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8 results on '"MESH: Cryptococcus neoformans"'

1. Panniculitis in a Woman With Opportunistic Pulmonary Coinfection by Pneumocystis jirovecii and Cryptococcus neoformans

Author

Tedbirt, Billal, Duval-Modeste, Anne-Benedicte, Courville, Philippe, Dominique, Stéphane, Vera, Pierre, Regaieg, Hamza, Equipe Quantification en Imagerie Fonctionnelle (QuantIF-LITIS), Laboratoire d'Informatique, de Traitement de l'Information et des Systèmes (LITIS), Institut national des sciences appliquées Rouen Normandie (INSA Rouen Normandie), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Université Le Havre Normandie (ULH), Normandie Université (NU)-Institut national des sciences appliquées Rouen Normandie (INSA Rouen Normandie), and Normandie Université (NU)

Subjects
MESH: Humans, MESH: Middle Aged, MESH: Fluorodeoxyglucose F18, [SDV]Life Sciences [q-bio], MESH: Cryptococcosis, MESH: Cryptococcus neoformans, MESH: Opportunistic Infections, MESH: Positron Emission Tomography Computed Tomography, MESH: Female, MESH: Pneumocystis carinii, MESH: Coinfection, MESH: Treatment Outcome, MESH: Pneumonia, Pneumocystis
Abstract

International audience; A 56-year-old woman, with history of psoriasis well controlled on ustekinumab, underwent 18F-FDG PET/CT to explore first onset of histologically proven skin panniculitis of unknown origin. PET/CT showed high uptake in panniculitis lesions in limbs and in a lung opacity suggestive of pneumonia. Based on PET/CT findings, a bronchoalveolar lavage revealed pulmonary coinfection by Pneumocystis jirovecii and Cryptococcus neoformans. Thus, hematogenous dissemination of infection was suspected as etiology of panniculitis. She was treated with fluconazole and trimethoprim-sulfamethoxazole, leading to total resolution of skin lesions. Posttherapeutic PET/CT showed complete metabolic response of skin and pulmonary lesions.

Published
2021
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2. Application of an optimized annotation pipeline to the Cryptococcus deuterogattii genome reveals dynamic primary metabolic gene clusters and genomic impact of RNAi loss

Author

Gröhs Ferrareze, Patrícia Aline, Maufrais, Corinne, Silva Araujo Streit, Rodrigo, Priest, Shelby, Cuomo, Christina, Heitman, Joseph, Staats, Charley Christian, Janbon, Guilhem, Biologie des ARN des Pathogènes fongiques - RNA Biology of Fungal Pathogens, Institut Pasteur [Paris] (IP)-Université Paris Cité (UPCité), Universidade Federal do Rio Grande do Sul [Porto Alegre] (UFRGS), Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB, Duke University Medical Center, Broad Institute of MIT and Harvard (BROAD INSTITUTE), Harvard Medical School [Boston] (HMS)-Massachusetts Institute of Technology (MIT)-Massachusetts General Hospital [Boston], PAGF was supported by a CAPES exchange grant (Advanced Network of Computational Biology—RABICÓ – Grant no. 23038.010041/2013-13). This work was supported by a CAPES COFECUB grant n°39712ZK to GJ, by a CNPq grant (309897/2017-3) to CCS, and by a NIH/NIAID R37 MERIT Award AI39115-23 and a NIH/NIAID R01 Award AI50113-16 to JH. JH is co-director and fellow of CIFAR program Fungal Kingdom: Threats & Opportunities. SJP was supported by the NIH/NIAID F31 Fellowship 1F31AI143136-02., and Members of the Heitman laboratory are acknowledged for valuable discussion.

Subjects
AcademicSubjects/SCI01140, AcademicSubjects/SCI00010, genome annotation pipeline, MESH: Genomics, [SDV]Life Sciences [q-bio], MESH: RNA Interference, MESH: Cryptococcus neoformans, Molecular Sequence Annotation, MESH: Molecular Sequence Annotation, Genomics, Cryptococus deuterogattii, AcademicSubjects/SCI01180, metabolic gene cluster, RNAi, Multigene Family, MESH: Genome, Fungal, Fungal Genetics and Genomics, Cryptococcus neoformans, MESH: Multigene Family, AcademicSubjects/SCI00960, RNA Interference, Genome, Fungal
Abstract

International audience; Evaluating the quality of a de novo annotation of a complex fungal genome based on RNA-seq data remains a challenge. In this study, we sequentially optimized a Cufflinks-CodingQuary-based bioinformatics pipeline fed with RNA-seq data using the manually annotated model pathogenic yeasts Cryptococcus neoformans and Cryptococcus deneoformans as test cases. Our results show that the quality of the annotation is sensitive to the quantity of RNA-seq data used and that the best quality is obtained with 5–10 million reads per RNA-seq replicate. We also showed that the number of introns predicted is an excellent a priori indicator of the quality of the final de novo annotation. We then used this pipeline to annotate the genome of the RNAi-deficient species Cryptococcus deuterogattii strain R265 using RNA-seq data. Dynamic transcriptome analysis revealed that intron retention is more prominent in C. deuterogattii than in the other RNAi-proficient species C. neoformans and C. deneoformans. In contrast, we observed that antisense transcription was not higher in C. deuterogattii than in the two other Cryptococcus species. Comparative gene content analysis identified 21 clusters enriched in transcription factors and transporters that have been lost. Interestingly, analysis of the subtelomeric regions in these three annotated species identified a similar gene enrichment, reminiscent of the structure of primary metabolic clusters. Our data suggest that there is active exchange between subtelomeric regions, and that other chromosomal regions might participate in adaptive diversification of Cryptococcus metabolite assimilation potential.

Published
2021
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3. From the environment to the host: How non-azole agrochemical exposure affects the antifungal susceptibility and virulence of Cryptococcus gattii

Author

Frédérique Moyrand, Guilhem Janbon, Hellem Cristina Silva Carneiro, Ludmila Gouveia-Eufrasio, Daniel Assis Santos, Rafael Wesley Bastos, Lorena Vívien Neves de Oliveira, Gustavo José Cota de Freitas, Corinne Maufrais, Anderson Philip Nonato Santos, Departamento de Microbiologia [Minas Gerais, Brazil], Instituto de Ciencias Biologicas [Minas Gerais], Universidade Federal de Minas Gerais [Belo Horizonte] (UFMG)-Universidade Federal de Minas Gerais [Belo Horizonte] (UFMG), Faculdade de Ciências Farmacêuticas de Ribeirão Preto [São Paulo], Universidade de São Paulo = University of São Paulo (USP), Biologie des ARN des Pathogènes fongiques - RNA Biology of Fungal Pathogens, Institut Pasteur [Paris] (IP), This study was supported by Fundação de Amparo a Pesquisa do Estado de Minas Gerais - FAPEMIG (Grants APQ-00727-16 and PPM-00061-18) and Conselho Nacional de Desenvolvimento Científico e Tecnológico - CNPq (Grants 403006/2016-3 and 440010/2018-7). RWB received fellowships from CNPq and Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (PDSE-CAPES-88881.131683/2016-01). DAS is a research fellow of the CNPq (Grant 302670/2017-3)., Universidade de São Paulo (USP), and Institut Pasteur [Paris]

Subjects
Antifungal Agents, 010504 meteorology & atmospheric sciences, 010501 environmental sciences, Ravuconazole, 01 natural sciences, Mice, Efflux pumps, MESH: Animals, Waste Management and Disposal, Fluconazole, [SDV.MP.MYC]Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, 2. Zero hunger, chemistry.chemical_classification, MESH: Microbial Sensitivity Tests, biology, MESH: Agrochemicals, Temperature, MESH: Strobilurins / toxicity, MESH: Cryptococcus neoformans, Strobilurins, Pollution, Agrochemicals, medicine.drug, Environmental Engineering, Itraconazole, Virulence, Microbial Sensitivity Tests, Microbiology, MESH: Antifungal Agents, Minimum inhibitory concentration, Drug Resistance, Fungal, parasitic diseases, medicine, Environmental Chemistry, Animals, Humans, Cross-resistance, Cryptococcus gattii, MESH: Mice, 0105 earth and related environmental sciences, MESH: Humans, biology.organism_classification, bacterial infections and mycoses, chemistry, MESH: Cryptococcus gattii / physiology, Cryptococcus neoformans, Pyraclostrobin, Azole, MESH: Drug Resistance, Fungal / physiology
Abstract

International audience; Agrochemicals such as the non-azoles, used to improve crop productivity, poses severe undesirable effects on the environment and human health. In addition, they induce cross-resistance (CR) with clinical drugs in pathogenic fungi. However, till date emphasis has been given to the role of azoles on the induction of CR. Herein, we analyzed the effect of a non-azole agrochemical, pyraclostrobin (PCT), on the antifungal susceptibility and virulence of the human and animal pathogens Cryptococcus gattii and C. neoformans. We determined the minimum inhibitory concentration (MIC) of fluconazole (FLC), itraconazole, ravuconazole, amphotericin B, and PCT on colonies: (i) that were not exposed to PCT (non-adapted-NA-cultures), (ii) were exposed at the maximum concentration of PCT (adapted-A-cultures) and (iii) the adapted colonies after cultivation 10 times in PCT-free media (10 passages-10p-cultures). Our results showed that exposure to PCT induced both temporary and permanent CR to clinical azoles in a temperature-dependent manner. With the objective to understand the mechanism of induction of CR through non-azoles, the transcriptomes of NA and 10p cells from C. gattii R265 were analyzed. The transcriptomic analysis showed that expression of the efflux-pump genes (AFR1 and MDR1) and PCT target was higher in resistant 10p cells than that in NA. Moreover, the virulence of 10p cells was reduced as compared to NA cells in mice, as observed by the differential gene expression analysis of genes related to ion-metabolism. Additionally, we observed that FLC could not increase the survival rate of mice infected with 10p cells, confirming the occurrence of permanent CR in vivo. The findings of the present study demonstrate that the non-azole agrochemical PCT can induce permanent CR to clinical antifungals through increased expression of efflux pump genes in resistant cells and that such phenomenon also manifests in vivo.

Published
2019
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4. Titan cells formation in Cryptococcus neoformans is finely tuned by environmental conditions and modulated by positive and negative genetic regulators

Author

James A. Fraser, Liliane Mukaremera, John R. Perfect, Arturo Casadevall, Françoise Dromer, Benjamin Hommel, Christopher A. Desjardins, Alexandre Alanio, Aude Sturny-Leclère, Guilhem Janbon, Christina A. Cuomo, Carolina Coelho, Kirsten Nielsen, Radames J. B. Cordero, Mycologie moléculaire - Molecular Mycology, Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], Université Paris Diderot - Paris 7 (UPD7), Laboratoire de Parasitologie-Mycologie [CHU Saint Louis, Paris], Groupe Hospitalier Saint Louis - Lariboisière - Fernand Widal [Paris], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), University of Minnesota [Twin Cities] (UMN), University of Minnesota System, Johns Hopkins University School of Medicine [Baltimore], Broad Institute of MIT and Harvard (BROAD INSTITUTE), Harvard Medical School [Boston] (HMS)-Massachusetts Institute of Technology (MIT)-Massachusetts General Hospital [Boston], Biologie des ARN des Pathogènes fongiques - RNA Biology of Fungal Pathogens, Institut Pasteur [Paris], Duke University [Durham], University of Queensland [Brisbane], BH’s salary was funded by Assistance Publique-Hôpitaux de Paris and Institut Pasteur (Poste d’ accueil APHP/CNRS/Institut Pasteur). http://recherche.aphp.fr/candidatures-internes/ KN grant funding National Institutes of Health, National Institute of Allergy and Infectious Diseases (NIAID) grant R01AI080275. https://www.niaid.nih.gov AC is supported in part by 5R01HL059842, 5R01AI033774, 5R37AI033142, and 5R01AI052733. https://www.niaid.nih.gov CAD and CAC were supported by National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services grant number U19AI110818. https://www.niaid.nih.gov The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript., Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris] (IP), and Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS)

Subjects
0301 basic medicine, Cell division, Cell, Vacuole, MESH: Quorum Sensing, MESH: Lung Diseases, Fungal, MESH: Animals, Biology (General), [SDV.MP.MYC]Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, 2. Zero hunger, education.field_of_study, 0303 health sciences, Chemistry, MESH: Cryptococcus neoformans, Phenotype, Cell biology, medicine.anatomical_structure, Interaction with host, symbols, Titan (rocket family), MESH: Mutation, QH301-705.5, 030106 microbiology, Immunology, Population, MESH: Cryptococcosis, Biology, MESH: Phenotype, Microbiology, Cell wall, symbols.namesake, 03 medical and health sciences, MESH: Hyphae, MESH: Mice, Inbred C57BL, Virology, Genetics, medicine, Progenitor cell, education, Molecular Biology, MESH: Mice, 030304 developmental biology, Cryptococcus neoformans, MESH: Humans, 030306 microbiology, fungi, MESH: Host-Pathogen Interactions, MESH: Models, Biological, RC581-607, biology.organism_classification, In vitro, Nucleic acid biosynthesis, Parasitology, Immunologic diseases. Allergy, MESH: Disease Models, Animal, MESH: Genes, Fungal, Biogenesis
Abstract

A remarkable aspect of the human fungal pathogen Cryptococcus neoformans is the morphological changes triggered by the interaction with the host. During infection, a specific morphological change in cell size is observed, particularly in lung tissue, from regular 5 to 7 µm cells (RCs) to titan cells (TCs, > 10 µm and up to 100 µm). However, the stable and reproducible generation of large quantity of TCs was only possible during experimental infection. We implemented here in vitro conditions allowing TCs generation with the aim to understand the ancestry of TC, the environmental determinants of TCs formation and perform easily phenotype/genotype analysis to uncover genetic factors underlying TCs formation. This paper reports robust in vitro conditions that generates yeasts cells harboring the main characteristics of TCs: large (>10 µm), uninucleate and polyploid cells harboring a single large vacuole with a dense capsule surrounding a thickened melanized cell wall. We observed that TCs formation begins as soon as 8 hours after induction, with a maximal proportion of TCs obtained after 24 hours. TCs derived for the initial oldest cells (mother cells) rather than from daughter cells. Hypoxia, nutrient starvation and low pH stresses were the main factors that trigger TCs formation, while quorum sensing factors like the initial inoculum concentration and the addition of pantothenic acid also impacted TCs formation. Antifungal drugs, resulting in inhibition of ergosterol (fluconazole), or proteins and nucleic acids (flucytosine), altered TCs formation, as did hosts-related products such as serum, phospholipids and anti-capsular antibodies in our settings. We then explored genetic factors important for TCs formation using two approaches. Using strains from H99 lineage strains among which few genetic differences have been described, we showed that TCs formation was dependent on Lmp1, Sgf29 and Gpr4/5-Rim101 proteins. Then, based on a the analysis of natural Pkr1 loss-of-function clinical isolates and serial clinical isolates, we observed the important role of Pkr1 protein, a negative regulator of the cyclic adenosine monophosphate / protein kinase A (cAMP/PKA), for TCs formation. These strains also emphasize the structural and functional relationship between Pkr1 and Pka. Our results provide new insights into TCs biogenesis with identification of multiple important factors/pathways involved. The implementation of such standardized and robust in vitro conditions pave the way for future research focusing on the genetic basis of TCs biogenesis, biology of TCs and the ontology of morphological changes in Cryptococcus neoformans. Author Summary Cryptococcus neoformans is a yeast that is capable of morphological change upon interaction with host. Particularly, in the lung of infected mice, a subpopulation of yeast evolves toward gigantism (titan cells size from 10 to 100 µm) that include other characteristics such as thickened cell wall, dense capsule, polyploidization, large vacuole with peripheral nucleus and cellular organelles. The generation of large number of such cells outside the lung of mice have been described but was not reproducible nor standardized. We here report standardized, reproducible, robust conditions of generation of titan cells and explored the environmental and genetic factors underlying the genesis of these cells. We showed that Titan cells were generated upon stresses such as change in the medium, nutrient deprivation, hypoxia and low pH. Using collection of well characterized reference strains and clinical isolates, we validated with our model the AMPc/PKA/Rim pathway as the major genetic determinant of titan cell formation. This study opens the way for a more comprehensive picture of the ontology of morphological changes in Cryptococcus neoformans.

Published
2018
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5. Fundamental niche prediction of the pathogenic yeasts Cryptococcus neoformans and Cryptococcus gattii in Europe

Author

Cogliati, Massimo, Puccianti, Erika, Montagna, Maria, de Donno, Antonella, Susever, Serdar, Ergin, Cagri, Velegraki, Aristea, Ellabib, Mohamed, Nardoni, Simona, Macci, Cristina, Trovato, Laura, Dipineto, Ludovico, Rickerts, Volker, Akcaglar, Sevim, Mlinaric-Missoni, Emilija, Bertout, Sébastien, Vencà, Ana, Sampaio, Ana, Criseo, Giuseppe, Ranque, Stéphane, Çerikçioğlu, Nilgün, Marchese, Anna, Vezzulli, Luigi, Ilkit, Macit, Desnos-Ollivier, Marie, Pasquale, Vincenzo, Polacheck, Itzhack, Scopa, Antonio, Meyer, Wieland, Ferreira-Paim, Kennio, Hagen, Ferry, Boekhout, Teun, Dromer, Françoise, Varma, Ashok, Kwon-Chung, Kyung, Inácio, Joäo, Colom, Maria, Università degli Studi di Milano = University of Milan (UNIMI), Università degli studi di Bari Aldo Moro = University of Bari Aldo Moro (UNIBA), Università del Salento [Lecce], University of Cyprus [Nicosia] (UCY), Pamukkale University, National and Kapodistrian University of Athens (NKUA), University of Tripoli - University Al Fateh, University of Pisa - Università di Pisa, Istituto per lo Studio degli Ecosistemi ISE-CNR, Istituto per lo Studio degli Ecosistemi, Università degli studi di Catania = University of Catania (Unict), University of Naples Federico II = Università degli studi di Napoli Federico II, Robert Koch Institute [Berlin] (RKI), Uludağ Üniversitesi = Uludag University, Croatian Institute of Public Health [Zagreb] (CIPH), Recherches Translationnelles sur le VIH et les maladies infectieuses endémiques et émergentes (TransVIHMI), Institut de Recherche pour le Développement (IRD)-Université de Yaoundé I-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa = NOVA University Lisbon (NOVA), Universidade de Trás-os-Montes e Alto Douro (UTAD), Universidade do Trás-os-Montes e Alto Douro, University of Messina, Aix Marseille Université (AMU), Marmara University [Kadıköy - İstanbul], Università degli studi di Genova = University of Genoa (UniGe), Istituto di ricovero e cura a carattere scientifico Azienda Ospedaliera Universitaria 'San Martino' (IRCCS AOU San Martino), Cukurova University, Mycologie moléculaire - Molecular Mycology, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Università degli Studi di Napoli 'Parthenope' = University of Naples (PARTHENOPE), Hadassah Hebrew University Medical Center [Jerusalem], Università degli studi della Basilicata [Potenza] (UNIBAS), The University of Sydney, Canisius-Wilhelmina Hospital [Nijmegen, The Netherlands], University of Amsterdam [Amsterdam] (UvA), National Institutes of Health [Bethesda] (NIH), University of Brighton, Universidad Miguel Hernández [Elche] (UMH), Dr. Ferreira‐Paim was supported by a CAPES Science without Borders visiting fellow (N° 9313133) from Brazil. We declare we have no conflict of interests., Università degli Studi di Milano [Milano] (UNIMI), Università degli studi di Bari Aldo Moro (UNIBA), University of Cyprus [Nicosia], Università degli studi di Catania [Catania], Università degli studi di Napoli Federico II, Recherches Translationnelles sur le VIH et les maladies infectieuses endémiques er émergentes (TransVIHMI), Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut de Recherche pour le Développement (IRD)-Université de Yaoundé I-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Université Montpellier 1 (UM1), Universita degli studi di Genova, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Universita degli studi di Napoli 'Parthenope' [Napoli], Cogliati, Massimo, Puccianti, Erika, Montagna, Maria Teresa, De Donno, Antonella, Susever, Serdar, Ergin, Cagri, Velegraki, Aristea, Ellabib, Mohamed S., Nardoni, Simona, Macci, Cristina, Trovato, Laura, Dipineto, Ludovico, Rickerts, Volker, Akcaglar, Sevim, Mlinaric-Missoni, Emilija, Bertout, Sebastien, Vencà, Ana C. F., Sampaio, Ana C., Criseo, Giuseppe, Ranque, Stéphane, Çerikçioğlu, Nilgün, Marchese, Anna, Vezzulli, Luigi, Ilkit, Macit, Desnos-Ollivier, Marie, Pasquale, Vincenzo, Polacheck, Itzhack, Scopa, Antonio, Meyer, Wieland, Ferreira-Paim, Kennio, Hagen, Ferry, Boekhout, Teun, Dromer, Françoise, Varma, Ashok, Kwon-Chung, Kyung J., Inácio, Joäo, Colom, Maria F., Evolutionary and Population Biology (IBED, FNWI), Montagna, Maria T., and Lisbino, PASQUALE VINCENZO

Subjects
Cellular Microenvironment, Cryptococcosis, Cryptococcus gattii, Cryptococcus neoformans, Europe, Mediterranean Region, Seasons, Soil, Weather, Environmental Microbiology, Soil Microbiology, Microbiology, Ecology, Evolution, Behavior and Systematics, Evolution, MESH: Cryptococcosis, MESH: Cryptococcus gattii, MESH: Soil, MESH: Mediterranean Region, Behavior and Systematics, parasitic diseases, Cryptococcosi, MESH: Weather, Niche prediction, [SDV.MP.MYC]Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, Ecology, MESH: Cryptococcus neoformans, MESH: Environmental Microbiology, bacterial infections and mycoses, Cellular Microenvironment/*physiology, Cryptococcosis/microbiology, Cryptococcus gattii/*growth & development/metabolism, Cryptococcus neoformans/*growth & development/metabolism, Soil/chemistry, MESH: Soil Microbiology, Cryptococcus neoforman, Season, MESH: Europe, MESH: Seasons
Abstract

Fundamental niche prediction of Cryptococcus neoformans and Cryptococcus gattii in Europe is an important tool to understand where these pathogenic yeasts have a high probability to survive in the environment and therefore to identify the areas with high risk of infection. In this study, occurrence data for C. neoformans and C. gattii were compared by MaxEnt software with several bioclimatic conditions as well as with soil characteristics and land use. The results showed that C. gattii distribution can be predicted with high probability along the Mediterranean coast. The analysis of variables showed that its distribution is limited by low temperatures during the coldest season, and by heavy precipitations in the driest season. C. neoformans var. grubii is able to colonize the same areas of C. gattii but is more tolerant to cold winter temperatures and summer precipitations. In contrast, the C. neoformans var. neoformans map was completely different. The best conditions for its survival were displayed in sub-continental areas and not along the Mediterranean coasts. In conclusion, we produced for the first time detailed prediction maps of the species and varieties of the C. neoformans and C. gattii species complex in Europe and Mediterranean area. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd

Published
2017
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6. Introns Protect Eukaryotic Genomes from Transcription-Associated Genetic Instability

Author

Vincent Géli, Ana Rita Grosso, Guilhem Janbon, Emeline Coleno, Sérgio F. de Almeida, Amandine Bonnet, Adrien Presle, Sree Rama Chaitanya Sridhara, Abdessamad El-Kaoutari, Benoit Palancade, Institut Jacques Monod (IJM (UMR_7592)), Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Faculdade de Medicina [Lisboa], Universidade de Lisboa = University of Lisbon (ULISBOA), Centre de Recherche en Cancérologie de Marseille (CRCM), Aix Marseille Université (AMU)-Institut Paoli-Calmettes, Fédération nationale des Centres de lutte contre le Cancer (FNCLCC)-Fédération nationale des Centres de lutte contre le Cancer (FNCLCC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Biologie des ARN des Pathogènes fongiques - RNA Biology of Fungal Pathogens, Institut Pasteur [Paris] (IP), This work was supported by CNRS (to B.P.), Fondation ARC pour la Recherche sur le Cancer (to B.P.), Ligue Nationale contre le Cancer (to B.P., fellowship to A.B. and Equipe Labellisée 2014 to V.G.), EMBO (short-term fellowship to A.B.), Cancéropole PACA (fellowship to A.E.), and Fundaçao para a Ciencia e Tecnologia, Portugal (PTDC/BIM-ONC/0016-2014 to S.F.d.A. and IF/00510/2014 to A.R.G.). Bioinformatic and computing support at CRCM was provided by the CRCM Integrative Bioinformatics and Datacentre IT and Scientific Computing platforms., Universidade de Lisboa (ULISBOA), Institut Pasteur [Paris], Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Paoli-Calmettes, Fédération nationale des Centres de lutte contre le Cancer (FNCLCC)-Fédération nationale des Centres de lutte contre le Cancer (FNCLCC)-Aix Marseille Université (AMU), and Biologie des ARN des Pathogènes fongiques

Subjects
0301 basic medicine, Transcription, Genetic, MESH: Introns, [SDV]Life Sciences [q-bio], Candida glabrata, mRNA splicing, MESH: Genotype, 0302 clinical medicine, MESH: Structure-Activity Relationship, Minor spliceosome, Gene Expression Regulation, Fungal, Databases, Genetic, DNA, Fungal, MESH: Candida glabrata, MESH: Databases, Genetic, Genetics, Splice site mutation, MESH: Genomic Instability, Nucleic Acid Heteroduplexes, genetic instability, MESH: Cryptococcus neoformans, Group II intron, R-loops, MESH: Saccharomyces cerevisiae, messenger ribonucleoparticle, Phenotype, MESH: Nucleic Acid Conformation, MESH: Schizosaccharomyces, Ribonucleoproteins, RNA splicing, MESH: Fungal Proteins, transcription, MESH: Spliceosomes, MESH: Gene Expression Regulation, Fungal, MESH: Computational Biology, Spliceosome, Genotype, intron, RNA Splicing, Saccharomyces cerevisiae, Biology, MESH: Phenotype, Genomic Instability, Cell Line, Fungal Proteins, Structure-Activity Relationship, 03 medical and health sciences, mRNP, MESH: Nucleic Acid Heteroduplexes, Schizosaccharomyces, Humans, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Molecular Biology, Gene, MESH: DNA Damage, MESH: Humans, MESH: RNA, Fungal, MESH: Transcription, Genetic, Intron, Computational Biology, RNA, RNA, Fungal, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Cell Biology, Introns, recombination, MESH: Cell Line, MESH: DNA, Fungal, MESH: Ribonucleoproteins, 030104 developmental biology, Cryptococcus neoformans, Spliceosomes, Nucleic Acid Conformation, MESH: RNA Splicing, 030217 neurology & neurosurgery, DNA Damage
Abstract

International audience; Transcription is a source of genetic instability that can notably result from the formation of genotoxic DNA:RNA hybrids, or R-loops, between the nascent mRNA and its template. Here we report an unexpected function for introns in counteracting R-loop accumulation in eukaryotic genomes. Deletion of endogenous introns increases R-loop formation, while insertion of an intron into an intronless gene suppresses R-loop accumulation and its deleterious impact on transcription and recombination in yeast. Recruitment of the spliceosome onto the mRNA, but not splicing per se, is shown to be critical to attenuate R-loop formation and transcription-associated genetic instability. Genome-wide analyses in a number of distant species differing in their intron content, including human, further revealed that intron-containing genes and the intron-richest genomes are best protected against R-loop accumulation and subsequent genetic instability. Our results thereby provide a possible rationale for the conservation of introns throughout the eukaryotic lineage.

Published
2017
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7. Multilocus sequence typing analysis reveals that Cryptococcus neoformans var. neoformans is a recombinant population

Author

Ashok Varma, Kathrin Tintelnot, Patricia Escandón, Tomoe Ichikawa, Aristea Velegraki, Volker Rickerts, Alberto Zani, Reiko Ikeda, Ilka McCormick, Anne-Lise Bienvenu, Sevim Akcaglar, Massimo Cogliati, Anna Maria Tortorano, Okan Töre, Marie Desnos-Ollivier, Shawn R. Lockhart, Uludağ Üniversitesi/Tıp Fakültesi/Tıbbi Mikrobiyoloji Anabilim Dalı., Töre, Okan, Akçağlar, Sevim, Università degli Studi di Milano = University of Milan (UNIMI), Robert Koch Institute [Berlin] (RKI), Centre National de Référence des Mycoses invasives et antifongiques - Mycologie moléculaire (CNRMA), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), National and Kapodistrian University of Athens (NKUA), Instituto Nacional de Salud [Bogota], Meiji Pharmaceutical University, Hospices Civils de Lyon (HCL), Université de Lyon, Uludağ Üniversitesi = Uludag University, Centers for Disease Control and Prevention [Atlanta] (CDC), Centers for Disease Control and Prevention, National Institutes of Health [Bethesda] (NIH), We thank Prof. F. Dromer and Prof. J. Kwon-Chung for providing some of the isolates and for her suggestions to improve this study, and Dr. T. Boekhout and Dr. B. Theelen for sequencing support., Università degli Studi di Milano [Milano] (UNIMI), and Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS)

Subjects
0301 basic medicine, Serotype, C neoformans var grubii, Serotypes, Denmark, Cryptococcus Gattii, Flucytosine, Cryptococcus Neoformans, Cryptococcus, Molecular typing, Population structure, Turkey (republic), law.invention, MESH: Genotype, Species complex, Belgium, Japan, law, Germany, Genotype, MESH: Genetic Variation, [SDV.MP.MYC]Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, Phylogeny, Priority journal, education.field_of_study, Phylogenetic tree, biology, Greece, MESH: Asia, Genetics & heredity, C. neoformans var. neoformans, Correlation analysis, MESH: Cryptococcus neoformans, Gene linkage disequilibrium, Cryptococcosis, Thailand, Classification, 3. Good health, Europe, Phylogeography, MESH: Multilocus Sequence Typing, Italy, MESH: Phylogeography, Molecular epidemiology, Recombinant DNA, MESH: Recombination, Genetic, Microbiological examination, France, MLST, Asia, 030106 microbiology, Population, C neoformans var neoformans, Multilocus sequence typing, MESH: Cryptococcosis, Mycology, Recombination, genetic, Colombia, Microbiology, Mating-type, Article, 03 medical and health sciences, C. neoformans var. grubii, C neoformans var. grubii, MESH: Mycological Typing Techniques, Genetics, MESH: Americas, Cutaneous cryptococcosis, Genetic variation, Western hemisphere, education, Cryptococcus neoformans, Genetic recombination, Mycological typing techniques, biology.organism_classification, Nonhuman, Recombination, United States, Gattii, 030104 developmental biology, Isolation and purification, Geographic origin, Fungus isolation, Genetic variability, MESH: Europe, Americas, Varietas
Abstract

Cryptococcus neoformans var. neoformans (serotype D) represents about 30% of the clinical isolates in Europe and is present less frequently in the other continents. It is the prevalent etiological agent in primary cutaneous cryptococcosis as well as in cryptococcal skin lesions of disseminated cryptococcosis. Very little is known about the genotypic diversity of this Cryptococcus subtype. The aim of this study was to investigate the genotypic diversity among a set of clinical and environmental C. neoformans var. neoformans isolates and to evaluate the relationship between genotypes, geographical origin and clinical manifestations. A total of 83 globally collected C neoformans var. neoformans isolates from Italy, Germany, France, Belgium, Denmark, Greece, Turkey, Thailand, Japan, Colombia, and the USA, recovered from different sources (primary and secondary cutaneous cryptococcosis, disseminated cryptococcosis, the environment, and animals), were included in the study. All isolates were confirmed to belong to genotype VNIV by molecular typing and they were further investigated by MLST analysis. Maximum likelihood phylogenetic as well as network analysis strongly suggested the existence of a recombinant rather than a clonal population structure. Geographical origin and source of isolation were not correlated with a specific MLST genotype. The comparison with a set of outgroup C neoformans var. grubii isolates provided clear evidence that the two varieties have different population structures. United States Department of Health & Human Services - Z99 AI999999 - P41 RR001646 National Institutes of Health (NIH) - USA NIH National Center for Research Resources (NCRR)

Published
2016
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8. Pulmonary cryptococcosis: localized and disseminated infections in 27 patients with AIDS

Author

J. L. Meynard, Christos Chouaid, Patricia Roux, Willy Rozenbaum, J. Frottier, Poirot Jl, Marie-Caroline Meyohas, Diane Bollens, Charles Mayaud, Laboratoire de Géophysique Interne et Tectonophysique (LGIT), Laboratoire Central des Ponts et Chaussées (LCPC)-Observatoire des Sciences de l'Univers de Grenoble (OSUG), Université Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Institut national des sciences de l'Univers (INSU - CNRS)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Université Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Institut national des sciences de l'Univers (INSU - CNRS)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Epidémiologie des maladies infectieuses et modélisation (ESIM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM), CHU Tenon [AP-HP], Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Meyohas MC, P Roux, Bollens D, C Chouaid, W Rozenbaum, JL Meynard, JL Poirot, Frottier J, C Mayaud, Observatoire des Sciences de l'Univers de Grenoble (OSUG), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Université Joseph Fourier - Grenoble 1 (UJF)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Université Joseph Fourier - Grenoble 1 (UJF)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Laboratoire Central des Ponts et Chaussées (LCPC)-Institut des Sciences de la Terre (ISTerre), Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-PRES Université de Grenoble-Institut de recherche pour le développement [IRD] : UR219-Institut national des sciences de l'Univers (INSU - CNRS)-Institut Français des Sciences et Technologies des Transports, de l'Aménagement et des Réseaux (IFSTTAR)-Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-PRES Université de Grenoble-Institut de recherche pour le développement [IRD] : UR219-Institut Français des Sciences et Technologies des Transports, de l'Aménagement et des Réseaux (IFSTTAR), CHU Tenon [APHP], Université Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Institut national des sciences de l'Univers (INSU - CNRS)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Université Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Institut national des sciences de l'Univers (INSU - CNRS)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Laboratoire Central des Ponts et Chaussées (LCPC)-Centre National de la Recherche Scientifique (CNRS), and Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)

Subjects
Male, Pathology, MESH: CD4 Lymphocyte Count, Pleural effusion, MESH: Lung Diseases, Fungal, 0302 clinical medicine, 030212 general & internal medicine, MESH: Middle Aged, medicine.diagnostic_test, biology, MESH: AIDS-Related Opportunistic Infections, Respiratory disease, MESH: Cryptococcus neoformans, Cryptococcosis, Middle Aged, Prognosis, 3. Good health, Infectious Diseases, Female, Bronchoalveolar Lavage Fluid, Microbiology (medical), Adult, medicine.medical_specialty, Antigens, Fungal, AIDS-Related Opportunistic Infections, MESH: Cryptococcosis, MESH: Prognosis, 03 medical and health sciences, medicine, Humans, Cryptococcal Pneumonia, Mycosis, MESH: Antigens, Fungal, Cryptococcus neoformans, MESH: Humans, Lung Diseases, Fungal, business.industry, MESH: Bronchoalveolar Lavage Fluid, MESH: Adult, biology.organism_classification, medicine.disease, MESH: Male, CD4 Lymphocyte Count, Bronchoalveolar lavage, 030228 respiratory system, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, business, MESH: Female
Abstract

International audience; We reviewed the records of 85 patients infected with both human immunodeficiency virus and Cryptococcus neoformans. Twenty-seven patients (32%) had pulmonary cryptococcosis. C. neoformans was cultured from bronchoalveolar lavage (BAL) or pleural fluid in 25 cases; the remaining two patients had cryptococcal antigen (CA) detected in BAL fluid and C. neoformans cultured from other sites. All but one of the 27 patients had detectable CA in serum. The CD4+ lymphocyte count was low in all cases (median, 24/mm3). Clinical manifestations of pulmonary cryptococcosis included fever (94%), cough (71%), dyspnea (7%), expectoration (4%), chest pain (2%), and hemoptysis (1%). Diffuse interstitial opacities (70.5%), focal interstitial abnormalities, alveolar opacities, adenopathies, cavitary lesions, and pleural effusions were evident. Outcome was poor (mean survival time, 23 weeks) despite treatment. Patients with localized pulmonary cryptococcosis appeared to have a higher CD4+ lymphocyte count, an earlier diagnosis, lower serum CA titers, fewer previous or concomitant infections, and a better prognosis than patients with disseminated cryptococcosis.

Published
1995

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