1
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Zeitz C, Navarro J, Azizzadeh Pormehr L, Méjécase C, Neves LM, Letellier C, Condroyer C, Albadri S, Amprou A, Antonio A, Ben-Yacoub T, Wohlschlegel J, Andrieu C, Serafini M, Bianco L, Antropoli A, Nassisi M, El Shamieh S, Chantot-Bastaraud S, Mohand-Saïd S, Smirnov V, Sahel JA, Del Bene F, Audo I. Variants in UBAP1L lead to autosomal recessive rod-cone and cone-rod dystrophy. Genet Med 2024:101081. [PMID: 38293907 DOI: 10.1016/j.gim.2024.101081] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 01/16/2024] [Accepted: 01/19/2024] [Indexed: 02/01/2024] Open
Abstract
PURPOSE Progressive inherited retinal degenerations (IRDs) affecting rods and cones are clinically and genetically heterogeneous and can lead to blindness with limited therapeutic options. The major gene defects have been identified in subjects of European and Asian descent with only few reports of North African descent. METHODS Genome, targeted next-generation, and Sanger sequencing was applied to cohort of ∼4000 IRDs cases. Expression analyses were performed including Chip-seq database analyses, on human-derived retinal organoids (ROs), retinal pigment epithelium cells, and zebrafish. Variants' pathogenicity was accessed using 3D-modeling and/or ROs. RESULTS Here, we identified a novel gene defect with three distinct pathogenic variants in UBAP1L in 4 independent autosomal recessive IRD cases from Tunisia. UBAP1L is expressed in the retinal pigment epithelium and retina, specifically in rods and cones, in line with the phenotype. It encodes Ubiquitin-associated protein 1-like, containing a solenoid of overlapping ubiquitin-associated domain, predicted to interact with ubiquitin. In silico and in vitro studies, including 3D-modeling and ROs revealed that the solenoid of overlapping ubiquitin-associated domain is truncated and thus ubiquitin binding most likely abolished secondary to all variants identified herein. CONCLUSION Biallelic UBAP1L variants are a novel cause of IRDs, most likely enriched in the North African population.
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Affiliation(s)
- Christina Zeitz
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France.
| | - Julien Navarro
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Leila Azizzadeh Pormehr
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France; Mass. Eye and Ear, Ocular Genomics Institute, Berman-Gund Laboratory for the Study of Retinal Degenerations, Harvard Medical School, Boston, MA
| | - Cécile Méjécase
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France; UCL Institute of Ophthalmology, London, UK; The Francis Crick Institute, London, UK
| | - Luiza M Neves
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France; Instituto Nacional de Saúde da Mulher, da Criança e do Adolescente Fernandes Figueira, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Camille Letellier
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | | | - Shahad Albadri
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Andréa Amprou
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Aline Antonio
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Tasnim Ben-Yacoub
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Juliette Wohlschlegel
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France; Department of Biological Structure, University of Washington, Seattle, WA
| | - Camille Andrieu
- Centre Hospitalier National d'Ophtalmologie des Quinze-Vingts, Centre de Référence Maladies Rares REFERET and INSERM-DGOS CIC 1423, Paris, France
| | - Malo Serafini
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Lorenzo Bianco
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France; Department of Ophthalmology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Alessio Antropoli
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France; Department of Ophthalmology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Marco Nassisi
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France; Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
| | - Said El Shamieh
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France; Molecular Testing Laboratory, Department of Medical Laboratory Technology, Faculty of Health Sciences, Beirut Arab University, Beirut, Lebanon
| | - Sandra Chantot-Bastaraud
- APHP, Hôpital Armand-Trousseau, Département de Génétique, UF de Génétique Chromosomique, Paris, France
| | - Saddek Mohand-Saïd
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France; Centre Hospitalier National d'Ophtalmologie des Quinze-Vingts, Centre de Référence Maladies Rares REFERET and INSERM-DGOS CIC 1423, Paris, France
| | - Vasily Smirnov
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France; Exploration de la Vision et Neuro-Ophtalmologie, CHU de Lille, Lille, France
| | - José-Alain Sahel
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France; Centre Hospitalier National d'Ophtalmologie des Quinze-Vingts, Centre de Référence Maladies Rares REFERET and INSERM-DGOS CIC 1423, Paris, France; Department of Ophthalmology, The University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Filippo Del Bene
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Isabelle Audo
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France; Centre Hospitalier National d'Ophtalmologie des Quinze-Vingts, Centre de Référence Maladies Rares REFERET and INSERM-DGOS CIC 1423, Paris, France.
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2
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Andrieu C, Loiseau L, Vergnes A, Gagnot S, Barré R, Aussel L, Collet JF, Ezraty B. Salmonella Typhimurium uses the Cpx stress response to detect N-chlorotaurine and promote the repair of oxidized proteins. Proc Natl Acad Sci U S A 2023; 120:e2215997120. [PMID: 36976766 PMCID: PMC10083560 DOI: 10.1073/pnas.2215997120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 03/01/2023] [Indexed: 03/29/2023] Open
Abstract
The cell envelope of gram-negative bacteria constitutes the first protective barrier between a cell and its environment. During host infection, the bacterial envelope is subjected to several stresses, including those induced by reactive oxygen species (ROS) and reactive chlorine species (RCS) produced by immune cells. Among RCS, N-chlorotaurine (N-ChT), which results from the reaction between hypochlorous acid and taurine, is a powerful and less diffusible oxidant. Here, using a genetic approach, we demonstrate that Salmonella Typhimurium uses the CpxRA two-component system to detect N-ChT oxidative stress. Moreover, we show that periplasmic methionine sulfoxide reductase (MsrP) is part of the Cpx regulon. Our findings demonstrate that MsrP is required to cope with N-ChT stress by repairing N-ChT-oxidized proteins in the bacterial envelope. By characterizing the molecular signal that induces Cpx when S. Typhimurium is exposed to N-ChT, we show that N-ChT triggers Cpx in an NlpE-dependent manner. Thus, our work establishes a direct link between N-ChT oxidative stress and the envelope stress response.
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Affiliation(s)
- Camille Andrieu
- Aix-Marseille University, CNRS, Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, 13402Marseille, France
| | - Laurent Loiseau
- Aix-Marseille University, CNRS, Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, 13402Marseille, France
| | - Alexandra Vergnes
- Aix-Marseille University, CNRS, Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, 13402Marseille, France
| | - Séverine Gagnot
- Aix-Marseille University, CNRS, Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, 13402Marseille, France
| | - Romain Barré
- Institut de Microbiologie de la Méditerranée, Plate-forme Transcriptomique, 13402Marseille, France
| | - Laurent Aussel
- Aix-Marseille University, CNRS, Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, 13402Marseille, France
| | | | - Benjamin Ezraty
- Aix-Marseille University, CNRS, Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, 13402Marseille, France
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3
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Smirnov VM, Nassisi M, Solis Hernandez C, Méjécase C, El Shamieh S, Condroyer C, Antonio A, Meunier I, Andrieu C, Defoort-Dhellemmes S, Mohand-Said S, Sahel JA, Audo I, Zeitz C. Retinal Phenotype of Patients With Isolated Retinal Degeneration Due to CLN3 Pathogenic Variants in a French Retinitis Pigmentosa Cohort. JAMA Ophthalmol 2021; 139:278-291. [PMID: 33507216 DOI: 10.1001/jamaophthalmol.2020.6089] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Importance Biallelic variants in CLN3 lead to a spectrum of diseases, ranging from severe neurodegeneration with retinal involvement (juvenile neuronal ceroid lipofuscinosis) to retina-restricted conditions. Objective To provide a detailed description of the retinal phenotype of patients with isolated retinal degeneration harboring biallelic CLN3 pathogenic variants and to attempt a phenotype-genotype correlation associated with this gene defect. Design, Setting, and Participants This retrospective cohort study included patients carrying biallelic CLN3 variants extracted from a cohort of patients with inherited retinal disorders (IRDs) investigated at the National Reference Center for Rare Ocular Diseases of the Centre Hospitalier National d'Ophtalmologie des Quinze-Vingts from December 2007 to August 2020. Data were analyzed from October 2019 to August 2020. Main Outcome and Measures Functional (best-corrected visual acuity, visual field, color vision, and full-field electroretinogram), morphological (multimodal retinal imaging), and clinical data from patients were collected and analyzed. Gene defect was identified by either next-generation sequencing or whole-exome sequencing and confirmed by Sanger sequencing, quantitative polymerase chain reaction, and cosegregation analysis. Results Of 1533 included patients, 843 (55.0%) were women and 690 (45.0%) were men. A total of 15 cases from 11 unrelated families harboring biallelic CLN3 variants were identified. All patients presented with nonsyndromic IRD. Two distinct patterns of retinal disease could be identified: a mild rod-cone degeneration of middle-age onset (n = 6; legal blindness threshold reached by 70s) and a severe retinal degeneration with early macular atrophic changes (n = 9; legal blindness threshold reached by 40s). Eleven distinct pathogenic variants were detected, of which 4 were novel. All but 1, p.(Arg405Trp), CLN3 point variants and their genotypic associations were clearly distinct between juvenile neuronal ceroid lipofuscinosis and retina-restricted disease. Mild and severe forms of retina-restricted CLN3-linked IRDs also had different genetic background. Conclusions and Relevance These findings suggest CLN3 should be included in next-generation sequencing panels when investigating patients with nonsyndromic rod-cone dystrophy. These results document phenotype-genotype correlations associated with specific variants in CLN3. However, caution seems warranted regarding the potential neurological outcome if a pathogenic variant in CLN3 is detected in a case of presumed isolated IRD for the onset of neurological symptoms could be delayed.
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Affiliation(s)
- Vasily M Smirnov
- Sorbonne Université, INSERM, Centre national de la recherche scientifique, Institut de la Vision, Paris, France.,Université de Lille, Faculté de Médecine, Lille, France.,Exploration de la Vision et Neuro-Ophtalmologie, CHU de Lille, Lille, France
| | - Marco Nassisi
- Sorbonne Université, INSERM, Centre national de la recherche scientifique, Institut de la Vision, Paris, France
| | - Cyntia Solis Hernandez
- Sorbonne Université, INSERM, Centre national de la recherche scientifique, Institut de la Vision, Paris, France
| | - Cécile Méjécase
- Sorbonne Université, INSERM, Centre national de la recherche scientifique, Institut de la Vision, Paris, France.,Institute of Ophthalmology, University College London, London, United Kingdom
| | - Said El Shamieh
- Sorbonne Université, INSERM, Centre national de la recherche scientifique, Institut de la Vision, Paris, France.,Department of Medical Laboratory Technology, Faculty of Health Sciences, Beirut Arab University, Beirut, Lebanon
| | - Christel Condroyer
- Sorbonne Université, INSERM, Centre national de la recherche scientifique, Institut de la Vision, Paris, France
| | - Aline Antonio
- Sorbonne Université, INSERM, Centre national de la recherche scientifique, Institut de la Vision, Paris, France
| | - Isabelle Meunier
- Institute for Neurosciences Montpellier, INSERM U1051, University of Monpellier, Montpellier, France.,National Center for Rare Genetic Retinal Dystrophies, Hôpital Guy de Chauliac, Montpellier, France
| | - Camille Andrieu
- Centre Hospitalier National d'Ophtalmologie des Quinze-Vingts, INSERM-DHOS CIC 1423, Paris, France
| | | | - Saddek Mohand-Said
- Centre Hospitalier National d'Ophtalmologie des Quinze-Vingts, INSERM-DHOS CIC 1423, Paris, France
| | - José-Alain Sahel
- Sorbonne Université, INSERM, Centre national de la recherche scientifique, Institut de la Vision, Paris, France.,Centre Hospitalier National d'Ophtalmologie des Quinze-Vingts, INSERM-DHOS CIC 1423, Paris, France.,Fondation Ophtalmologique Adolphe de Rothschild, Paris, France.,Académie des Sciences, Institut de France, Paris, France.,Department of Ophthalmology, The University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Isabelle Audo
- Sorbonne Université, INSERM, Centre national de la recherche scientifique, Institut de la Vision, Paris, France.,Institute of Ophthalmology, University College London, London, United Kingdom.,Centre Hospitalier National d'Ophtalmologie des Quinze-Vingts, INSERM-DHOS CIC 1423, Paris, France
| | - Christina Zeitz
- Sorbonne Université, INSERM, Centre national de la recherche scientifique, Institut de la Vision, Paris, France
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4
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Smirnov V, Grunewald O, Muller J, Zeitz C, Obermaier CD, Devos A, Pelletier V, Bocquet B, Andrieu C, Bacquet JL, Lebredonchel E, Mohand-Saïd S, Defoort-Dhellemmes S, Sahel JA, Dollfus H, Zanlonghi X, Audo I, Meunier I, Boulanger-Scemama E, Dhaenens CM. Novel TTLL5 Variants Associated with Cone-Rod Dystrophy and Early-Onset Severe Retinal Dystrophy. Int J Mol Sci 2021; 22:ijms22126410. [PMID: 34203883 PMCID: PMC8232641 DOI: 10.3390/ijms22126410] [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] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 06/07/2021] [Accepted: 06/09/2021] [Indexed: 01/05/2023] Open
Abstract
Variants of the TTLL5 gene, which encodes tubulin tyrosine ligase-like family member five, are a rare cause of cone dystrophy (COD) or cone-rod dystrophy (CORD). To date, only a few TTLL5 patients have been clinically and genetically described. In this study, we report five patients harbouring biallelic variants of TTLL5. Four adult patients presented either COD or CORD with onset in the late teenage years. The youngest patient had a phenotype of early onset severe retinal dystrophy (EOSRD). Genetic analysis was performed by targeted next generation sequencing of gene panels and assessment of copy number variants (CNV). We identified eight variants, of which six were novel, including two large multiexon deletions in patients with COD or CORD, while the EOSRD patient harboured the novel homozygous p.(Trp640*) variant and three distinct USH2A variants, which might explain the observed rod involvement. Our study highlights the role of TTLL5 in COD/CORD and the importance of large deletions. These findings suggest that COD or CORD patients lacking variants in known genes may harbour CNVs to be discovered in TTLL5, previously undetected by classical sequencing methods. In addition, variable phenotypes in TTLL5-associated patients might be due to the presence of additional gene defects.
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Affiliation(s)
- Vasily Smirnov
- Université de Lille, Faculté de Médecine, 59037 Lille, France;
- CHU Lille, Service d’Exploration Fonctionnelle de la Vision et de Neuro-Ophtalmologie, Hôpital Salengro, 59037 Lille, France;
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 75012 Paris, France; (C.Z.); (S.M.-S.); (J.-A.S.); (I.A.)
| | - Olivier Grunewald
- Univ. Lille, Inserm, CHU Lille, U1172-LilNCog-Lille Neuroscience & Cognition, 59045 Lille, France;
| | - Jean Muller
- Laboratoire de Génétique Médicale, Institut de Génétique Médicale d’Alsace (IGMA), INSERM U1112, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg UMRS_1112, 67000 Strasbourg, France;
- Laboratoire de Diagnostic Génétique, Hôpitaux Universitaires de Strasbourg, Institut de Génétique Médicale d’Alsace (IGMA), 67000 Strasbourg, France
| | - Christina Zeitz
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 75012 Paris, France; (C.Z.); (S.M.-S.); (J.-A.S.); (I.A.)
| | - Carolin D. Obermaier
- Praxis für Humangenetik Tuebingen & Center for Genomics and Transcriptomics, CeGaT GmbH, 72076 Tuebingen, Germany;
| | - Aurore Devos
- Univ. Lille, CHU Lille, Service de Toxicologie et Génopathies, 59037 Lille, France; (A.D.); (E.L.)
| | - Valérie Pelletier
- Centre de Référence pour les Affections Rares en Génétique Ophtalmologiques, Hopitaux Universitaires de Strasbourg, 67000 Strasbourg, France; (V.P.); (J.-L.B.); (H.D.)
| | - Béatrice Bocquet
- National Reference Centre for Inherited Sensory Diseases, University of Montpellier, Montpellier University Hospital, Sensgene Care Network, ERN-EYE Network, 34295 Montpellier, France; (B.B.); (I.M.)
- Institute for Neurosciences of Montpellier (INM), INSERM, University of Montpellier, INSERM, 34295 Montpellier, France
| | - Camille Andrieu
- Centre Hospitalier National d’Ophtalmologie des Quinze-Vingts, INSERM-DHOS CIC 1423, 75012 Paris, France;
| | - Jean-Louis Bacquet
- Centre de Référence pour les Affections Rares en Génétique Ophtalmologiques, Hopitaux Universitaires de Strasbourg, 67000 Strasbourg, France; (V.P.); (J.-L.B.); (H.D.)
| | - Elodie Lebredonchel
- Univ. Lille, CHU Lille, Service de Toxicologie et Génopathies, 59037 Lille, France; (A.D.); (E.L.)
| | - Saddek Mohand-Saïd
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 75012 Paris, France; (C.Z.); (S.M.-S.); (J.-A.S.); (I.A.)
- Centre Hospitalier National d’Ophtalmologie des Quinze-Vingts, INSERM-DHOS CIC 1423, 75012 Paris, France;
| | - Sabine Defoort-Dhellemmes
- CHU Lille, Service d’Exploration Fonctionnelle de la Vision et de Neuro-Ophtalmologie, Hôpital Salengro, 59037 Lille, France;
| | - José-Alain Sahel
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 75012 Paris, France; (C.Z.); (S.M.-S.); (J.-A.S.); (I.A.)
- Centre Hospitalier National d’Ophtalmologie des Quinze-Vingts, INSERM-DHOS CIC 1423, 75012 Paris, France;
- Fondation Ophtalmologique Adolphe de Rothschild, 75019 Paris, France;
- Department of Ophthalmology, The University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Hélène Dollfus
- Centre de Référence pour les Affections Rares en Génétique Ophtalmologiques, Hopitaux Universitaires de Strasbourg, 67000 Strasbourg, France; (V.P.); (J.-L.B.); (H.D.)
| | | | - Isabelle Audo
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 75012 Paris, France; (C.Z.); (S.M.-S.); (J.-A.S.); (I.A.)
- Centre Hospitalier National d’Ophtalmologie des Quinze-Vingts, INSERM-DHOS CIC 1423, 75012 Paris, France;
- Institute of Ophthalmology, University College London, London EC1V 9EL, UK
| | - Isabelle Meunier
- National Reference Centre for Inherited Sensory Diseases, University of Montpellier, Montpellier University Hospital, Sensgene Care Network, ERN-EYE Network, 34295 Montpellier, France; (B.B.); (I.M.)
- Institute for Neurosciences of Montpellier (INM), INSERM, University of Montpellier, INSERM, 34295 Montpellier, France
| | | | - Claire-Marie Dhaenens
- Univ. Lille, Inserm, CHU Lille, U1172-LilNCog-Lille Neuroscience & Cognition, 59045 Lille, France;
- Correspondence: ; Tel.: +33-320-444-953
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5
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Zeitz C, Nassisi M, Laurent-Coriat C, Andrieu C, Boyard F, Condroyer C, Démontant V, Antonio A, Lancelot ME, Frederiksen H, Kloeckener-Gruissem B, El-Shamieh S, Zanlonghi X, Meunier I, Roux AF, Mohand-Saïd S, Sahel JA, Audo I. CHM mutation spectrum and disease: An update at the time of human therapeutic trials. Hum Mutat 2021; 42:323-341. [PMID: 33538369 DOI: 10.1002/humu.24174] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 07/16/2020] [Revised: 12/21/2020] [Accepted: 01/20/2021] [Indexed: 12/15/2022]
Abstract
Choroideremia is an X-linked inherited retinal disorder (IRD) characterized by the degeneration of retinal pigment epithelium, photoreceptors, choriocapillaris and choroid affecting males with variable phenotypes in female carriers. Unlike other IRD, characterized by a large clinical and genetic heterogeneity, choroideremia shows a specific phenotype with causative mutations in only one gene, CHM. Ongoing gene replacement trials raise further interests in this disorder. We describe here the clinical and genetic data from a French cohort of 45 families, 25 of which carry novel variants, in the context of 822 previously reported choroideremia families. Most of the variants represent loss-of-function mutations with eleven families having large (i.e. ≥6 kb) genomic deletions, 18 small insertions, deletions or insertion deletions, six showing nonsense variants, eight splice site variants and two missense variants likely to affect splicing. Similarly, 822 previously published families carry mostly loss-of-function variants. Recurrent variants are observed worldwide, some of which linked to a common ancestor, others arisen independently in specific CHM regions prone to mutations. Since all exons of CHM may harbor variants, Sanger sequencing combined with quantitative polymerase chain reaction or multiplex ligation-dependent probe amplification experiments are efficient to achieve the molecular diagnosis in patients with typical choroideremia features.
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Affiliation(s)
- Christina Zeitz
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Marco Nassisi
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | | | - Camille Andrieu
- CHNO des Quinze-Vingts, DHU Sight Restore, INSERM-DHOS CIC1423, Paris, France
| | - Fiona Boyard
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | | | - Vanessa Démontant
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Aline Antonio
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | | | - Helen Frederiksen
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Barbara Kloeckener-Gruissem
- Institute of Medical Molecular Genetics, University of Zurich, Schlieren, Switzerland.,Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Said El-Shamieh
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France.,Department of Medical Laboratory Technology, Faculty of Health Sciences, Beirut Arab University, Beirut, Lebanon
| | - Xavier Zanlonghi
- Clinique Pluridisciplinaire Jules Verne, Institut Ophtalmologique de l'Ouest, Nantes, France
| | - Isabelle Meunier
- National Reference Centre for Inherited Sensory Diseases, University of Montpellier, Montpellier University Hospital, Montpellier, France.,Institute for Neurosciences of Montpellier (INM), University of Montpellier, INSERM, Montpellier, France
| | - Anne-Françoise Roux
- Laboratoire de Génétique Moléculaire, CHU de Montpellier, Université de Montpellier, Montpellier, France
| | - Saddek Mohand-Saïd
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France.,CHNO des Quinze-Vingts, DHU Sight Restore, INSERM-DHOS CIC1423, Paris, France
| | - José-Alain Sahel
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France.,CHNO des Quinze-Vingts, DHU Sight Restore, INSERM-DHOS CIC1423, Paris, France.,Fondation Ophtalmologique Adolphe de Rothschild, Paris, France.,Académie des Sciences-Institut de France, Paris, France.,Department of Ophthalmology, The University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Isabelle Audo
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France.,CHNO des Quinze-Vingts, DHU Sight Restore, INSERM-DHOS CIC1423, Paris, France.,Department of Genetics, UCL-Institute of Ophthalmology, London, UK
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6
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Andrieu C, Vergnes A, Loiseau L, Aussel L, Ezraty B. Characterisation of the periplasmic methionine sulfoxide reductase (MsrP) from Salmonella Typhimurium. Free Radic Biol Med 2020; 160:506-512. [PMID: 32750406 DOI: 10.1016/j.freeradbiomed.2020.06.031] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 06/17/2020] [Indexed: 11/23/2022]
Abstract
The oxidation of free methionine (Met) and Met residues inside proteins leads to the formation of methionine sulfoxide (Met-O). The reduction of Met-O to Met is catalysed by a ubiquitous enzyme family: the methionine sulfoxide reductases (Msr). The importance of Msr systems in bacterial physiology and virulence has been reported in many species. Salmonella Typhimurium, a facultative intracellular pathogen, contains four cytoplasmic Msr. Recently, a periplasmic Msr enzyme (MsrP) has been identified in Escherichia coli. In the present study, the STM14_4072 gene from Salmonella was shown to encode the MsrP protein (StMsrP). We describe the experimental procedure and precautions for the production of this molybdo-enzyme. StMsrP was also demonstrated to reduce free Met-O and to catalyse the complete repair of an oxidized protein. More importantly, this study provides for the first time access to the exhaustive list of the Msr systems of a pathogen, including four cytoplasmic enzymes (MsrA, MsrB, MsrC, BisC) and one periplasmic enzyme (MsrP).
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Affiliation(s)
- Camille Andrieu
- Aix-Marseille Univ, CNRS, Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, Marseille, France
| | - Alexandra Vergnes
- Aix-Marseille Univ, CNRS, Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, Marseille, France
| | - Laurent Loiseau
- Aix-Marseille Univ, CNRS, Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, Marseille, France
| | - Laurent Aussel
- Aix-Marseille Univ, CNRS, Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, Marseille, France
| | - Benjamin Ezraty
- Aix-Marseille Univ, CNRS, Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, Marseille, France.
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7
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Nassisi M, Mohand-Saïd S, Andrieu C, Antonio A, Condroyer C, Méjécase C, Dhaenens CM, Sahel JA, Zeitz C, Audo I. Peripapillary Sparing With Near Infrared Autofluorescence Correlates With Electroretinographic Findings in Patients With Stargardt Disease. Invest Ophthalmol Vis Sci 2020; 60:4951-4957. [PMID: 31790517 DOI: 10.1167/iovs.19-27100] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Purpose To evaluate the correlation between the quantification of peripapillary sparing and electroretinogram (ERG) outcomes in autosomal recessive Stargardt disease (STGD1). Methods Near infrared fundus autofluorescence (NIR-FAF) images of 101 eyes of 101 patients were retrospectively reviewed. Peripapillary sparing was assessed both qualitatively and quantitatively. The area of spared tissue (AST) was calculated in a 1-mm-wide ring around the optic disc after binarization of the 55° NIR-FAF. These measurements were correlated with the presence of normal ERG (group I), abnormal photopic responses (group II), or abnormal photopic and scotopic responses (group III). Results AST showed significant correlations with ERG groups (R = -0.802, P < 0.001). While qualitative assessment of peripapillary sparing (i.e., present or not) also showed a significant correlation with ERG groups (R = -0.435, P < 0.001), it was weaker than by AST quantification. The ordinal regression analysis showed that the increase in AST was associated with a decrease in the odds of belonging to ERG groups II and III, with an odds ratio of 0.82 (95% confidence interval [CI] 0.78-0.87), P < 0.001. Conclusions The AST around the optic disc in eyes with STGD1 correlates with the impairment of photoreceptors as shown in the ERG. If replicated in future longitudinal studies, the quantification of peripapillary sparing may prove to be a useful parameter for evaluating the visual prognosis of these eyes.
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Affiliation(s)
- Marco Nassisi
- Sorbonne Université, Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche Scientfique, Institut de la Vision, Paris, France
| | - Saddek Mohand-Saïd
- Centre Hospitalier National d'Ophtalmologie des Quinze-Vingts, DHU Sight Restore, INSERM-DHOS CIC 1423, Paris, France
| | - Camille Andrieu
- Centre Hospitalier National d'Ophtalmologie des Quinze-Vingts, DHU Sight Restore, INSERM-DHOS CIC 1423, Paris, France
| | - Aline Antonio
- Sorbonne Université, Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche Scientfique, Institut de la Vision, Paris, France
| | - Christel Condroyer
- Sorbonne Université, Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche Scientfique, Institut de la Vision, Paris, France
| | - Cécile Méjécase
- Sorbonne Université, Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche Scientfique, Institut de la Vision, Paris, France
| | - Claire-Marie Dhaenens
- University of Lille, Institut National de la Santé et de la Recherche Médicale UMR-S 1172, CHU Lille, Biochemistry and Molecular Biology Department-UF Génopathies, Lille, France
| | - José-Alain Sahel
- Sorbonne Université, Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche Scientfique, Institut de la Vision, Paris, France.,Centre Hospitalier National d'Ophtalmologie des Quinze-Vingts, DHU Sight Restore, INSERM-DHOS CIC 1423, Paris, France.,Fondation Ophtalmologique Adolphe de Rothschild, Paris, France.,Académie des Sciences-Institut de France, Paris, France.,Department of Ophthalmology, The University of Pittsburgh School of Medicine, Pittsburg, Pennsylvania, United States
| | - Christina Zeitz
- Sorbonne Université, Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche Scientfique, Institut de la Vision, Paris, France
| | - Isabelle Audo
- Sorbonne Université, Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche Scientfique, Institut de la Vision, Paris, France.,Centre Hospitalier National d'Ophtalmologie des Quinze-Vingts, DHU Sight Restore, INSERM-DHOS CIC 1423, Paris, France.,Institute of Ophthalmology, University College of London, London, United Kingdom
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8
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Anani H, Guilhot E, Andrieu C, Fontanini A, Raoult D, Fournier PE. Prevotella ihumii sp. nov., a new bacterium isolated from a stool specimen of a healthy woman. New Microbes New Infect 2019; 32:100607. [PMID: 31719996 PMCID: PMC6838980 DOI: 10.1016/j.nmni.2019.100607] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [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: 06/11/2019] [Revised: 09/10/2019] [Accepted: 09/29/2019] [Indexed: 12/22/2022] Open
Abstract
Prevotella ihumii strain Marseille-P3385T (= CSURP3385T; = DSM106428T) is a new species isolated from a fresh stool specimen of a healthy woman.
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Affiliation(s)
- H Anani
- UMR VITROME, SSA, Aix-Marseille Université, IRD, AP-HM, IHU Méditerranée Infection, Marseille, France.,IHU Méditerranée Infection, Marseille, France
| | - E Guilhot
- IHU Méditerranée Infection, Marseille, France.,UMR MEPHI, Aix Marseille Université, IRD, AP-HM, IHU Méditerranée Infection, Marseille, France
| | - C Andrieu
- IHU Méditerranée Infection, Marseille, France.,UMR MEPHI, Aix Marseille Université, IRD, AP-HM, IHU Méditerranée Infection, Marseille, France
| | - A Fontanini
- IHU Méditerranée Infection, Marseille, France.,UMR MEPHI, Aix Marseille Université, IRD, AP-HM, IHU Méditerranée Infection, Marseille, France
| | - D Raoult
- IHU Méditerranée Infection, Marseille, France.,UMR MEPHI, Aix Marseille Université, IRD, AP-HM, IHU Méditerranée Infection, Marseille, France.,Special Infections Agents Unit, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah, Saudi Arabia
| | - P E Fournier
- UMR VITROME, SSA, Aix-Marseille Université, IRD, AP-HM, IHU Méditerranée Infection, Marseille, France.,IHU Méditerranée Infection, Marseille, France
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9
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Zeitz C, Michiels C, Neuillé M, Friedburg C, Condroyer C, Boyard F, Antonio A, Bouzidi N, Milicevic D, Veaux R, Tourville A, Zoumba A, Seneina I, Foussard M, Andrieu C, N Preising M, Blanchard S, Saraiva JP, Mesrob L, Le Floch E, Jubin C, Meyer V, Blanché H, Boland A, Deleuze JF, Sharon D, Drumare I, Defoort-Dhellemmes S, De Baere E, Leroy BP, Zanlonghi X, Casteels I, de Ravel TJ, Balikova I, Koenekoop RK, Laffargue F, McLean R, Gottlob I, Bonneau D, Schorderet DF, L Munier F, McKibbin M, Prescott K, Pelletier V, Dollfus H, Perdomo-Trujillo Y, Faure C, Reiff C, Wissinger B, Meunier I, Kohl S, Banin E, Zrenner E, Jurklies B, Lorenz B, Sahel JA, Audo I. Where are the missing gene defects in inherited retinal disorders? Intronic and synonymous variants contribute at least to 4% of CACNA1F-mediated inherited retinal disorders. Hum Mutat 2019; 40:765-787. [PMID: 30825406 DOI: 10.1002/humu.23735] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [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: 01/09/2019] [Revised: 02/15/2019] [Accepted: 02/26/2019] [Indexed: 12/27/2022]
Abstract
Inherited retinal disorders (IRD) represent clinically and genetically heterogeneous diseases. To date, pathogenic variants have been identified in ~260 genes. Albeit that many genes are implicated in IRD, for 30-50% of the cases, the gene defect is unknown. These cases may be explained by novel gene defects, by overlooked structural variants, by variants in intronic, promoter or more distant regulatory regions, and represent synonymous variants of known genes contributing to the dysfunction of the respective proteins. Patients with one subgroup of IRD, namely incomplete congenital stationary night blindness (icCSNB), show a very specific phenotype. The major cause of this condition is the presence of a hemizygous pathogenic variant in CACNA1F. A comprehensive study applying direct Sanger sequencing of the gene-coding regions, exome and genome sequencing applied to a large cohort of patients with a clinical diagnosis of icCSNB revealed indeed that seven of the 189 CACNA1F-related cases have intronic and synonymous disease-causing variants leading to missplicing as validated by minigene approaches. These findings highlight that gene-locus sequencing may be a very efficient method in detecting disease-causing variants in clinically well-characterized patients with a diagnosis of IRD, like icCSNB.
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Affiliation(s)
- Christina Zeitz
- INSERM, CNRS, Institut de la Vision, Sorbonne Université, Paris, France
| | | | - Marion Neuillé
- INSERM, CNRS, Institut de la Vision, Sorbonne Université, Paris, France
| | | | | | - Fiona Boyard
- INSERM, CNRS, Institut de la Vision, Sorbonne Université, Paris, France
| | - Aline Antonio
- INSERM, CNRS, Institut de la Vision, Sorbonne Université, Paris, France.,CHNO des Quinze-Vingts, DHU Sight Restore, INSERM-DGOS CIC 1423, Paris, France
| | - Nassima Bouzidi
- INSERM, CNRS, Institut de la Vision, Sorbonne Université, Paris, France
| | - Diana Milicevic
- INSERM, CNRS, Institut de la Vision, Sorbonne Université, Paris, France
| | - Robin Veaux
- INSERM, CNRS, Institut de la Vision, Sorbonne Université, Paris, France
| | - Aurore Tourville
- INSERM, CNRS, Institut de la Vision, Sorbonne Université, Paris, France
| | - Axelle Zoumba
- INSERM, CNRS, Institut de la Vision, Sorbonne Université, Paris, France
| | - Imene Seneina
- INSERM, CNRS, Institut de la Vision, Sorbonne Université, Paris, France
| | - Marine Foussard
- INSERM, CNRS, Institut de la Vision, Sorbonne Université, Paris, France
| | - Camille Andrieu
- CHNO des Quinze-Vingts, DHU Sight Restore, INSERM-DGOS CIC 1423, Paris, France
| | - Markus N Preising
- Department of Ophthalmology, Justus-Liebig-University Giessen, Germany
| | | | | | - Lilia Mesrob
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, CEA, Université Paris-Saclay, Evry, France.,INSERM, Sorbonne Université, Paris, France
| | - Edith Le Floch
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - Claire Jubin
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - Vincent Meyer
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - Hélène Blanché
- Fondation Jean Dausset-CEPH (Centre d'Etude du Polymorphisme Humain), Paris, France
| | - Anne Boland
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - Jean-François Deleuze
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, CEA, Université Paris-Saclay, Evry, France.,Fondation Jean Dausset-CEPH (Centre d'Etude du Polymorphisme Humain), Paris, France
| | - Dror Sharon
- Department of Ophthalmology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Isabelle Drumare
- Service d'Exploration de la Vision et Neuro-ophtalmologie, CHRU de Lille, Lille, France
| | | | - Elfride De Baere
- Center for Medical Genetics, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Bart P Leroy
- Center for Medical Genetics, Ghent University and Ghent University Hospital, Ghent, Belgium.,Department of Ophthalmology, Ghent University and Ghent University Hospital, Ghent, Belgium.,Division of Ophthalmology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Xavier Zanlonghi
- Clinique Jules Verne, Centre de Compétence Maladies Rares, Nantes, France
| | - Ingele Casteels
- Department of Ophthalmology, University Hospitals Leuven, Leuven, Belgium
| | | | - Irina Balikova
- Department of Ophthalmology, Ghent University and Ghent University Hospital, Ghent, Belgium.,Department of Ophthalmology, Queen Fabiola Children's University Hospital, Brussels, Belgium
| | - Rob K Koenekoop
- Departments of Ophthalmology, Human Genetics, and Pediatric Surgery, Montreal Children's Hospital, McGill University Health Centre, McGill University, Montreal, Quebec, Canada
| | | | - Rebecca McLean
- Department of Neuroscience, Psychology and Behaviour, Ulverscroft Eye Unit, University of Leicester, Leicester, United Kingdom
| | - Irene Gottlob
- Department of Neuroscience, Psychology and Behaviour, Ulverscroft Eye Unit, University of Leicester, Leicester, United Kingdom
| | - Dominique Bonneau
- Département de Biochimie et Génétique, Centre Hospitalier Universitaire, Angers, France.,Mitovasc, UMR CNRS 6015-INSERM 1083, Université d'Angers, France
| | - Daniel F Schorderet
- Department of Ophthalmology, Jules-Gonin Eye Hospital, University of Lausanne, Lausanne, Switzerland.,IRO-Institute for Research in Ophthalmology, Sion, Switzerland.,Faculty of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Francis L Munier
- Department of Ophthalmology, Jules-Gonin Eye Hospital, University of Lausanne, Lausanne, Switzerland
| | - Martin McKibbin
- Department of Ophthalmology, St. James's University Hospital, Leeds, United Kingdom
| | | | - Valerie Pelletier
- Centre de référence pour les Affections Rares en Génétique Ophtalmologique (CARGO), Hôpital Civil, Strasbourg, France.,Service de Génétique Médicale, Hôpital de Hautepierre, Strasbourg, France
| | - Hélène Dollfus
- Centre de référence pour les Affections Rares en Génétique Ophtalmologique (CARGO), Hôpital Civil, Strasbourg, France.,Service de Génétique Médicale, Hôpital de Hautepierre, Strasbourg, France.,Laboratoire de Génétique Médicale, INSERM U1112, Strasbourg, France
| | - Yaumara Perdomo-Trujillo
- Centre de référence pour les Affections Rares en Génétique Ophtalmologique (CARGO), Hôpital Civil, Strasbourg, France
| | - Céline Faure
- CHNO des Quinze-Vingts, DHU Sight Restore, INSERM-DGOS CIC 1423, Paris, France.,Hôpital Privé Saint Martin, Ramsay Générale de Santé, Caen, France
| | | | - Bernd Wissinger
- Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tübingen, Tübingen, Germany
| | - Isabelle Meunier
- Centre de Référence Maladies Sensorielles Génétiques, Hôpital Gui de Chauliac, Montpellier, France.,Institute for Neurosciences of Montpellier, Montpellier University and INSERM U1051, Montpellier, France
| | - Susanne Kohl
- Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tübingen, Tübingen, Germany
| | - Eyal Banin
- Department of Ophthalmology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Eberhart Zrenner
- Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tübingen, Tübingen, Germany.,Werner Reichardt Center for Integrative Neuroscience, University of Tübingen, Tübingen, Germany
| | | | - Birgit Lorenz
- Department of Ophthalmology, Justus-Liebig-University Giessen, Germany
| | - José-Alain Sahel
- INSERM, CNRS, Institut de la Vision, Sorbonne Université, Paris, France.,CHNO des Quinze-Vingts, DHU Sight Restore, INSERM-DGOS CIC 1423, Paris, France.,Fondation Ophtalmologique Adolphe de Rothschild, Paris, France.,Academie des Sciences, Institut de France, Paris, France.,Department of Ophthalmology, The University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Isabelle Audo
- INSERM, CNRS, Institut de la Vision, Sorbonne Université, Paris, France.,CHNO des Quinze-Vingts, DHU Sight Restore, INSERM-DGOS CIC 1423, Paris, France.,Institute of Ophthalmology, University College of London, London, United Kingdom
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10
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Méjécase C, Hummel A, Mohand-Saïd S, Andrieu C, El Shamieh S, Antonio A, Condroyer C, Boyard F, Foussard M, Blanchard S, Letexier M, Saraiva JP, Sahel JA, Zeitz C, Audo I. Whole exome sequencing resolves complex phenotype and identifies CC2D2A mutations underlying non-syndromic rod-cone dystrophy. Clin Genet 2018; 95:329-333. [PMID: 30267408 DOI: 10.1111/cge.13453] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [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: 07/09/2018] [Revised: 09/11/2018] [Accepted: 09/25/2018] [Indexed: 01/20/2023]
Abstract
Genetic investigations were performed in three brothers from a consanguineous union, the two oldest diagnosed with rod-cone dystrophy (RCD), the youngest with early-onset cone-rod dystrophy and the two youngest with nephrotic-range proteinuria. Targeted next-generation sequencing did not identify homozygous pathogenic variant in the oldest brother. Whole exome sequencing (WES) applied to the family identified compound heterozygous variants in CC2D2A (c.2774G>C p.(Arg925Pro); c.4730_4731delinsTGTATA p.(Ala1577Valfs*5)) in the three brothers with a homozygous deletion in CNGA3 (c.1235_1236del p.(Glu412Valfs*6)) in the youngest correcting his diagnosis to achromatopsia plus RCD. None of the three subjects had cerebral abnormalities or learning disabilities inconsistent with Meckel-Gruber and Joubert syndromes, usually associated with CC2D2A mutations. Interestingly, an African woman with RCD shared the CC2D2A missense variant (c.2774G>C p.(Arg925Pro); with c.3182+355_3825del p.(?)). The two youngest also carried compound heterozygous variants in CUBN (c.7906C>T rs137998687 p.(Arg2636*); c.10344C>G p.(Cys3448Trp)) that may explain their nephrotic-range proteinuria. Our study identifies for the first time CC2D2A mutations in isolated RCD and underlines the power of WES to decipher complex phenotypes.
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Affiliation(s)
- Cécile Méjécase
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Aurélie Hummel
- Department of Nephrology, Necker-Enfants Malades Hospital, Paris, France
| | - Saddek Mohand-Saïd
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France.,CHNO des Quinze-Vingts, DHU Sight Restore, INSERM-DGOS CIC 1423, Paris, France
| | - Camille Andrieu
- CHNO des Quinze-Vingts, DHU Sight Restore, INSERM-DGOS CIC 1423, Paris, France
| | - Said El Shamieh
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France.,Department of Medical Laboratory Technology, Faculty of Health Sciences, Beirut Arab University, Beirut, Lebanon
| | - Aline Antonio
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France.,CHNO des Quinze-Vingts, DHU Sight Restore, INSERM-DGOS CIC 1423, Paris, France
| | | | - Fiona Boyard
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Marine Foussard
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | | | | | | | - José-Alain Sahel
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France.,CHNO des Quinze-Vingts, DHU Sight Restore, INSERM-DGOS CIC 1423, Paris, France.,Institute of Ophthalmology, University College of London, London, UK.,Fondation Ophtalmologique Adolphe de Rothschild, Paris, France.,Académie des Sciences, Institut de France, Paris, France.,Department of Ophthalmology, The University of Pittsburgh School of Medicine, Pittsburg, Pennsylvania, USA
| | - Christina Zeitz
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Isabelle Audo
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France.,CHNO des Quinze-Vingts, DHU Sight Restore, INSERM-DGOS CIC 1423, Paris, France.,Institute of Ophthalmology, University College of London, London, UK
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11
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Andrieu C, Mailhe M, Ricaboni D, Fonkou MDM, Bilen M, Cadoret F, Tomei E, Armstrong N, Vitton V, Benezech A, Davoust B, Levasseur A, Lagier JC, Fournier PE, Raoult D. Noncontiguous finished genome sequences and description of Bacteroides mediterraneensis sp. nov., Bacteroides ihuae sp. nov., Bacteroides togonis sp. nov., Bacteroides ndongoniae sp. nov., Bacteroides ilei sp. nov. and Bacteroides congonensis sp. nov. identified by culturomics. New Microbes New Infect 2018; 26:73-88. [PMID: 30258636 PMCID: PMC6154776 DOI: 10.1016/j.nmni.2018.06.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [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: 04/20/2018] [Revised: 06/08/2018] [Accepted: 06/13/2018] [Indexed: 12/22/2022] Open
Abstract
Culturomics is a concept developing different culture conditions in order to enlarge our knowledge of the human microbiota through the discovery of previously uncultured bacteria. This enabled us to isolate six new species of the Bacteroides genus: Bacteroides mediterraneensis strain Marseille-P2644, Bacteroides ihuae strain Marseille-P2824, Bacteroides togonis strain Marseille-P3166, Bacteroides ndongoniae strain Marseille-P3108, Bacteroides ilei strain Marseille-P3208 and Bacteroides congonensis strain Marseille-P3132. Those bacteria are Gram-negative anaerobic bacilli. We describe here their phenotypic features, together with phylogenetic analysis, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry spectrum, fatty acid composition, and genome sequencing and annotation.
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Affiliation(s)
- C Andrieu
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - M Mailhe
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - D Ricaboni
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France.,Département des Sciences Cliniques et Biomédicales, Luigi Sacco, Division des Maladies Infectieuses III, Université de Milan, Milan, Italy
| | - M D M Fonkou
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - M Bilen
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - F Cadoret
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - E Tomei
- Aix-Marseille Université, IRD, AP-HM, SSA, VITROME, IHU-Méditerranée Infection, Marseille, France
| | - N Armstrong
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - V Vitton
- Service de Gastroentérologie, Hopital Nord, Assistance Publique-Hopitaux de Marseille, Marseille, France
| | - A Benezech
- Service de Gastroentérologie, Hopital Nord, Assistance Publique-Hopitaux de Marseille, Marseille, France
| | - B Davoust
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - A Levasseur
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - J-C Lagier
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - P-E Fournier
- Aix-Marseille Université, IRD, AP-HM, SSA, VITROME, IHU-Méditerranée Infection, Marseille, France
| | - D Raoult
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France.,Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
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12
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Mbogning Fonkou M, Mailhe M, Ndongo S, Ricaboni D, Morand A, Cornu F, Tidjani Alou M, Bilen M, Andrieu C, Levasseur A, Cadoret F, Raoult D. Noncontiguous finished genome sequences and descriptions of Actinomyces ihuae, Actinomyces bouchesdurhonensis, Actinomyces urinae, Actinomyces marseillensis, Actinomyces mediterranea and Actinomyces oralis sp. nov. identified by culturomics. New Microbes New Infect 2018; 25:30-44. [PMID: 29992027 PMCID: PMC6036942 DOI: 10.1016/j.nmni.2018.06.004] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 06/05/2018] [Accepted: 06/10/2018] [Indexed: 11/22/2022] Open
Abstract
The taxonogenomic approach, including the culturomics techniques, is now currently used to isolate and characterize new bacteria. These approaches notably allowed us to discover six new species of the Actinomyces genus: Actinomyces ihuae strain SD1, Actinomyces bouchesdurhonensis strain Marseille-P2825, Actinomyces urinae strain Marseille-P2225, Actinomyces marseillensis strain Marseille-P2818, Actinomyces mediterranea strain Marseille-P3257 and Actinomyces oralis strain Marseille-P3109. Each is the type strain of the corresponding bacterial species. 16S ribosomal RNA gene sequence comparison was used to classify these strains among the Actinomyces genus. These strains are all Gram positive, rod shaped and facultative aerobic. We describe the main characteristics of each bacterium and present their complete genome sequence and annotation.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - D. Raoult
- Aix Marseille Université, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France
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13
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Nassisi M, Mohand-Saïd S, Dhaenens CM, Boyard F, Démontant V, Andrieu C, Antonio A, Condroyer C, Foussard M, Méjécase C, Eandi CM, Sahel JA, Zeitz C, Audo I. Expanding the Mutation Spectrum in ABCA4: Sixty Novel Disease Causing Variants and Their Associated Phenotype in a Large French Stargardt Cohort. Int J Mol Sci 2018; 19:E2196. [PMID: 30060493 PMCID: PMC6121640 DOI: 10.3390/ijms19082196] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 06/18/2018] [Accepted: 07/22/2018] [Indexed: 12/18/2022] Open
Abstract
Here we report novel mutations in ABCA4 with the underlying phenotype in a large French cohort with autosomal recessive Stargardt disease. The DNA samples of 397 index subjects were analyzed in exons and flanking intronic regions of ABCA4 (NM_000350.2) by microarray analysis and direct Sanger sequencing. At the end of the screening, at least two likely pathogenic mutations were found in 302 patients (76.1%) while 95 remained unsolved: 40 (10.1%) with no variants identified, 52 (13.1%) with one heterozygous mutation, and 3 (0.7%) with at least one variant of uncertain significance (VUS). Sixty-three novel variants were identified in the cohort. Three of them were variants of uncertain significance. The other 60 mutations were classified as likely pathogenic or pathogenic, and were identified in 61 patients (15.4%). The majority of those were missense (55%) followed by frameshift and nonsense (30%), intronic (11.7%) variants, and in-frame deletions (3.3%). Only patients with variants never reported in literature were further analyzed herein. Recruited subjects underwent complete ophthalmic examination including best corrected visual acuity, kinetic and static perimetry, color vision test, full-field and multifocal electroretinography, color fundus photography, short-wavelength and near-infrared fundus autofluorescence imaging, and spectral domain optical coherence tomography. Clinical evaluation of each subject confirms the tendency that truncating mutations lead to a more severe phenotype with electroretinogram (ERG) impairment (p = 0.002) and an earlier age of onset (p = 0.037). Our study further expands the mutation spectrum in the exonic and flanking regions of ABCA4 underlying Stargardt disease.
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Affiliation(s)
- Marco Nassisi
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, F-75012 Paris, France.
- Department of Surgical Sciences, Eye Clinic, University of Turin, 10126 Turin, Italy.
| | - Saddek Mohand-Saïd
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, F-75012 Paris, France.
- Centre Hospitalier National d'Ophtalmologie des Quinze-Vingts, DHU Sight Restore, INSERM-DHOS CIC 1423, F-75012 Paris, France.
| | - Claire-Marie Dhaenens
- Univ. Lille, Inserm UMR-S 1172, CHU Lille, Biochemistry and Molecular Biology Department-UF Génopathies, F-59000 Lille, France.
| | - Fiona Boyard
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, F-75012 Paris, France.
| | - Vanessa Démontant
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, F-75012 Paris, France.
| | - Camille Andrieu
- Centre Hospitalier National d'Ophtalmologie des Quinze-Vingts, DHU Sight Restore, INSERM-DHOS CIC 1423, F-75012 Paris, France.
| | - Aline Antonio
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, F-75012 Paris, France.
| | - Christel Condroyer
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, F-75012 Paris, France.
| | - Marine Foussard
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, F-75012 Paris, France.
| | - Cécile Méjécase
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, F-75012 Paris, France.
| | - Chiara Maria Eandi
- Department of Surgical Sciences, Eye Clinic, University of Turin, 10126 Turin, Italy.
| | - José-Alain Sahel
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, F-75012 Paris, France.
- Centre Hospitalier National d'Ophtalmologie des Quinze-Vingts, DHU Sight Restore, INSERM-DHOS CIC 1423, F-75012 Paris, France.
- Fondation Ophtalmologique Adolphe de Rothschild, F-75019 Paris, France.
- Académie des Sciences-Institut de France, F-75006 Paris, France.
- Department of Ophthalmology, The University of Pittsburgh School of Medicine, Pittsburg, PA 15213, USA.
| | - Christina Zeitz
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, F-75012 Paris, France.
| | - Isabelle Audo
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, F-75012 Paris, France.
- Centre Hospitalier National d'Ophtalmologie des Quinze-Vingts, DHU Sight Restore, INSERM-DHOS CIC 1423, F-75012 Paris, France.
- Institute of Ophthalmology, University College of London, London EC1V 9EL, UK.
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14
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Orès R, Mohand-Said S, Dhaenens CM, Antonio A, Zeitz C, Augstburger E, Andrieu C, Sahel JA, Audo I. Phenotypic Characteristics of a French Cohort of Patients with X-Linked Retinoschisis. Ophthalmology 2018; 125:1587-1596. [PMID: 29739629 DOI: 10.1016/j.ophtha.2018.03.057] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 03/25/2018] [Accepted: 03/28/2018] [Indexed: 10/17/2022] Open
Abstract
PURPOSE To analyze the retinal structure in patients with X-linked retinoschisis (XLRS) using spectral-domain OCT and to correlate the morphologic findings with visual acuity, electroretinographic results, and patient age. DESIGN Retrospective, observational study. PARTICIPANTS Data from 52 consecutive male patients with molecularly confirmed XLRS were collected retrospectively. METHODS Complete clinical evaluation included best-corrected visual acuity, full-field electroretinography, fundus photography, spectral-domain OCT, and fundus autofluorescence. Spectral-domain OCT images were analyzed to determine full thickness of the retina and tomographic structural changes. MAIN OUTCOME MEASURES Relationships between age, OCT, and visual acuity were assessed. RESULTS One hundred four eyes of 52 patients were included. The mean age at inclusion was 24±15 years (range, 3-57 years). The best-corrected visual acuity ranged from no light perception to 0.1 logarithm of the minimum angle of resolution (mean, 0.6±0.38 logarithm of the minimum angle of resolution). Macular schisis was found in 88% of eyes and macular atrophy was found in 11% of eyes, whereas peripheral schisis was present in 30% of eyes. A spoke-wheel pattern of high and low intensity was the most frequently observed fundus autofluorescence abnormality (51/94 eyes [54%]). The b-to-a amplitude ratio on bright-flash dark-adapted electroretinography was reduced significantly in 45 of 64 eyes (70%). Spectral-domain OCT was available for 97 eyes and showed foveoschisis in 76 of 97 eyes (78%), parafoveal schisis in 10 of 97 eyes (10%), and foveal atrophy in 11 of 97 eyes (11%). Mean central macular thickness (CMT) was of 373.6±140 μm. Cystoid changes were localized mainly in the inner nuclear layer (85/97 eyes [88%]). Qualitative defects in photoreceptor structures were found in most eyes (79/97 eyes [81%]), and the most frequent abnormality was an interruption of the photoreceptor cell outer segment tips (79/79 eyes [100%]). Older age correlated well with lower CMT (correlation coefficient [CC], -0.44; P < 0.001) and with lower photoreceptor outer segment (PROS) length (CC, -0.42; P < 0.001). Lower visual acuity correlated strongly with lower PROS length (CC, -0.53; P < 0.001). CONCLUSIONS This study underlined the wide variety of clinical features of XLRS. It highlighted the correlation between visual acuity, patient age, and OCT features, emphasizing the relevance of the latter as potential outcome measure in clinical trials.
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Affiliation(s)
- Raphaëlle Orès
- Centre de Maladies Rares "Dystrophies Rétiniennes d'Origine Génétique," DHU Sight Restore INSERM-DHOS CIC 1423, Centre Hospitalier National d'Ophtalmologie des Quinze-Vingts, Paris, France
| | - Saddek Mohand-Said
- Centre de Maladies Rares "Dystrophies Rétiniennes d'Origine Génétique," DHU Sight Restore INSERM-DHOS CIC 1423, Centre Hospitalier National d'Ophtalmologie des Quinze-Vingts, Paris, France; INSERM, CNRS, Institut de la Vision, Sorbonne Université, Paris, France
| | - Claire-Marie Dhaenens
- Department of Biochemistry and Molecular Biology-UF Génopathies, Université Lille, Inserm UMR-S 1172, CHU Lille, Lille, France
| | - Aline Antonio
- INSERM, CNRS, Institut de la Vision, Sorbonne Université, Paris, France
| | - Christina Zeitz
- INSERM, CNRS, Institut de la Vision, Sorbonne Université, Paris, France
| | - Edouard Augstburger
- Centre de Maladies Rares "Dystrophies Rétiniennes d'Origine Génétique," DHU Sight Restore INSERM-DHOS CIC 1423, Centre Hospitalier National d'Ophtalmologie des Quinze-Vingts, Paris, France
| | - Camille Andrieu
- Centre de Maladies Rares "Dystrophies Rétiniennes d'Origine Génétique," DHU Sight Restore INSERM-DHOS CIC 1423, Centre Hospitalier National d'Ophtalmologie des Quinze-Vingts, Paris, France
| | - José-Alain Sahel
- Centre de Maladies Rares "Dystrophies Rétiniennes d'Origine Génétique," DHU Sight Restore INSERM-DHOS CIC 1423, Centre Hospitalier National d'Ophtalmologie des Quinze-Vingts, Paris, France; INSERM, CNRS, Institut de la Vision, Sorbonne Université, Paris, France; Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Isabelle Audo
- Centre de Maladies Rares "Dystrophies Rétiniennes d'Origine Génétique," DHU Sight Restore INSERM-DHOS CIC 1423, Centre Hospitalier National d'Ophtalmologie des Quinze-Vingts, Paris, France; INSERM, CNRS, Institut de la Vision, Sorbonne Université, Paris, France.
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15
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Al-Bayssari C, Dubourg G, Cimmino T, Okdah L, Mathlouthi N, Nguyen TT, Andrieu C, Rathored J, Fournier PE, Raoult D, Rolain JM. Genome sequence and description of Paenibacillus ihuae strain GD6 sp. nov., isolated from the stool of a 62-year-old Frenchman. New Microbes New Infect 2018; 23:77-82. [PMID: 29692909 PMCID: PMC5913357 DOI: 10.1016/j.nmni.2018.02.010] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 02/14/2018] [Accepted: 02/20/2018] [Indexed: 11/30/2022] Open
Abstract
Paenibacillus ihuae strain GD6 (=CSUR P892 = DSMZ 45751T) is the new type strain collected from the stool of a 69-year-old Frenchman admitted to an intensive care unit and receiving a 10-day course of imipenem at the time of stool collection. This is a Gram-positive, facultative anaerobic, rod-shaped bacterium. We describe here the features of this organism, together with its complete genome sequence and annotation. The genome size is 6 719 043 bp with 49.6% G+C content and contains 6211 protein-coding and 65 sRNA genes, including four 5S rRNA genes, one 16S rRNA gene and one 23S rRNA gene.
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Affiliation(s)
- C Al-Bayssari
- Aix-Marseille Université IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - G Dubourg
- Aix-Marseille Université IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - T Cimmino
- Aix-Marseille Université IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - L Okdah
- Aix-Marseille Université IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - N Mathlouthi
- Aix-Marseille Université IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - T T Nguyen
- Aix-Marseille Université IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - C Andrieu
- Aix-Marseille Université IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - J Rathored
- Aix-Marseille Université IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - P-E Fournier
- Aix-Marseille Université IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - D Raoult
- Aix-Marseille Université IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - J-M Rolain
- Aix-Marseille Université IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France
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16
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Spyratos F, Andrieu C, Vidaud D, Briffod M, Vidaud M, Lidereau R, Bièche I. CCND1 mRNA Overexpression is Highly Related to Estrogen Receptor Positivity but not to Proliferative Markers in Primary Breast Cancer. Int J Biol Markers 2018. [DOI: 10.1177/172460080001500301] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
To elucidate the role of CCND1 alterations in sporadic breast cancer we investigated the possible link between CCND1 mRNA levels versus estrogen-receptor (ER) status and a proliferation marker, S-phase fraction (SPF), measured by flow cytometry. CCND1 expression was quantified by means of real-time quantitative RT-PCR in a well-characterized series of 33 primary breast cancer patients. Eighteen tumors (54.5%) showed CCND1 overexpression ranging from 3.3 to 29.5 times the level observed in normal breast tissue. Seventeen (94.4%) of the 18 cases with CCND1 overexpression were ER-positive compared to seven (46.7%) of the 15 cases with normal CCND1 expression (p=0.0074). CCND1 overexpression was independent of SPF and DNA-ploidy status. These data suggest that the CCND1 gene does not act as an oncogene responsible for more rapid cell proliferation in breast cancer, but could be involved in the regulation of hormone sensitivity associated with ER.
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Affiliation(s)
- F. Spyratos
- Département d'Anatomo-cytopathologie Faculté des Sciences Pharmaceutiques et Biologiques de Paris - France
- Centre René Huguenin, Saint-Cloud
| | - C. Andrieu
- Laboratoire d'Oncobiologie Faculté des Sciences Pharmaceutiques et Biologiques de Paris - France
- Laboratoire de Génétique Moléculaire
- Centre René Huguenin, Saint-Cloud
| | - D. Vidaud
- Département d'Anatomo-cytopathologie Faculté des Sciences Pharmaceutiques et Biologiques de Paris - France
- Centre René Huguenin, Saint-Cloud
| | - M. Briffod
- Laboratoire d'Oncogénétique Faculté des Sciences Pharmaceutiques et Biologiques de Paris - France
- Centre René Huguenin, Saint-Cloud
| | - M. Vidaud
- Département d'Anatomo-cytopathologie Faculté des Sciences Pharmaceutiques et Biologiques de Paris - France
- Centre René Huguenin, Saint-Cloud
| | - R. Lidereau
- Laboratoire de Génétique Moléculaire
- Centre René Huguenin, Saint-Cloud
| | - I. Bièche
- Département d'Anatomo-cytopathologie Faculté des Sciences Pharmaceutiques et Biologiques de Paris - France
- Laboratoire de Génétique Moléculaire
- Centre René Huguenin, Saint-Cloud
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17
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Alou MT, Ndongo S, Frégère L, Labas N, Andrieu C, Richez M, Couderc C, Baudoin JP, Abrahão J, Brah S, Diallo A, Sokhna C, Cassir N, La Scola B, Cadoret F, Raoult D. Taxonogenomic description of four new Clostridium species isolated from human gut: 'Clostridium amazonitimonense', 'Clostridium merdae', 'Clostridium massilidielmoense' and 'Clostridium nigeriense'. New Microbes New Infect 2017; 21:128-139. [PMID: 29348922 PMCID: PMC5767839 DOI: 10.1016/j.nmni.2017.11.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [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: 08/18/2017] [Revised: 11/09/2017] [Accepted: 11/16/2017] [Indexed: 12/29/2022] Open
Abstract
Culturomics investigates microbial diversity of the human microbiome by combining diversified culture conditions, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and 16S rRNA gene identification. The present study allowed identification of four putative new Clostridium sensu stricto species: ‘Clostridium amazonitimonense’ strain LF2T, ‘Clostridium massilidielmoense’ strain MT26T, ‘Clostridium nigeriense’ strain Marseille-P2414T and ‘Clostridium merdae’ strain Marseille-P2953T, which we describe using the concept of taxonogenomics. We describe the main characteristics of each bacterium and present their complete genome sequence and annotation.
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Affiliation(s)
- M T Alou
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - S Ndongo
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - L Frégère
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - N Labas
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - C Andrieu
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - M Richez
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - C Couderc
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - J-P Baudoin
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - J Abrahão
- Laboratório de Vírus, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - S Brah
- Hopital National de Niamey, BP 247, Niamey, Niger
| | - A Diallo
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France.,Campus Commun UCAD-IRD of Hann, Route des pères Maristes, Hann Maristes, BP 1386, CP 18524, Dakar, Senegal
| | - C Sokhna
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France.,Campus Commun UCAD-IRD of Hann, Route des pères Maristes, Hann Maristes, BP 1386, CP 18524, Dakar, Senegal
| | - N Cassir
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - B La Scola
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - F Cadoret
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - D Raoult
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France.,Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
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18
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Ndongo S, Andrieu C, Fournier PE, Lagier JC, Raoult D. ' Actinomyces provencensis' sp. nov., ' Corynebacterium bouchesdurhonense' sp. nov., ' Corynebacterium provencense' sp. nov. and ' Xanthomonas massiliensis' sp. nov., 4 new species isolated from fresh stools of obese French patients. New Microbes New Infect 2017; 18:24-27. [PMID: 28507764 PMCID: PMC5423319 DOI: 10.1016/j.nmni.2017.01.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [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: 01/05/2017] [Revised: 01/19/2017] [Accepted: 01/30/2017] [Indexed: 12/22/2022] Open
Abstract
We report the main characteristics of ‘Actinomyces provencensis’ strain SN12T sp. nov., ‘Corynebacterium bouchesdurhonense’ strain SN14T sp. nov., ‘Corynebacterium provencense’ strain SN15T sp. nov. and ‘Xanthomonas massiliensis’ strain SN8T sp. nov., which were all isolated from stool samples from obese French patients.
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Affiliation(s)
| | | | | | | | - D. Raoult
- Corresponding author: D. Raoult, Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), CNRS 7278, IRD 198, INSERM 1095, UM63, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, 27 Boulevard Jean Moulin, 13385, Marseille cedex 5, France.Aix-Marseille UniversitéUnité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE)CNRS 7278IRD 198INSERM 1095UM63Institut Hospitalo-Universitaire Méditerranée-InfectionFaculté de médecine27 Boulevard Jean MoulinMarseille cedex 513385France
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19
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Cadoret F, Alou MT, Afouda P, Traore IS, Bréchard L, Michelle C, Di Pinto F, Andrieu C, Delerce J, Levasseur A, Fournier PE, Raoult D. Noncontiguous finished genome sequences and description of Bacillus massiliglaciei, Bacillus mediterraneensis, Bacillus massilinigeriensis, Bacillus phocaeensis and Bacillus tuaregi, five new species identified by culturomics. New Microbes New Infect 2017; 19:45-59. [PMID: 28706723 PMCID: PMC5496451 DOI: 10.1016/j.nmni.2017.04.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [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: 12/01/2016] [Revised: 04/06/2017] [Accepted: 04/13/2017] [Indexed: 11/02/2022] Open
Abstract
Microbial culturomics, which investigates microbial diversity by combining diversified culture conditions, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and 16S rDNA identification, allowed to identify five new species within the Bacillus genus. Bacillus massiliglaciei strain Marseille-P2600T, Bacillus mediterraneensis strain Marseille-P2384T, Bacillus massilinigeriensis strain Marseille-P2366T, Bacillus tuaregi strain Marseille-P2489T and Bacillus phocaeensis strain SIT16T are each the type strain of the corresponding bacterial species. These strains, the genomes of which are described here, are facultative anaerobic Gram-positive bacilli. Here, we describe the main characteristics of each bacterium and present their complete genome sequence and annotation.
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Affiliation(s)
- F Cadoret
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, INSERM 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
| | - M T Alou
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, INSERM 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
| | - P Afouda
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, INSERM 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
| | - I S Traore
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, INSERM 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
| | - L Bréchard
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, INSERM 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
| | - C Michelle
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, INSERM 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
| | - F Di Pinto
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, INSERM 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
| | - C Andrieu
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, INSERM 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
| | - J Delerce
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, INSERM 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
| | - A Levasseur
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, INSERM 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
| | - P-E Fournier
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, INSERM 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
| | - D Raoult
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, INSERM 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France.,Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
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Ricaboni D, Mailhe M, Benezech A, Andrieu C, Fournier PE, Raoult D. ' Pseudoflavonifractor phocaeensis' gen. nov., sp. nov., isolated from human left colon. New Microbes New Infect 2016; 17:15-17. [PMID: 28275431 PMCID: PMC5328723 DOI: 10.1016/j.nmni.2016.12.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [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: 11/18/2016] [Revised: 12/07/2016] [Accepted: 12/07/2016] [Indexed: 12/31/2022] Open
Abstract
We describe here characteristics of ‘Pseudoflavonifractor phocaeensis’ strain Marseille-P3064T, which was isolated from a human left colon wash sample.
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Affiliation(s)
- D Ricaboni
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France; Department of Biomedical and Clinical Sciences, 3rd Division of Clinical Infectious Disease, University of Milan, Luigi Sacco Hospital, Italy
| | - M Mailhe
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
| | - A Benezech
- Service de Gastroenterologie, Hopital Nord, Assistance Publique-Hopitaux de Marseille, Marseille, France
| | - C Andrieu
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
| | - P-E Fournier
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
| | - D Raoult
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
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Tidjani Alou M, Rathored J, Nguyen TT, Andrieu C, Couderc C, Brah S, Diallo BA, Fournier PE, Raoult D, Dubourg G. Paenibacillus phocaensis sp. nov., isolated from the gut microbiota of a healthy infant. New Microbes New Infect 2016; 16:13-24. [PMID: 28116105 PMCID: PMC5233791 DOI: 10.1016/j.nmni.2016.12.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [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: 09/20/2016] [Revised: 11/28/2016] [Accepted: 12/01/2016] [Indexed: 12/20/2022] Open
Abstract
Paenibacillus phocaensis sp. nov. strain mt24T (= CSUR P2238 = DSM 101777) is a Gram-negative, facultative anaerobic, spore-forming and motile bacilli. This strain was isolated from the stool sample of a healthy infant from Niger. Its genome was estimated to a size of 5 521 415 bp with a 53.54% GC content. It contains 4835 protein-coding genes and 89 RNAs, among which two were 16S rRNA genes. There were also 101 genes (2.09%) identified as ORFans.
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Affiliation(s)
- M Tidjani Alou
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - J Rathored
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - T T Nguyen
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - C Andrieu
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - C Couderc
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - S Brah
- Hôpital National de Niamey, BP 238, Niamey, Niger
| | - B A Diallo
- Laboratoire de microbiologie, département de biologie, Université Abdou Moumouni de Niamey, BP 237, Niamey, Niger
| | - P-E Fournier
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - D Raoult
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France; Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - G Dubourg
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
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Mailhe M, Ricaboni D, Vitton V, Benezech A, Dubourg G, Michelle C, Andrieu C, Armstrong N, Bittar F, Fournier PE, Raoult D, Million M. Noncontiguous finished genome sequence and description of Fusobacterium massiliense sp. nov. isolated from human duodenum. New Microbes New Infect 2016; 16:3-12. [PMID: 28116104 PMCID: PMC5225283 DOI: 10.1016/j.nmni.2016.12.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [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: 10/28/2016] [Accepted: 12/01/2016] [Indexed: 11/13/2022] Open
Abstract
The strain Marseille-P2749T (= CSUR P2749 = DSM 103085) was isolated as part of culturomics study from a liquid duodenum sample from a French man. Bacterial cells were Gram-negative bacilli, fusiform shaped and non–spore forming, and they grew in microaerophilic and anaerobic atmosphere. Its genome is 1 809 169 bp long and contains 1646 protein-coding genes. The DNA G+C content was 27.33 mol%. This strain exhibited a 95.9% sequence similarity with Fusobacterium periodonticum, the phylogenetically closest species with standing in nomenclature. Strain Marseille-P2749T is suggested to be a novel species belonging to the genus Fusobacterium, for which the name Fusobacterium massiliense sp. nov. is proposed.
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Affiliation(s)
- M Mailhe
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, INSERM 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
| | - D Ricaboni
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, INSERM 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France; Département des sciences cliniques et biomédicales, Luigi Sacco, Division des Maladies Infectieuses III, Université de Milan, Milan, Italy
| | - V Vitton
- Service de Gastroentérologie, Hopital Nord, Assistance Publique-Hopitaux de Marseille, Marseille, France
| | - A Benezech
- Service de Gastroentérologie, Hopital Nord, Assistance Publique-Hopitaux de Marseille, Marseille, France
| | - G Dubourg
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, INSERM 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
| | - C Michelle
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, INSERM 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
| | - C Andrieu
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, INSERM 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
| | - N Armstrong
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, INSERM 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
| | - F Bittar
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, INSERM 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
| | - P-E Fournier
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, INSERM 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
| | - D Raoult
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, INSERM 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France; Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - M Million
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, INSERM 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
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23
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Ricaboni D, Mailhe M, Vitton V, Andrieu C, Fournier PE, Raoult D. "Negativibacillus massiliensis" gen. nov., sp. nov., isolated from human left colon. New Microbes New Infect 2016; 17:36-38. [PMID: 28275439 PMCID: PMC5328706 DOI: 10.1016/j.nmni.2016.11.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [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: 10/17/2016] [Revised: 11/04/2016] [Accepted: 11/09/2016] [Indexed: 12/13/2022] Open
Abstract
We report here the main characteristics of “Negativibacillus massiliensis” strain Marseille-P3213T, isolated from a human left-colon wash sample.
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Affiliation(s)
- D. Ricaboni
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, France
- Department of Biomedical and Clinical Sciences, 3rd Division of Clinical Infectious Disease, University of Milan, Luigi Sacco Hospital, Milan, Italy
| | - M. Mailhe
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, France
| | - V. Vitton
- Service de Gastroenterologie, Hopital Nord, Assistance Publique-Hopitaux de Marseille, Marseille, France
| | - C. Andrieu
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, France
| | - P.-E. Fournier
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, France
| | - D. Raoult
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, France
- Corresponding author: D. Raoult, Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, 27 Boulevard Jean Moulin, 13385, Marseille cedex 05, FranceAix-Marseille UniversitéURMITEUM63CNRS7278IRD198Inserm 1095Institut Hospitalo-Universitaire Méditerranée-InfectionFaculté de médecine27 Boulevard Jean MoulinMarseille cedex 0513385France
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Andrieu C, Taieb D, Baylot V, Ettinger S, Soubeyran P, De-Thonel A, Nelson C, Garrido C, So A, Fazli L, Bladou F, Gleave M, Iovanna JL, Rocchi P. Heat shock protein 27 confers resistance to androgen ablation and chemotherapy in prostate cancer cells through eIF4E. Oncogene 2010; 29:1883-96. [DOI: 10.1038/onc.2009.479] [Citation(s) in RCA: 106] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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Tozlu-Kara S, Roux V, Andrieu C, Vendrell J, Vacher S, Lazar V, Spyratos F, Tubiana-Hulin M, Cohen P, Dessen P, Lidereau R, Bièche I. Oligonucleotide microarray analysis of estrogen receptor alpha-positive postmenopausal breast carcinomas: identification of HRPAP20 and TIMELESS as outstanding candidate markers to predict the response to tamoxifen. J Mol Endocrinol 2007; 39:305-18. [PMID: 17909269 DOI: 10.1677/jme-07-0001] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The estrogen receptor alpha (ER alpha) status of breast tumors is used to identify patients who may respond to endocrine agents such as tamoxifen. However, ER alpha status alone is not perfectly predictive, and there is a pressing need for more reliable markers of endocrine responsiveness. In this aim, we used a two-step strategy. We first screened genes of interest by a pangenomic 44 K oligonucleotide microarray in a series of ten ER alpha-positive tumors from five tamoxifen-treated postmenopausal patients who relapsed (distant metastasis) and five tamoxifen-treated postmenopausal patients who did not relapse, matched with respect to age, Scarff-Bloom-Richardson grade, lymph node status, and macroscopic tumor size. Genes of interest (n=24) were then investigated in an independent well-characterized series of ER alpha-positive unilateral invasive primary breast tumors from postmenopausal women who received tamoxifen alone as adjuvant hormone therapy after primary surgery. We identified four genes (HRPAP20, TIMELESS, PTPLB, and MGC29814) for which high mRNA levels were significantly associated with shorter relapse-free survival (log-rank test). We also showed that hormone-regulated proliferation-associated 20 kDa protein (HRPAP20) and TIMELESS are 17beta-estradiol-regulated in vitro and are ectopically expressed in OH-Tam-resistant cell lines. In conclusion, these findings point to HRPAP20 and TIMELESS as promising markers of tamoxifen resistance in women with ER alpha-positive breast tumors.
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Affiliation(s)
- S Tozlu-Kara
- Centre René Huguenin, FNCLCC, F-92210 St-Cloud, France
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Rouleau E, Lefol C, Tozlu S, Andrieu C, Guy C, Copigny F, Nogues C, Bieche I, Lidereau R. High-resolution oligonucleotide array-CGH applied to the detection and characterization of large rearrangements in the hereditary breast cancer gene BRCA1. Clin Genet 2007; 72:199-207. [PMID: 17718857 DOI: 10.1111/j.1399-0004.2007.00849.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [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: 11/26/2022]
Abstract
We have developed a new method for detecting and characterizing large rearrangements in the BRCA1 gene based on high-resolution oligonucleotide array-CGH technology. We designed a specific CGH array for the BRCA1 gene and its flanking regions. We then used this approach to analyze nine DNA samples known to contain large deletions and large duplications. When possible, the deleted or duplicated region was sequenced to identify the break point. All the large rearrangements were detected by the new method, and their size was estimated to be within 1--2 kb. This enabled us to develop a simple polymerase chain reaction screening test for other family members. A refined choice of oligonucleotides should improve the precision of the breakpoint determination. Finally, the high resolution of oligonucleotide array-CGH should help to detect new large rearrangements missed by other current methods.
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Affiliation(s)
- E Rouleau
- Laboratoire d'Oncogénétique, Centre René Huguenin, St Cloud, France.
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Tozlu S, Girault I, Vacher S, Vendrell J, Andrieu C, Spyratos F, Cohen P, Lidereau R, Bieche I. Identification of novel genes that co-cluster with estrogen receptor alpha in breast tumor biopsy specimens, using a large-scale real-time reverse transcription-PCR approach. Endocr Relat Cancer 2006; 13:1109-20. [PMID: 17158757 DOI: 10.1677/erc.1.01120] [Citation(s) in RCA: 176] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The estrogen receptor alpha (ERalpha) plays a critical role in the pathogenesis and clinical behavior of breast cancer. To obtain further insights into the molecular basis of estrogen-dependent forms of this malignancy, we used real-time quantitative reverse transcription (RT)-PCR to compare the mRNA expression of 560 selected genes in ERalpha-positive and ERalpha-negative breast tumors. Fifty-one (9.1%) of the 560 genes were significantly upregulated in ERalpha-positive breast tumors compared with ERalpha-negative breast tumors. In addition to well-known ERalpha-induced genes (PGR, TFF1/PS2, BCL2, ERBB4, CCND1, etc.) and genes recently identified by cDNA microarray-based approaches (GATA3, TFF3, MYB, STC2, HPN/HEPSIN, FOXA1, XBP1, SLC39A6/LIV-1, etc.), an appreciable number of novel genes were identified, many of, which were weakly expressed. This validates the use of large-scale real-time RT-PCR as a method complementary to cDNA microarrays for molecular tumor profiling. Most of the new genes identified here encoded secreted proteins (SEMA3B and CLU), growth factors (BDNF, FGF2 and EGF), growth factor receptors (IL6ST, PTPRT, RET, VEGFR1 and FGFR2) or metabolic enzymes (CYP2B6, CA12, ACADSB, NAT1, LRBA, SLC7A2 and SULT2B1). Importantly, we also identified a large number of genes encoding proteins with either pro-apoptotic (PUMA, NOXA and TATP73) or anti-apoptotic properties (BCL2, DNTP73 and TRAILR3). Surprisingly, only a small proportion of the 51 genes identified in breast tumor biopsy specimens were confirmed to be ERalpha-regulated and/or E2-regulated in vitro (cultured cell lines). Therefore, this study identified a limited number of genes and signaling pathways, which better delineate the role of ERalpha in breast cancer. Some of the genes identified here could be useful for diagnosis or for predicting endocrine responsiveness, and could form the basis for novel therapeutic strategies.
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Affiliation(s)
- S Tozlu
- Centre René Huguenin, FNCLCC, St-Cloud F-92210, France
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Andrieu C, Gautrand D, Presseq P, Castel M. Le passage aux 35 heures : son vécu dans deux entreprises. ARCH MAL PROF ENVIRO 2004. [DOI: 10.1016/s1775-8785(04)93157-8] [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: 11/29/2022]
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Andrieu C, Gautrand D, Presseq P, Castel M. La sous charge au travail : quels enjeux ? ARCH MAL PROF ENVIRO 2004. [DOI: 10.1016/s1775-8785(04)93128-1] [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: 10/22/2022]
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Berdugo M, Valamanesh F, Andrieu C, Klein C, Benezra D, Courtois Y, Behar-Cohen F. Delivery of antisense oligonucleotide to the cornea by iontophoresis. Antisense Nucleic Acid Drug Dev 2003; 13:107-14. [PMID: 12804037 DOI: 10.1089/108729003321629647] [Citation(s) in RCA: 48] [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] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
We wished to evaluate the potential of iontophoresis to promote the delivery of antisense oligonucleotides (ODN) directed at the vascular endothelial growth factor (VEGF)-R2 receptor (KDR/Flk) to the cornea of the rat eye. Fluorescence (CY5)-labeled ODNs in phosphate-buffered saline (PBS) (20 microM) were locally administered to rat eyes, and their fate within the anterior segment was studied. Thirty-four male, 5-week-old Wistar rats were used for all experiments. The rats were divided in four groups. In group I (12 rats, 12 eyes), the ODNs (20 microM) were delivered by iontophoresis (300 microA for 5 minutes) using a specially designed corneal applicator. In group II (12 rats, 12 eyes), the ODNs (20 microM) were delivered using the same applicator, but no electrical current was applied. In group III (6 rats, 6 eyes), a corneal neovascular reaction was induced prior to the application of ODNs (20 microM), and iontophoresis electrical current was delivered as for group I rats. Group IV (4 rats, 4 eyes) received ODN (60 microM) iontophoresis application (300 microA for 5 minutes) and were used for ODN integrity studies. The animals were killed 5 minutes, 90 minutes, and 24 hours after a single ODN application and studied. Topically applied ODNs using the same iontophoresis applicator but without current do not penetrate the cornea and remain confined to the superficial epithelial layer. ODNs delivered with transcorneoscleral iontophoresis penetrate into all corneal layers and are also detected in the iris. In corneas with neovascularization, ODNs were particularly localized within the vascular endothelial cells of the stroma. ODNs extracted from eye tissues 24 hours after iontophoresis remained unaltered. The iontophoresis current did not cause any detectable ocular damage under these conditions. Iontophoresis promotes the delivery of ODNs to the anterior segment of the eye, including all corneal layers. Iontophoresis of ODNs directed at VEGF-R2 may be used for the design of specific antiangiogenic strategy in diseases of the cornea.
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Affiliation(s)
- M Berdugo
- Association Claude Bermond, INSERM U450, Paris, France
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33
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Hitchcock AP, Tourillon G, Garrett R, Williams GP, Mahatsekake C, Andrieu C. Inner-shell excitation of gas-phase and polymer thin-film 3-alkylthiophenes by electron energy loss and x-ray photoabsorption spectroscopy. ACTA ACUST UNITED AC 2002. [DOI: 10.1021/j100369a026] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Bièche I, Onody P, Lerebours F, Tozlu S, Hacene K, Andrieu C, Vidaud M, Tubiana-Hulin M, Spyratos F, Lidereau R. ERBB2 status and benefit from adjuvant tamoxifen in ERalpha-positive postmenopausal breast carcinoma. Cancer Lett 2001; 174:173-8. [PMID: 11689293 DOI: 10.1016/s0304-3835(01)00696-6] [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: 11/17/2022]
Abstract
We examined the relation between ERBB2 gene expression (as determined by a real-time quantitative RT-PCR assay) and the response to adjuvant tamoxifen therapy in a well-defined cohort of 125 ERalpha-positive postmenopausal patients with breast cancer. Although ERBB2 overexpression was associated with shorter relapse-free survival in univariate analysis (P=0.00029), ERBB2 did not persist as an independent prognostic factor in multivariate analysis. Nevertheless, when we analyzed the ERBB2 mRNA level as a continuous variable, the higher the ERBB2RNA level, the poorer the outcome (P=0.00036). The results point to the need for a quantitative ERBB2 expression assay for use in future studies of ERBB2-based clinical management of breast cancer.
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Affiliation(s)
- I Bièche
- Laboratoire d'Oncogénétique, INSERM E0017, 35 rue Dailly, F-92211 St-Cloud, France.
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36
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Bièche I, Parfait B, Noguès C, Andrieu C, Vidaud D, Spyratos F, Lidereau R, Vidaud M. The CGA gene as new predictor of the response to endocrine therapy in ER alpha-positive postmenopausal breast cancer patients. Oncogene 2001; 20:6955-9. [PMID: 11687975 DOI: 10.1038/sj.onc.1204739] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2001] [Revised: 05/29/2001] [Accepted: 06/18/2001] [Indexed: 11/09/2022]
Abstract
We recently identified CGA (coding for the alpha subunit of glycoprotein hormones) as a new estrogen receptor alpha (ER alpha)-responsive gene in human breast tumors. Here, we assessed the relationship between CGA status (as determined by real-time quantitative RT-PCR) and the response to tamoxifen therapy in a well-defined cohort of 125 ER alpha-positive postmenopausal breast cancer patients treated with primary surgery followed by adjuvant tamoxifen alone. CGA overexpression, observed in 37.6% of patients, was associated with good relapse-free survival (P=0.037; univariate analysis). CGA status, combined with ERBB2 status (a marker of poor outcome), was an independent predictor of the response to tamoxifen (P=0.020; multivariate analysis). CGA status, especially when combined with ERBB2 status, may thus provide useful predictive information on tamoxifen responsiveness in breast cancer.
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Affiliation(s)
- I Bièche
- Laboratoire de Génétique Moléculaire-UPRES JE 2195, Faculté des Sciences Pharmaceutiques et Biologiques, Université René Descartes-Paris V, 4 Avenue de l'Observatoire, F-75006 Paris, France
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Abstract
We propose a hierarchical full Bayesian model for radial basis networks. This model treats the model dimension (number of neurons), model parameters, regularization parameters, and noise parameters as unknown random variables. We develop a reversible-jump Markov chain Monte Carlo (MCMC) method to perform the Bayesian computation. We find that the results obtained using this method are not only better than the ones reported previously, but also appear to be robust with respect to the prior specification. In addition, we propose a novel and computationally efficient reversible-jump MCMC simulated annealing algorithm to optimize neural networks. This algorithm enables us to maximize the joint posterior distribution of the network parameters and the number of basis function. It performs a global search in the joint space of the parameters and number of parameters, thereby surmounting the problem of local minima to a large extent. We show that by calibrating the full hierarchical Bayesian prior, we can obtain the classical Akaike information criterion, Bayesian information criterion, and minimum description length model selection criteria within a penalized likelihood framework. Finally, we present a geometric convergence theorem for the algorithm with homogeneous transition kernel and a convergence theorem for the reversible-jump MCMC simulated annealing method.
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Affiliation(s)
- C Andrieu
- Cambridge University Engineering Department, Cambridge CB2 1PZ, England
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Spyratos F, Andrieu C, Vidaud D, Briffod M, Vidaud M, Lidereau R, Bièche I. CCND1 mRNA overexpression is highly related to estrogen receptor positivity but not to proliferative markers in primary breast cancer. Int J Biol Markers 2000; 15:210-4. [PMID: 11012095] [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: 02/17/2023]
Abstract
To elucidate the role of CCND1 alterations in sporadic breast cancer we investigated the possible link between CCND1 mRNA levels versus estrogen-receptor (ER) status and a proliferation marker, S-phase fraction (SPF), measured by flow cytometry. CCND1 expression was quantified by means of real-time quantitative RT-PCR in a well-characterized series of 33 primary breast cancer patients. Eighteen tumors (54.5%) showed CCND1 overexpression ranging from 3.3 to 29.5 times the level observed in normal breast tissue. Seventeen (94.4%) of the 18 cases with CCND1 overexpression were ER-positive compared to seven (46.7%) of the 15 cases with normal CCND1 expression (p=0.0074). CCND1 overexpression was independent of SPF and DNA-ploidy status. These data suggest that the CCND1 gene does not act as an oncogene responsible for more rapid cell proliferation in breast cancer, but could be involved in the regulation of hormone sensitivity associated with ER.
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Affiliation(s)
- F Spyratos
- Laboratoire d'Oncobiologie, Centre René Huguenin, Saint-Cloud, France
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39
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Bouchet-Bernet C, Spyratos F, Andrieu C, Deytieux S, Bécette V, Oglobine J. Influence of the extraction procedure on plasminogen activator inhibitor-2 (PAI-2) and urokinase receptor (uPAR) assays in breast cancer tissues. Breast Cancer Res Treat 1996; 41:141-6. [PMID: 8944332 DOI: 10.1007/bf01807159] [Citation(s) in RCA: 11] [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: 02/03/2023]
Abstract
The levels of uPA, its inhibitors PAI-1 and PAI-2, and the uPA receptor (uPAR) have prognostic value in breast cancer. However, different extraction methods and assays kits are used in different laboratories and may directly influence the levels observed. To define a buffer suitable for both PAI-2 and uPAR extraction from breast cancer tissue compatible with hormone receptors and other cytosolic prognosticator assays, we compared PAI-2 and uPAR values obtained by immunoenzymatic assays (American Diagnostica, Greenwhich, USA) in several extraction conditions: 1) cytosol obtained with the standard hormone receptor buffer; 2) solubilized pellets obtained by Triton X100 extraction of the pelleted membranes obtained with standard hormone receptor buffer; 3) cytosol obtained by direct extraction in the buffer (containing Triton X100) recommended by the manufacturer, after 2 hours or 12 hours of incubation. Cytosol extracts prepared using the standard procedure recommended for hormone receptors gave the highest PAI-2 values. The highest uPAR values were obtained in the subsequent detergent extraction of the pelleted membranes. PAI-2 levels obtained with the kit manufacturer's method after 12 hours of incubation were lower than those obtained after 2 hours of incubation, whereas uPAR levels were similar. We conclude that the most suitable extraction protocol employs standard hormone receptor extraction buffer to obtain a supernatant cytosol fraction for PAI-2 assay, and subsequent detergent extraction of the pelleted membranes to obtain an extract suitable for uPAR.
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Affiliation(s)
- C Bouchet-Bernet
- Laboratoire d'Immunochimie, Centre René Huguenin, St. Cloud, France
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40
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Colombel MC, Pous MF, Abbou CC, Vanvelthoven R, Bellot J, Spyratos F, Andrieu C, de Launoit Y, Chopin DK. Computer assisted image analysis of bladder tumour nuclei for morphonuclear and ploidy assessment. Anal Cell Pathol 1994; 6:137-47. [PMID: 8167096] [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: 01/29/2023] Open
Abstract
Morphonuclear analysis using a quantitative image analysis system has been demonstrated to be a potentially useful technique in the prognostic evaluation of bladder carcinoma. The integrated optical density parameter permits DNA content evaluation in addition to 15 other morphonuclear parameters. We assessed the reliability of morphonuclear analysis by image analysis and flow cytometry for 46 bladder carcinomas and 14 normal bladder specimens. Frozen sample material was obtained from endoscopic resection, radical cystectomy and from cadaveric donors. The grade and staging of the tumours according to the World Health Organization was as follows: 8 G1, 18 G2, 20 G3 and 28 T1, 7 T2, 7 T3, 4 T4. Quantitative image analysis was made on imprint smears stained by the Feulgen method. Simultaneously cell suspensions were obtained by mechanical dissociation and stained with propidium iodide for Flow cytometry analysis. There was a good agreement between quantitative image analysis and flow cytometry for DNA content measurement indicating that image analysis is a reliable method for the quantitation of DNA content (P = 0.001). Moreover we found a good correlation between five of the morphonuclear parameters: surface (P < 0.001), chromatin clumps distribution (P < 0.001), frequency of small (P < 0.001) to large chromatin clumps (P < 0.001) and the grade of bladder tumours. These results indicate that morphonuclear analysis may be a valuable method of quantitating DNA and morphonuclear parameters in a single analysis to provide information which may have some prognostic significance for patients with bladder carcinoma.
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Affiliation(s)
- M C Colombel
- Service d'urologie, Hôpital H. Mondor CHU, Créteil, France
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Abstract
We reviewed 319 primary breast tumours for cytosolic pS2 content, with a median follow-up of 6 years. pS2 status correlated positively with oestradiol and progesterone receptors and negatively with Scarff, Bloom and Richardson grade. pS2 positivity was associated with longer overall survival, particularly in patients who received hormone therapy, in whom pS2 status was also predictive of the response to therapy.
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Affiliation(s)
- F Spyratos
- Centre René Huguenin, Saint-Cloud, France
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42
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Spyratos F, Martin PM, Hacène K, Andrieu C, Romain S, Floiras JL, Magdelénat H. Prognostic value of a solubilized fraction of EGF receptors in primary breast cancer using an immunoenzymatic assay--a retrospective study. Breast Cancer Res Treat 1994; 29:85-95. [PMID: 8018965 DOI: 10.1007/bf00666184] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [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: 01/28/2023]
Abstract
In a retrospective study of 319 primary breast cancers, we show that an immunoenzymatic assay of a solubilized fraction of EGF receptors indicates a prognostic value for EGFR which is in contradiction with some (but not all) other studies. It appears that different methodological approaches of measuring EGFR are not equivalent in terms of prognostic power. We emphasize the need for rigorous multicentric standardization and quality control of assays, followed by multistep validation of parameters oriented towards clinical use.
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Affiliation(s)
- F Spyratos
- Centre René Huguenin, Saint-Cloud, France
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Le Doussal V, Spyratos F, Andrieu C, Briffod M. Improvement in the prognostic value of nuclear components of cytological-histological MSBR grading and its dependent relationship to ploidy and S-phase status in primary operable breast carcinoma. Eur J Cancer 1993. [DOI: 10.1016/0959-8049(93)90914-2] [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: 11/29/2022]
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Spyratos F, Martin PM, Hacène K, Romain S, Andrieu C, Ferrero-Poüs M, Deytieux S, Le Doussal V, Tubiana-Hulin M, Brunet M. Multiparametric prognostic evaluation of biological factors in primary breast cancer. J Natl Cancer Inst 1992; 84:1266-72. [PMID: 1640487 DOI: 10.1093/jnci/84.16.1266] [Citation(s) in RCA: 99] [Impact Index Per Article: 3.1] [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: 12/28/2022] Open
Abstract
BACKGROUND An array of biological features related to tumor cell differentiation status, growth rate, and invasive potential have been identified as potential prognostic factors in breast cancer. We were interested in determining their relative importance in predicting patient survival. PURPOSE We evaluated the relative weight of the following four biological factors in predicting survival of patients with breast cancer: tumor cell DNA content (determined by flow cytometry), tumor cell proliferation rate (determined by thymidine kinase activity), expression levels of cathepsin D and urokinase plasminogen activator, and several "classical" clinical and histological factors. METHODS Selected from a prospectively updated database, the study population consisted of 319 primary breast cancer patients who received treatment and follow-up care (median, 6 years) in the Centre René Huguenin. To determine the profile of biological factors for each patient, we used frozen tumor specimens and (except for the flow cytometric DNA content assay) commercially available assay kits. We determined by Cox multivariate analysis the relationships of the biological factors to each other, to classical prognostic factors, and to disease-free and metastasis-free survival. RESULTS In the overall population, disease-free survival was best predicted by node status (P = .004), clinical tumor size (P = .02), and cathepsin D expression (P = .01), whereas metastasis-free survival was best predicted by node status (P = .0004), clinical tumor size (P = .009), and urokinase plasminogen activator expression (P = .04). In node-negative patients, thymidine kinase activity was the only factor selected for disease-free (P = .04) and metastasis-free (P = .05) survival. In node-positive patients, the number of positive axillary lymph nodes was the only factor selected for disease-free (P = .0008) and metastasis-free (P = .00017) survival. CONCLUSIONS Our retrospective analysis has identified protease expression and tumor cell proliferation rate as important biological prognostic factors in breast cancer. Prospective clinical trials should be undertaken to confirm these results.
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Affiliation(s)
- F Spyratos
- Laboratoire des Récepteurs Hormonaux, Centre René Huguenin, St-Cloud, France
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Predine J, Spyratos F, Prud'homme JF, Andrieu C, Hacene K, Brunet M, Pallud C, Milgrom E. Enzyme-linked immunosorbent assay of pS2 in breast cancers, benign tumors, and normal breast tissues. Correlation with prognosis and adjuvant hormone therapy. Cancer 1992; 69:2116-23. [PMID: 1544118 DOI: 10.1002/1097-0142(19920415)69:8<2116::aid-cncr2820690818>3.0.co;2-b] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.4] [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: 12/27/2022]
Abstract
An enzyme-linked immunosorbent assay using monoclonal and polyclonal antibodies against recombinant pS2 was devised. It was used to measure pS2 concentration in the cytosol of 339 breast cancer, 15 fibroadenomas, 16 cases of benign breast disease, and 6 normal breast tissues. The mean value of pS2 concentration was higher in cancer, but the protein could be detected readily in benign tumors and even in normal breast. The concentration of pS2 was significantly lower in postmenopausal women and tumors of differentiation Grade 3. The pS2 concentration was correlated strongly with the presence of estrogen receptors (ER) and progesterone receptors (PR). No correlation was observed with the size, histologic type of the tumor, and lymph node status. The prognostic value of pS2 appeared relatively limited. It was clear cut only for a relatively small group of patients (approximately 15%), who had low concentrations of pS2 (less than or equal to 0.32 ng/mg of protein). These patients had a shorter disease-free interval and overall survival time. The most striking correlation was observed with the outcome of adjuvant hormone therapy. pS2 concentration was shown to be the most potent prognostic factor, preceding even ER.
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Affiliation(s)
- J Predine
- Unité de Recherches Hormones et Reproduction, Faculté de Médecine, Le Kremlin-Bicêtre, France
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Spyratos F, Briffod M, Tubiana-Hulin M, Andrieu C, Mayras C, Pallud C, Lasry S, Rouëssé J. Sequential cytopunctures during preoperative chemotherapy for primary breast carcinoma. II. DNA flow cytometry changes during chemotherapy, tumor regression, and short-term follow-up. Cancer 1992; 69:470-5. [PMID: 1728376 DOI: 10.1002/1097-0142(19920115)69:2<470::aid-cncr2820690233>3.0.co;2-l] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.5] [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: 12/28/2022]
Abstract
Between May 1986 and May 1987, 35 primary noninflammatory breast carcinomas (T3N0-N1M0) were studied by means of DNA flow cytometry (FCM-DNA) before and after each of three courses of preoperative chemotherapy (doxorubicin, vincristine, cyclophosphamide, methotrexate, and 5-fluorouracil) to assess initial nuclear DNA content, initial S-phase fraction (SPF), and the impact of chemotherapy on these parameters. Correlations were sought with objective regression and short-term follow-up. Four sequential cytopunctures were performed for cytologic examination and FCM-DNA analyses. Ten tumors were diploid and 25 aneuploid. No significant changes in FCM-DNA parameters during chemotherapy were observed in diploid tumors, and no regression was seen in nine of the ten cases. Among the 25 aneuploid tumors, 10 showed changes in DNA content and/or kinetic parameters. A significant correlation was observed between objective regression and initial FCM-DNA content (P = 0.008), initial SPF (P = 0.004), and changes in FCM-DNA patterns observed during chemotherapy (P = 0.00005). During the follow-up period (range, 27 to 41 months), 13 patients had relapses. Patients with aneuploid tumors were more likely to have relapses (n = 11) than patients with diploid tumors (n = 2), and patients with high SPF were more likely to have relapses than patients with low SPF, but the differences were not significant. Similarly, changes in FCM-DNA parameters were observed more often in patients who had relapses, but, again, the difference was not significant. In 5 of the 13 patients who had relapses, FCM-DNA analyses were performed on cytopunctures of the recurrences: patterns were identical to those observed before treatment even when the primary tumor regressed or showed changes in FCM-DNA parameters during chemotherapy.
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Affiliation(s)
- F Spyratos
- Department of Biology, Centre René Huguenin, Saint-Cloud, France
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Spyratos F, Delarue JC, Andrieu C, Lidereau R, Champème MH, Hacène K, Brunet M. Epidermal growth factor receptors and prognosis in primary breast cancer. Breast Cancer Res Treat 1990; 17:83-9. [PMID: 2096996 DOI: 10.1007/bf01806288] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.4] [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: 12/30/2022]
Abstract
A retrospective study was performed on 109 human breast tumors stored in liquid nitrogen in order to assess the prognostic value of epidermal growth factor receptor (EGF-R) (median patient follow-up 5 years). A significant inverse relationship was observed between EGF-R and both estrogen (ER) and progesterone receptors (PR). Univariate analysis showed a trend towards a shorter metastasis-free survival both in the overall population and in node-negative patients with EGF-R positive tumors. Multivariate analysis of the overall population showed that lymph-node involvement and PR status were the only significant variables in predicting metastasis-free survival. However, in patients receiving no adjuvant treatment (hormone therapy or chemotherapy). EGF was the only significant variable in the multivariate Cox analysis. No c-erbB-1 amplification was detected in these tumors.
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Affiliation(s)
- F Spyratos
- Laboratoire des récepteurs hormonaux, Centre René Huguenin, Saint-Cloud, France
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Spyratos F, Maudelonde T, Brouillet JP, Brunet M, Defrenne A, Andrieu C, Hacene K, Desplaces A, Rouëssé J, Rochefort H. Cathepsin D: an independent prognostic factor for metastasis of breast cancer. Lancet 1989; 2:1115-8. [PMID: 2572846 DOI: 10.1016/s0140-6736(89)91487-6] [Citation(s) in RCA: 248] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
122 patients with primary breast cancer were followed-up for a median of 4.6 years after surgery. The concentration of cathepsin D in tumour cytosol was strongly related to both metastasis-free survival and disease-free survival and was independent of nine conventional prognostic indices. Cathepsin D assay may prove particularly useful in identifying women who, though without lymph node involvement at presentation, are at high risk of metastatic disease.
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Affiliation(s)
- F Spyratos
- Centre René Huguenin, Saint-Cloud, France
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