 Workshop are summarized in this report. In agreement with all participating groups, three main antigenic domains were identified: free PSA-specific epitopes located in or close to amino acids 86-91; discontinuous epitopes specific for PSA without human kallikrein (hK2) cross-reactivity located at or close to amino acids 158-163; and continuous or linear epitopes shared between PSA and hK2 located close to amino acids 3-11. In addition, several minor and partly overlapping domains were also identified. Clearly, the characterization of antibodies from this workshop and the location of their epitopes on the 3-D model of PSA illustrate the importance of selecting appropriate antibody pairs for use in immunoassays. It is hoped that these findings and the epitope nomenclature described in this TD-3 Workshop are used as a standard for future evaluation of anti-PSA antibodies.
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Affiliation(s)
- U H Stenman
- Department of Clinical Chemistry, Helsinki University Central Hospital, Finland
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10
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Stigbrand T, Andrés C, Bellanger L, Bishr Omary M, Bodenmüller H, Bonfrer H, Brundell J, Einarsson R, Erlandsson A, Johansson A, Leca JF, Levi M, Meier T, Nap M, Nustad K, Seguin P, Sjödin A, Sundström B, van Dalen A, Wiebelhaus E, Wiklund B, Arlestig L, Hilgers J. Epitope specificity of 30 monoclonal antibodies against cytokeratin antigens: the ISOBM TD5-1 Workshop. Tumour Biol 2000; 19:132-52. [PMID: 9486565 DOI: 10.1159/000029984] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.3] [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: 11/19/2022] Open
Abstract
The epitope specificities of 30 monoclonal antibodies (MAbs) against the most common human cytokeratins. i.e., Nos. 8, 18, and 19, in epithelial cells were investigated in the ISOBM TD-5 Workshop. Seven research groups from universities or companies participated independently in the evaluation of the antibody specificities. The complex assembly of cytokeratins in vivo, with obligatory heterologous dimeric combinations of different cytokeratins from each of the two major groups, comprising together more than 20 different individual cytokeratins, made analysis of the antibody reactivity patterns with isolated single cytokeratins necessary. The concordance of the evaluations was striking and independent of the technologies used. As antigens purified individual cytokeratins, chemically degraded purified cytokeratins, recombinant intact and truncated cytokeratins, as well as specific synthesized shorter peptides were used. In order to elucidate the epitope specificity, reactivity patterns in ELISA assays and immunoblots with partial enzymatic degradation of the antigens were performed. Competitive cross-inhibition experiments between antibodies using antigens and antibodies in all possible combinations were performed with radioimmunometric assays, BIAcore, and ELISA technology. All 30 antibodies could convincingly be classified with regard to target cytokeratin. One MAb (192) had to be deleted due to dual specificities in both isotype and epitope specificity against its target. Six antibodies bound selectively to cytokeratin 8, 14 to cytokeratin 18, and 10 to cytokeratin 19, as demonstrated by using native, recombinant, and synthesized antigens. The immunodominant part of the molecule for all three types of cytokeratins was located in the region of amino acid (aa) 270-400. Out of the six MAbs reactive with cytokeratin 8, four MAbs, i.e., 178, 199, 202, and 206, were reactive with a sequence in the interval aa 340-365, and MAb 191 reacted with a closely related epitope. The remaining antibody, 192, presented dual specificities. At least two closely related major immunogenic epitopes could be identified in cytokeratin 8. In cytokeratin 18 four distinct epitopes could be documented, again with the dominating sequence region 270-429 as target for 10 (181, 184, 186, 188, 189, 190, 193, 196, 198, and 200) out of 14 antibodies. Since MAb 193 is known to react with the M3 epitope, aa 322-342 in cytokeratin 18, this entire group is reactive in the region close to the charge shift, in the middle of the rod 2B region, as shown by competitive binding. The remaining four anticytokeratin 18 antibodies (180, 185, 203, and 205) displayed unique, noncompetitive binding to this filament. Cytokeratin 19, reactive with altogether ten antibodies, displayed two major epitopes, all of them also within the large immunodominant region. MAbs 179, 195, 197, and 204 were reactive with the peptides aa 311-335 also known as the KS 19.1 epitope, and MAbs 182, 183, 187, 194, and 201 bound to peptide aa 346-367, known as the BM 19.21 epitope. One antibody, 231, was selectively reactive with aa 356-370 in cytokeratin 19. A complex pattern of binding specificities comprising at least ten different, noncompetitive epitopes, mainly situated in the rod portion, 2A and 2B, situated close to the charge shift in the rod of all three cytokeratins was documented. Out of the 29 classifiable antibodies, altogether 22 were reactive in this very short region, i.e., from aa 311 to 370 in all cytokeratin filaments. The remaining seven antibodies displayed unique binding properties. The implications of the findings are of significance both for immunohistochemistry and for assaying circulating heterodimeric, partially degraded complexes in patients' blood for tumor marker evaluation.
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Affiliation(s)
- T Stigbrand
- Department of Immunology, University of Umeå, Sweden
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11
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Abstract
A panel of 53 antibodies from the ISOBM TD-3 PSA Workshop were tested for reactivity with iodinated derivatives of free PSA or the alpha1-antichymotrypsin PSA complex using the BIAcore system. Two antibodies (#69 and #83) showed low binding (<8%) for both antigens. One group of antibodies (#25, #26, #33, #54, #68, #73, #77, #78 and #91) had a much lower affinity for the complex (<12%) than for the free antigen (>65%). According to the mapping study, it was possible to categorize the antibodies into 29 different groups. Four antibodies were not classified. The two-dimensional representation of all interactions between the antibodies showed a complex network on the PSA molecule. Antibodies with lower affinity for the complex than for the free PSA appeared to bind epitopes in a common region, and thus it was not possible to perform sandwich assays with antibodies specific for free PSA.
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Affiliation(s)
- L Bellanger
- CIS Bio International, Division of In Vitro Technologies, Bagnols-sur-Cèze, France.
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12
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Degorce F, Goumon Y, Jacquemart L, Vidaud C, Bellanger L, Pons-Anicet D, Seguin P, Metz-Boutigue MH, Aunis D. A new human chromogranin A (CgA) immunoradiometric assay involving monoclonal antibodies raised against the unprocessed central domain (145-245). Br J Cancer 1999; 79:65-71. [PMID: 10408695 PMCID: PMC2362168 DOI: 10.1038/sj.bjc.6690013] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Chromogranin A (CgA), a major protein of chromaffin granules, has been described as a potential marker for neuroendocrine tumours. Because of an extensive proteolysis which leads to a large heterogeneity of circulating fragments, its presence in blood has been assessed in most cases either by competitive immunoassays or with polyclonal antibodies. In the present study, 24 monoclonal antibodies were raised against native or recombinant human CgA. Their mapping with proteolytic peptides showed that they defined eight distinct epitopic groups which spanned two-thirds of the C-terminal part of human CgA. All monoclonal antibodies were tested by pair and compared with a reference radioimmunoassay (RIA) involving CGS06, one of the monoclonal antibodies against the 198-245 sequence. It appears that CgA C-terminal end seems to be highly affected by proteolysis and the association of C-terminal and median-part monoclonal antibodies is inadequate for total CgA assessment. Our new immunoradiometric assay involves two monoclonal antibodies, whose contiguous epitopes lie within the median 145-245 sequence. This assay allows a sensitive detection of total human CgA and correlates well with RIA because dibasic cleavage sites present in the central domain do not seem to be affected by degradation. It has been proved to be efficient in measuring CgA levels in patients with neuroendocrine tumours.
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Affiliation(s)
- F Degorce
- CIS Biointernational, Division In Vitro Technologies, Bagnols-sur-Cèze, France
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13
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Delage V, Deytieux S, Le Doussal V, Degorce F, Bellanger L, Hacene K, Seguin P, Descotes F, Saez S, Spyratos F. Comparison of a new microplate oestrogen receptor (ER) enzyme immunoassay with other ER detection methods. Br J Cancer 1997; 76:519-25. [PMID: 9275030 PMCID: PMC2227993 DOI: 10.1038/bjc.1997.418] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [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] [Indexed: 02/05/2023] Open
Abstract
In a study involving 50 breast cancer tumours, we compared two oestrogen receptor (ER) detection methods developed by us--a microplate immunoenzymometric assay (EIA96) and an immunohistochemistry kit (HistoCIS-ER)--with the radioligand assay (RLA), the Abbott immunoenzymometric assay ER-EIA and the reverse transcriptase polymerase chain reaction technique (RT-PCR). Among the three ER protein cytosolic assays (EIA96, ER-EIA and RLA), the two EIAs showed the best agreement (y = 1.086x - 7.840; r2 = 0.876). At the calculated optimal cut-off values (8 and 14 fmol mg(-1) protein for EIA96 and RLA respectively), EIA96 was more sensitive than RLA (0.94 for EIA96, 0.88 for RLA), but slightly less specific (0.82 for EIA96, 0.94 for RLA). The Cox logistical regression model applied to EIA96, RLA and RT-PCR showed that EIA96 discriminated the best between ER-EIA+ and ER-EIA- samples. The RT-PCR technique and HistoCIS-ER both had a positivity-negativity concordance of 86% with EIA96.
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Affiliation(s)
- V Delage
- CIS Bio International, Division In Vitro Technologies, Bagnols-sur-Cèze, France
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14
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Delage V, Teulon JM, Bellanger L, Seguin P, Descotes F, Saez S. Microtiter plate immunoenzymometric assay for estrogen receptor. Clin Chem 1996; 42:1955-60. [PMID: 8969632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The estrogen receptor (ER) status of breast cancer is used both as a prognostic factor and as a predictor of response to endocrine therapy. An immunoenzymometric assay for ER was developed on 96-well microtiter plates (EIA96). This technique involves two monoclonal antibodies directed against different epitopes in the B domain of ER. The two-step protocol (16-18 h and 3 h at 4 degrees C) requires 100 microL of cytosol. This assay showed a detection limit of 0.58 pmol/L. Intra- and interassay CVs of clinical specimens were < or = 5% except for the least concentrated sample (6.5 pmol/L, CV = 6.7%). In a comparison study involving cytosols of breast adenocarcinoma tissue biopsies, we compared the EIA96 with the radioligand assay (RLA) and the Abbott ER-EIA, widely used techniques for determining ER concentration in cytosols of breast cancer tumors. The two EIAs showed excellent agreement; however, two samples showed discrepant results by EIA96 and RLA.
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Affiliation(s)
- V Delage
- CIS Bio International, Division In Vitro Technologies, Bagnols-sur-Cèze, France
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15
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Abstract
Abstract
The estrogen receptor (ER) status of breast cancer is used both as a prognostic factor and as a predictor of response to endocrine therapy. An immunoenzymometric assay for ER was developed on 96-well microtiter plates (EIA96). This technique involves two monoclonal antibodies directed against different epitopes in the B domain of ER. The two-step protocol (16-18 h and 3 h at 4 degrees C) requires 100 microL of cytosol. This assay showed a detection limit of 0.58 pmol/L. Intra- and interassay CVs of clinical specimens were < or = 5% except for the least concentrated sample (6.5 pmol/L, CV = 6.7%). In a comparison study involving cytosols of breast adenocarcinoma tissue biopsies, we compared the EIA96 with the radioligand assay (RLA) and the Abbott ER-EIA, widely used techniques for determining ER concentration in cytosols of breast cancer tumors. The two EIAs showed excellent agreement; however, two samples showed discrepant results by EIA96 and RLA.
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Affiliation(s)
- V Delage
- CIS Bio International, Division In Vitro Technologies, Bagnols-sur-Cèze, France
| | - J M Teulon
- CIS Bio International, Division In Vitro Technologies, Bagnols-sur-Cèze, France
| | - L Bellanger
- CIS Bio International, Division In Vitro Technologies, Bagnols-sur-Cèze, France
| | - P Seguin
- CIS Bio International, Division In Vitro Technologies, Bagnols-sur-Cèze, France
| | - F Descotes
- CIS Bio International, Division In Vitro Technologies, Bagnols-sur-Cèze, France
| | - S Saez
- CIS Bio International, Division In Vitro Technologies, Bagnols-sur-Cèze, France
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16
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Chanussot C, Bellanger L, Ligny-Lemaire C, Seguin P, Ménez A, Boulain JC. Engineering of a recombinant colorimetric fusion protein for immunodiagnosis of insulin. J Immunol Methods 1996; 197:39-49. [PMID: 8890893 DOI: 10.1016/0022-1759(96)00109-3] [Citation(s) in RCA: 9] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
A synthetic DNA encoding human proinsulin was inserted in frame in the bacterial alkaline phosphatase gene. A homogeneous recombinant human proinsulin-alkaline phosphatase conjugate was obtained directly from the periplasm of Escherichia coli transformed with a plasmid carrying the hybrid gene. The recombinant conjugate was stable and could be produced in the bacteria. The immunological properties of the recombinant conjugate and those of the human insulin and human proinsulin were compared using a panel of six different human insulin-specific monoclonal antibodies. Three immunological groups were thus distinguished and one of them indiscriminately recognized all of the insulin-like molecules. One monoclonal antibody from this group was used in combination with the recombinant conjugate to develop successfully a competitive immunoenzymatic assay for detecting insulin.
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Affiliation(s)
- C Chanussot
- Département d'Ingénierie et d'Etudes des Protéines, C.E.A. Saclay, Gif sur Yvette, France
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17
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Bedeau N, Bellanger L, Malard V, Pons D, Seguin P, Guillet J. 1261 Clinical evaluation of specific assays for free PSA and total PSA. Eur J Cancer 1995. [DOI: 10.1016/0959-8049(95)96507-a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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18
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Guillet J, Role C, Pans D, Malard V, Bedeau N, Bellanger L, Seguin P. 466 Free and α 1 antichymotrypsin bound PSA in prostate diseases. Eur J Cancer 1995. [DOI: 10.1016/0959-8049(95)95720-q] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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