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1. Dataset of the de novo assembly and annotation of the marbled crayfish and the noble crayfish hepatopancreas transcriptomes

Author

Ljudevit Luka Boštjančić, Caterina Francesconi, Christelle Rutz, Lucien Hoffbeck, Laetitia Poidevin, Arnaud Kress, Japo Jussila, Jenny Makkonen, Barbara Feldmeyer, Miklós Bálint, Klaus Schwenk, Odile Lecompte, and Kathrin Theissinger

Subjects
Freshwater crayfish, Astacus astacus, Procambarus virginalis, Crayfish plague, RNA sequencing, Medicine, Biology (General), QH301-705.5, Science (General), Q1-390
Abstract

Abstract Objectives Crayfish plague disease, caused by the oomycete pathogen Aphanomyces astaci represents one of the greatest risks for the biodiversity of the freshwater crayfish. This data article covers the de novo transcriptome assembly and annotation data of the noble crayfish and the marbled crayfish challenged with Ap. astaci. Following the controlled infection experiment (Francesconi et al. in Front Ecol Evol, 2021, https://doi.org/10.3389/fevo.2021.647037 ), we conducted a differential gene expression analysis described in (Boštjančić et al. in BMC Genom, 2022, https://doi.org/10.1186/s12864-022-08571-z ) Data description In total, 25 noble crayfish and 30 marbled crayfish were selected. Hepatopancreas tissue was isolated, followed by RNA sequencing using the Illumina NovaSeq 6000 platform. Raw data was checked for quality with FastQC, adapter and quality trimming were conducted using Trimmomatic followed by de novo assembly with Trinity. Assembly quality was assessed with BUSCO, at 93.30% and 93.98% completeness for the noble crayfish and the marbled crayfish, respectively. Transcripts were annotated using the Dammit! pipeline and assigned to KEGG pathways. Respective transcriptome and raw datasets may be reused as the reference transcriptome assemblies for future expression studies.

Published
2022
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2. Host-pathogen coevolution drives innate immune response to Aphanomyces astaci infection in freshwater crayfish: transcriptomic evidence

Author

Ljudevit Luka Boštjančić, Caterina Francesconi, Christelle Rutz, Lucien Hoffbeck, Laetitia Poidevin, Arnaud Kress, Japo Jussila, Jenny Makkonen, Barbara Feldmeyer, Miklós Bálint, Klaus Schwenk, Odile Lecompte, and Kathrin Theissinger

Subjects
Crayfish plague, Astacus astacus, Invertebrate immune mechanisms, Innate immune system, Procambarus virginalis, Differential gene expression, Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background For over a century, scientists have studied host-pathogen interactions between the crayfish plague disease agent Aphanomyces astaci and freshwater crayfish. It has been hypothesised that North American crayfish hosts are disease-resistant due to the long-lasting coevolution with the pathogen. Similarly, the increasing number of latent infections reported in the historically sensitive European crayfish hosts seems to indicate that similar coevolutionary processes are occurring between European crayfish and A. astaci. Our current understanding of these host-pathogen interactions is largely focused on the innate immunity processes in the crayfish haemolymph and cuticle, but the molecular basis of the observed disease-resistance and susceptibility remain unclear. To understand how coevolution is shaping the host’s molecular response to the pathogen, susceptible native European noble crayfish and invasive disease-resistant marbled crayfish were challenged with two A. astaci strains of different origin: a haplogroup A strain (introduced to Europe at least 50 years ago, low virulence) and a haplogroup B strain (signal crayfish in lake Tahoe, USA, high virulence). Here, we compare the gene expression profiles of the hepatopancreas, an integrated organ of crayfish immunity and metabolism. Results We characterised several novel innate immune-related gene groups in both crayfish species. Across all challenge groups, we detected 412 differentially expressed genes (DEGs) in the noble crayfish, and 257 DEGs in the marbled crayfish. In the noble crayfish, a clear immune response was detected to the haplogroup B strain, but not to the haplogroup A strain. In contrast, in the marbled crayfish we detected an immune response to the haplogroup A strain, but not to the haplogroup B strain. Conclusions We highlight the hepatopancreas as an important hub for the synthesis of immune molecules in the response to A. astaci. A clear distinction between the innate immune response in the marbled crayfish and the noble crayfish is the capability of the marbled crayfish to mobilise a higher variety of innate immune response effectors. With this study we outline that the type and strength of the host immune response to the pathogen is strongly influenced by the coevolutionary history of the crayfish with specific A. astaci strains.

Published
2022
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3. Polyamines as Quality Control Metabolites Operating at the Post-Transcriptional Level

Author

Laetitia Poidevin, Dilek Unal, Borja Belda-Palazón, and Alejandro Ferrando

Subjects
polyamines, spermidine, thermospermine, nonsense-mediated decay, no-go decay, non-stop decay, quality control, translation, Botany, QK1-989
Abstract

Plant polyamines (PAs) have been assigned a large number of physiological functions with unknown molecular mechanisms in many cases. Among the most abundant and studied polyamines, two of them, namely spermidine (Spd) and thermospermine (Tspm), share some molecular functions related to quality control pathways for tightly regulated mRNAs at the level of translation. In this review, we focus on the roles of Tspm and Spd to facilitate the translation of mRNAs containing upstream ORFs (uORFs), premature stop codons, and ribosome stalling sequences that may block translation, thus preventing their degradation by quality control mechanisms such as the nonsense-mediated decay pathway and possible interactions with other mRNA quality surveillance pathways.

Published
2019
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4. Dataset of the de novo assembly and annotation of the marbled and noble crayfish hepatopancreas transcriptomes

Author

Ljudevit Luka Boštjančić, Caterina Francesconi, Christelle Rutz, Lucien Hoffbeck, Laetitia Poidevin, Arnaud Kress, Japo Jussila, Jenny Makkonen, Barbara Feldmeyer, Miklós Bálint, Klaus Schwenk, Odile Lecompte, Kathrin Theissinger, Centre for Translational Biodiversity Genomics [Frankfurt, Germany] (LOEWE-TBG), University of Koblenz-Landau, Laboratoire des sciences de l'ingénieur, de l'informatique et de l'imagerie (ICube), École Nationale du Génie de l'Eau et de l'Environnement de Strasbourg (ENGEES)-Université de Strasbourg (UNISTRA)-Institut National des Sciences Appliquées - Strasbourg (INSA Strasbourg), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Les Hôpitaux Universitaires de Strasbourg (HUS)-Centre National de la Recherche Scientifique (CNRS)-Matériaux et Nanosciences Grand-Est (MNGE), Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Réseau nanophotonique et optique, Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Centre de Recherche en Biomédecine de Strasbourg (CRBS), Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM), University of Eastern Finland, and univOAK, Archive ouverte

Subjects
[INFO.INFO-AI] Computer Science [cs]/Artificial Intelligence [cs.AI], Freshwater crayfish, Sequence Analysis, RNA, Hepatopancreas, RNA sequencing, General Medicine, Astacoidea, Aphanomyces, General Biochemistry, Genetics and Molecular Biology, [INFO.INFO-AI]Computer Science [cs]/Artificial Intelligence [cs.AI], Informatique [cs]/Intelligence artificielle [cs.AI], Crayfish plague, Animals, Procambarus virginalis, Transcriptome, Astacus astacus
Abstract

Objectives Crayfish plague disease, caused by the oomycete pathogen Aphanomyces astaci represents one of the greatest risks for the biodiversity of the freshwater crayfish. This data article covers the de novo transcriptome assembly and annotation data of the noble crayfish and the marbled crayfish challenged with Ap. astaci. Following the controlled infection experiment (Francesconi et al. in Front Ecol Evol, 2021, https://doi.org/10.3389/fevo.2021.647037), we conducted a differential gene expression analysis described in (Boštjančić et al. in BMC Genom, 2022, https://doi.org/10.1186/s12864-022-08571-z) Data description In total, 25 noble crayfish and 30 marbled crayfish were selected. Hepatopancreas tissue was isolated, followed by RNA sequencing using the Illumina NovaSeq 6000 platform. Raw data was checked for quality with FastQC, adapter and quality trimming were conducted using Trimmomatic followed by de novo assembly with Trinity. Assembly quality was assessed with BUSCO, at 93.30% and 93.98% completeness for the noble crayfish and the marbled crayfish, respectively. Transcripts were annotated using the Dammit! pipeline and assigned to KEGG pathways. Respective transcriptome and raw datasets may be reused as the reference transcriptome assemblies for future expression studies.

Published
2022
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5. Identification of an Alternative Splicing Product of the Otx2 Gene Expressed in the Neural Retina and Retinal Pigmented Epithelial Cells.

Author

Christo Kole, Naomi Berdugo, Corinne Da Silva, Najate Aït-Ali, Géraldine Millet-Puel, Delphine Pagan, Frédéric Blond, Laetitia Poidevin, Raymond Ripp, Valérie Fontaine, Patrick Wincker, Donald J Zack, José-Alain Sahel, Olivier Poch, and Thierry Léveillard

Subjects
Medicine, Science
Abstract

To investigate the complexity of alternative splicing in the retina, we sequenced and analyzed a total of 115,706 clones from normalized cDNA libraries from mouse neural retina (66,217) and rat retinal pigmented epithelium (49,489). Based upon clustering the cDNAs and mapping them with their respective genomes, the estimated numbers of genes were 9,134 for the mouse neural retina and 12,050 for the rat retinal pigmented epithelium libraries. This unique collection of retinal of messenger RNAs is maintained and accessible through a web-base server to the whole community of retinal biologists for further functional characterization. The analysis revealed 3,248 and 3,202 alternative splice events for mouse neural retina and rat retinal pigmented epithelium, respectively. We focused on transcription factors involved in vision. Among the six candidates suitable for functional analysis, we selected Otx2S, a novel variant of the Otx2 gene with a deletion within the homeodomain sequence. Otx2S is expressed in both the neural retina and retinal pigmented epithelium, and encodes a protein that is targeted to the nucleus. OTX2S exerts transdominant activity on the tyrosinase promoter when tested in the physiological environment of primary RPE cells. By overexpressing OTX2S in primary RPE cells using an adeno associated viral vector, we identified 10 genes whose expression is positively regulated by OTX2S. We find that OTX2S is able to bind to the chromatin at the promoter of the retinal dehydrogenase 10 (RDH10) gene.

Published
2016
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6. Integrated annotation and analysis of in situ hybridization images using the ImAnno system: application to the ear and sensory organs of the fetal mouse.

Author

Raymond Romand, Raymond Ripp, Laetitia Poidevin, Marcel Boeglin, Lars Geffers, Pascal Dollé, and Olivier Poch

Subjects
Medicine, Science
Abstract

An in situ hybridization (ISH) study was performed on 2000 murine genes representing around 10% of the protein-coding genes present in the mouse genome using data generated by the EURExpress consortium. This study was carried out in 25 tissues of late gestation embryos (E14.5), with a special emphasis on the developing ear and on five distinct developing sensory organs, including the cochlea, the vestibular receptors, the sensory retina, the olfactory organ, and the vibrissae follicles. The results obtained from an analysis of more than 11,000 micrographs have been integrated in a newly developed knowledgebase, called ImAnno. In addition to managing the multilevel micrograph annotations performed by human experts, ImAnno provides public access to various integrated databases and tools. Thus, it facilitates the analysis of complex ISH gene expression patterns, as well as functional annotation and interaction of gene sets. It also provides direct links to human pathways and diseases. Hierarchical clustering of expression patterns in the 25 tissues revealed three main branches corresponding to tissues with common functions and/or embryonic origins. To illustrate the integrative power of ImAnno, we explored the expression, function and disease traits of the sensory epithelia of the five presumptive sensory organs. The study identified 623 genes (out of 2000) concomitantly expressed in the five embryonic epithelia, among which many (∼12%) were involved in human disorders. Finally, various multilevel interaction networks were characterized, highlighting differential functional enrichments of directly or indirectly interacting genes. These analyses exemplify an under-represention of "sensory" functions in the sensory gene set suggests that E14.5 is a pivotal stage between the developmental stage and the functional phase that will be fully reached only after birth.

Published
2015
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7. Comparisons of Ribosomal Protein Gene Promoters Indicate Superiority of Heterologous Regulatory Sequences for Expressing Transgenes in Phytophthora infestans.

Author

Laetitia Poidevin, Kalina Andreeva, Careen Khachatoorian, and Howard S Judelson

Subjects
Medicine, Science
Abstract

Molecular genetics approaches in Phytophthora research can be hampered by the limited number of known constitutive promoters for expressing transgenes and the instability of transgene activity. We have therefore characterized genes encoding the cytoplasmic ribosomal proteins of Phytophthora and studied their suitability for expressing transgenes in P. infestans. Phytophthora spp. encode a standard complement of 79 cytoplasmic ribosomal proteins. Several genes are duplicated, and two appear to be pseudogenes. Half of the genes are expressed at similar levels during all stages of asexual development, and we discovered that the majority share a novel promoter motif named the PhRiboBox. This sequence is enriched in genes associated with transcription, translation, and DNA replication, including tRNA and rRNA biogenesis. Promoters from the three P. infestans genes encoding ribosomal proteins S9, L10, and L23 and their orthologs from P. capsici were tested for their ability to drive transgenes in stable transformants of P. infestans. Five of the six promoters yielded strong expression of a GUS reporter, but the stability of expression was higher using the P. capsici promoters. With the RPS9 and RPL10 promoters of P. infestans, about half of transformants stopped making GUS over two years of culture, while their P. capsici orthologs conferred stable expression. Since cross-talk between native and transgene loci may trigger gene silencing, we encourage the use of heterologous promoters in transformation studies.

Published
2015
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8. A DNA Repair and Cell Cycle Gene Expression Signature in Pediatric High-Grade Gliomas: Prognostic and Therapeutic Value

Author

Eric Guérin, Hélène Burckel, Georges Noël, Benoit Lhermitte, Quentin Fuchs, David Castel, Marie Pierre Chenard, Olivier Poch, Eric Van Dyck, Laetitia Poidevin, Laurence Choulier, Monique Dontenwill, Petr V. Nazarov, Natacha Entz-Werle, Laboratoire de Bioimagerie et Pathologies (LBP), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), CHU Strasbourg, Laboratoire des sciences de l'ingénieur, de l'informatique et de l'imagerie (ICube), Institut National des Sciences Appliquées - Strasbourg (INSA Strasbourg), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-École Nationale du Génie de l'Eau et de l'Environnement de Strasbourg (ENGEES)-Réseau nanophotonique et optique, Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Matériaux et nanosciences d'Alsace (FMNGE), Institut de Chimie du CNRS (INC)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), CRBS - Centre de Recherche en Biomédecine de Strasbourg (Inserm UMS38/UNISTRA), Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM), Luxembourg Institute of Health (LIH), Institut de Cancérologie de Strasbourg Europe (ICANS), Université de Strasbourg (UNISTRA), UNICANCER, CRLCC Paul Strauss, Biomarqueurs prédictifs et nouvelles stratégies moléculaires en thérapeutique anticancéreuse (U981), Université Paris-Sud - Paris 11 (UP11)-Institut Gustave Roussy (IGR)-Institut National de la Santé et de la Recherche Médicale (INSERM), Vectorologie et thérapeutiques anti-cancéreuses [Villejuif] (UMR 8203), Centre National de la Recherche Scientifique (CNRS)-Institut Gustave Roussy (IGR)-Université Paris-Sud - Paris 11 (UP11), École Nationale du Génie de l'Eau et de l'Environnement de Strasbourg (ENGEES)-Université de Strasbourg (UNISTRA)-Institut National des Sciences Appliquées - Strasbourg (INSA Strasbourg), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Les Hôpitaux Universitaires de Strasbourg (HUS)-Centre National de la Recherche Scientifique (CNRS)-Matériaux et Nanosciences Grand-Est (MNGE), Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Réseau nanophotonique et optique, Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Centre de Recherche en Biomédecine de Strasbourg (CRBS), Université Paris-Sud - Paris 11 (UP11)-Institut Gustave Roussy (IGR)-Centre National de la Recherche Scientifique (CNRS), and univOAK, Archive ouverte

Subjects
[INFO.INFO-AI] Computer Science [cs]/Artificial Intelligence [cs.AI], 0301 basic medicine, Cancer Research, pediatric high-grade gliomas, DNA damage repair, prognostic clustering, PARP1, XRCC1, DNA repair, DNA damage, Biology, Article, [INFO.INFO-AI]Computer Science [cs]/Artificial Intelligence [cs.AI], Transcriptome, 03 medical and health sciences, 0302 clinical medicine, Radioresistance, Gene expression, RC254-282, Neoplasms. Tumors. Oncology. Including cancer and carcinogens, Cell cycle, Cell Cycle Gene, 3. Good health, 030104 developmental biology, Oncology, 030220 oncology & carcinogenesis, Cancer research
Abstract

Simple Summary Pediatric high-grade gliomas are incurable brain tumors for which there is a critical need for new therapeutic strategies as well as treatment-predictive biomarkers. This study examined the expression of DNA repair and cell cycle genes in pediatric high-grade gliomas with distinct driving mutations. The aim is to propose a novel classification of these tumors based on sub-groups exposing therapeutic vulnerabilities. Several DNA repair factors were identified that might become new diagnostic markers. Abstract Background: Pediatric high-grade gliomas (pHGGs) are the leading cause of mortality in pediatric neuro-oncology, displaying frequent resistance to standard therapies. Profiling DNA repair and cell cycle gene expression has recently been proposed as a strategy to classify adult glioblastomas. To improve our understanding of the DNA damage response pathways that operate in pHGGs and the vulnerabilities that these pathways might expose, we sought to identify and characterize a specific DNA repair and cell-cycle gene expression signature of pHGGs. Methods: Transcriptomic analyses were performed to identify a DNA repair and cell-cycle gene expression signature able to discriminate pHGGs (n = 6) from low-grade gliomas (n = 10). This signature was compared to related signatures already established. We used the pHGG signature to explore already transcriptomic datasets of DIPGs and sus-tentorial pHGGs. Finally, we examined the expression of key proteins of the pHGG signature in 21 pHGG diagnostic samples and nine paired relapses. Functional inhibition of one DNA repair factor was carried out in four patients who derived H3.3 K27M mutant cell lines. Results: We identified a 28-gene expression signature of DNA repair and cell cycle that clustered pHGGs cohorts, in particular sus-tentorial locations, in two groups. Differential protein expression levels of PARP1 and XRCC1 were associated to TP53 mutations and TOP2A amplification and linked significantly to the more radioresistant pHGGs displaying the worst outcome. Using patient-derived cell lines, we showed that the PARP-1/XRCC1 expression balance might be correlated with resistance to PARP1 inhibition. Conclusion: We provide evidence that PARP1 overexpression, associated to XRCC1 expression, TP53 mutations, and TOP2A amplification, is a new theranostic and potential therapeutic target.

Published
2021
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9. Comparative transcriptome analysis of noble crayfish and marbled crayfish immune response to Aphanomyces astaci challenges

Author

Odile Lecompte, Hoffbeck L, Japo Jussila, Jenny Makkonen, Kathrin Theissinger, Rutz C, Arnaud Kress, Feldmeyer B, Laetitia Poidevin, Boštjančić Ll, Francesconi C, Miklós Bálint, Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Goethe-Universität Frankfurt am Main-Senckenberg – Leibniz Institution for Biodiversity and Earth System Research - Senckenberg Gesellschaft für Naturforschung, Leibniz Association-Leibniz Association, University of Koblenz-Landau, Laboratoire des sciences de l'ingénieur, de l'informatique et de l'imagerie (ICube), Institut National des Sciences Appliquées - Strasbourg (INSA Strasbourg), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-École Nationale du Génie de l'Eau et de l'Environnement de Strasbourg (ENGEES)-Réseau nanophotonique et optique, Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Matériaux et nanosciences d'Alsace (FMNGE), Institut de Chimie du CNRS (INC)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), CRBS - Centre de Recherche en Biomédecine de Strasbourg (Inserm UMS38/UNISTRA), Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM), University of Eastern Finland, École Nationale du Génie de l'Eau et de l'Environnement de Strasbourg (ENGEES)-Université de Strasbourg (UNISTRA)-Institut National des Sciences Appliquées - Strasbourg (INSA Strasbourg), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Les Hôpitaux Universitaires de Strasbourg (HUS)-Centre National de la Recherche Scientifique (CNRS)-Matériaux et Nanosciences Grand-Est (MNGE), Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Réseau nanophotonique et optique, Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Centre de Recherche en Biomédecine de Strasbourg (CRBS), and univOAK, Archive ouverte

Subjects
[INFO.INFO-AI] Computer Science [cs]/Artificial Intelligence [cs.AI], Zoology, Virulence, de novo assembly, Haplogroup, [INFO.INFO-AI]Computer Science [cs]/Artificial Intelligence [cs.AI], 03 medical and health sciences, 0302 clinical medicine, differential gene expression, Pathogen, innate immunity, 030304 developmental biology, 0303 health sciences, Astacus, biology, musculoskeletal, neural, and ocular physiology, Prophenoloxidase, Crayfish, biology.organism_classification, crayfish plague, nervous system, Hepatopancreas, Procambarus virginalis, Haplogroup A, 030217 neurology & neurosurgery, Astacus astacus
Abstract

Introduction of invasive North American crayfish species and their pathogen Aphanomyces astaci has significantly contributed to the decline of European freshwater crayfish populations. In this study, noble crayfish, a susceptible native European species, and marbled crayfish, an invasive disease-resistant species, were challenged with haplogroup A (low virulence) and haplogroup B (high virulence) strain of A. astaci. Hepatopancreatic tissue was isolated 3 and 21 days post-challenge. Our results revealed strong up-regulation in expression levels of the prophenoloxidase cascade immune-related genes in the haplogroup B challenged noble crayfish 3 days post-challenge. In the marbled crayfish, we observed an up-regulation of immune system relevant genes (DSCAM, AP, ALFs, CTLs and hemocyanin) 3 days post-challenge. This response highlights the marbled crayfish capability of building the immune tolerance. Furthermore, we successfully characterised several novel immune related gene groups in both crayfish species, contributing to our current understanding of crayfish immune related genes landscape.Graphical abstracta) Study species noble crayfish (Astacus astacus) in purple and marbled crayfish (Procambarus virginalis) in green challenged with the pathogen Aphanomyces astaci haplogroup A (Hap A) strain of low virulence and haplogroup B (Hap B) strain of high virulence. b) Sampling scheme of the infection experiment: 5 individuals were taken from the experiment three- and 21-days post-challenge. From each individual, a hepatopancreas sample was taken, followed by RNA isolation and sequencing. c)De novo transcriptome assembly and annotation were conducted for each species. d) Differential gene expression analysis revealed the distinct immune response in the noble crayfish 3 days post-challenge with the Hap B strain of A. astaci and marbled crayfish 3 days post-challenge with the Hap A strain of A. astaci. Immune related DEGs were not present in either species 21 days post-challenge with A. astaci.e) Noble crayfish challenged with the Hap B strain of A. astaci were acutely infected and ultimately moribund, while the A. astaci Hap A challenged marbled crayfish showed high resistance to the pathogen, resulting infected without any mortality.

Published
2021
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10. Correction to: Characterization of novel pollen-expressed transcripts reveals their potential roles in pollen heat stress response in Arabidopsis thaliana

Author

Nicholas Rutley, Laetitia Poidevin, Tirza Doniger, Richard L. Tillett, Abhishek Rath, Javier Forment, Gilad Luria, Karen A. Schlauch, Alejandro Ferrando, Jeffery F. Harper, and Gad Miller

Subjects
Arabidopsis Proteins, Arabidopsis, Correction, Pollen, Cell Biology, Plant Science, Heat-Shock Response, Phylogeny
Abstract

Arabidopsis pollen transcriptome analysis revealed new intergenic transcripts of unknown function, many of which are long non-coding RNAs, that may function in pollen-specific processes, including the heat stress response. The male gametophyte is the most heat sensitive of all plant tissues. In recent years, long noncoding RNAs (lncRNAs) have emerged as important components of cellular regulatory networks involved in most biological processes, including response to stress. While examining RNAseq datasets of developing and germinating Arabidopsis thaliana pollen exposed to heat stress (HS), we identified 66 novel and 246 recently annotated intergenic expressed loci (XLOCs) of unknown function, with the majority encoding lncRNAs. Comparison with HS in cauline leaves and other RNAseq experiments indicated that 74% of the 312 XLOCs are pollen-specific, and at least 42% are HS-responsive. Phylogenetic analysis revealed that 96% of the genes evolved recently in Brassicaceae. We found that 50 genes are putative targets of microRNAs and that 30% of the XLOCs contain small open reading frames (ORFs) with homology to protein sequences. Finally, RNAseq of ribosome-protected RNA fragments together with predictions of periodic footprint of the ribosome P-sites indicated that 23 of these ORFs are likely to be translated. Our findings indicate that many of the 312 unknown genes might be functional and play a significant role in pollen biology, including the HS response.

Published
2021

11. Novel approach combining transcriptional and evolutionary signatures to identify new multiciliation genes

Author

Odile Lecompte, Dorine Merlat, Yannis Nevers, Olivier Poch, Arnaud Kress, Audrey Defosset, Laetitia Poidevin, Laboratoire des sciences de l'ingénieur, de l'informatique et de l'imagerie (ICube), Institut National des Sciences Appliquées - Strasbourg (INSA Strasbourg), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-École Nationale du Génie de l'Eau et de l'Environnement de Strasbourg (ENGEES)-Réseau nanophotonique et optique, Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Matériaux et nanosciences d'Alsace (FMNGE), Institut de Chimie du CNRS (INC)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), univOAK, Archive ouverte, École Nationale du Génie de l'Eau et de l'Environnement de Strasbourg (ENGEES)-Université de Strasbourg (UNISTRA)-Institut National des Sciences Appliquées - Strasbourg (INSA Strasbourg), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Les Hôpitaux Universitaires de Strasbourg (HUS)-Centre National de la Recherche Scientifique (CNRS)-Matériaux et Nanosciences Grand-Est (MNGE), Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Réseau nanophotonique et optique, and Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Fish Proteins, [INFO.INFO-AI] Computer Science [cs]/Artificial Intelligence [cs.AI], Candidate gene, Cellular differentiation, Gene Expression, Computational biology, comparative genomics, Biology, QH426-470, Article, [INFO.INFO-AI]Computer Science [cs]/Artificial Intelligence [cs.AI], Transcriptome, 03 medical and health sciences, 0302 clinical medicine, Databases, Genetic, evolution, Genetics, Animals, Humans, Cilia, Gene, Phylogeny, Genetics (clinical), 030304 developmental biology, Comparative genomics, multiciliation, 0303 health sciences, Phylogenetic tree, Fishes, rare diseases, Cell Differentiation, Genomics, Biological Evolution, Informatique [cs]/Intelligence artificielle [cs.AI], multi-omics data integration, Motile cilium, Functional genomics, functional genomics, 030217 neurology & neurosurgery
Abstract

Multiciliogenesis is a complex process that allows the generation of hundreds of motile cilia on the surface of specialized cells, to create fluid flow across epithelial surfaces. Dysfunction of human multiciliated cells is associated with diseases of the brain, airway and reproductive tracts. Despite recent efforts to characterize the transcriptional events responsible for the differentiation of multiciliated cells, a lot of actors remain to be identified. In this work, we capitalize on the ever-growing quantity of high-throughput data to search for new candidate genes involved in multiciliation. After performing a large-scale screening using 10 transcriptomics datasets dedicated to multiciliation, we established a specific evolutionary signature involving Otomorpha fish to use as a criterion to select the most likely targets. Combining both approaches highlighted a list of 114 potential multiciliated candidates. We characterized these genes first by generating protein interaction networks, which showed various clusters of ciliated and multiciliated genes, and then by computing phylogenetic profiles. In the end, we selected 11 poorly characterized genes that seem like particularly promising multiciliated candidates. By combining functional and comparative genomics methods, we developed a novel type of approach to study biological processes and identify new promising candidates linked to that process.

Published
2021
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12. RNA polymerase II pausing downstream of core histone genes is different from genes producing polyadenylated transcripts.

Author

Krishanpal Anamika, Àkos Gyenis, Laetitia Poidevin, Olivier Poch, and Làszlò Tora

Subjects
Medicine, Science
Abstract

Recent genome-wide chromatin immunoprecipitation coupled high throughput sequencing (ChIP-seq) analyses performed in various eukaryotic organisms, analysed RNA Polymerase II (Pol II) pausing around the transcription start sites of genes. In this study we have further investigated genome-wide binding of Pol II downstream of the 3' end of the annotated genes (EAGs) by ChIP-seq in human cells. At almost all expressed genes we observed Pol II occupancy downstream of the EAGs suggesting that Pol II pausing 3' from the transcription units is a rather common phenomenon. Downstream of EAGs Pol II transcripts can also be detected by global run-on and sequencing, suggesting the presence of functionally active Pol II. Based on Pol II occupancy downstream of EAGs we could distinguish distinct clusters of Pol II pause patterns. On core histone genes, coding for non-polyadenylated transcripts, Pol II occupancy is quickly dropping after the EAG. In contrast, on genes, whose transcripts undergo polyA tail addition [poly(A)(+)], Pol II occupancy downstream of the EAGs can be detected up to 4-6 kb. Inhibition of polyadenylation significantly increased Pol II occupancy downstream of EAGs at poly(A)(+) genes, but not at the EAGs of core histone genes. The differential genome-wide Pol II occupancy profiles 3' of the EAGs have also been confirmed in mouse embryonic stem (mES) cells, indicating that Pol II pauses genome-wide downstream of the EAGs in mammalian cells. Moreover, in mES cells the sharp drop of Pol II signal at the EAG of core histone genes seems to be independent of the phosphorylation status of the C-terminal domain of the large subunit of Pol II. Thus, our study uncovers a potential link between different mRNA 3' end processing mechanisms and consequent Pol II transcription termination processes.

Published
2012
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13. HGG-34. A DNA DAMAGE REPAIR SIGNATURE IN PRIMARY AND RECURRENT PEDIATRIC HIGH-GRADE GLIOMAS: PROGNOSTIC AND THERAPEUTIC VALUE

Author

Monique Dontenwill, Benoit Lhermitte, Olivier Poch, Laetitia Poidevin, Eric Van Dyck, Marie Pierre Chenard, Natacha Entz-Werle, and Petr V. Nazarov

Subjects
Cancer Research, Mutation, biology, DNA repair, Cell cycle, Stem cell marker, medicine.disease_cause, medicine.disease, body regions, XRCC1, Histone, PARP1, Oncology, Glioma, biology.protein, Cancer research, medicine, AcademicSubjects/MED00300, AcademicSubjects/MED00310, Neurology (clinical), High Grade Gliomas
Abstract

Pediatric high-grade gliomas (pHGGs), including diffuse intrinsic pontine gliomas (DIPGs), despite their low incidence, are the leading cause of mortality in pediatric neuro-oncology. Frequently, pHGGs, harboring mainly histone mutations, are or become resistant to standard therapies like irradiation or chemotherapies. Recent insights showed in adult HGG the predominant role of DNA damage repair (DDR) as a way of prognostic classification. Given the recent evidence that transcription conflicts like in histone-mutated gliomas can induce replication stress and be linked to DDR abnormalities, this study is aiming to establish a DDR signature able to classify specifically pHGGs and to cluster among them poor responders to radiation. Transcriptomic analyses were performed to discriminate seven pHGGs comparatively to a cohort of 10 pilocytic astrocytomas with specific DDR deregulations. The specific transcriptomic signature obtained from this differential gene expression analysis was compared to the aHGG signature already established. To strengthen, refine and finalize the DDR signature able to classify and cluster the pHGGs, we explored both signatures and their common genes in already published transcriptomic analyses of DIPGs and sus-tentorial pHGGs. To check DDR protein expressions correlated to loss of trimethylation as well as histone and TP53 mutations, an immunohistochemical assessment of several DDR markers was performed on a collection of 21 pHGG diagnostic samples and 9 paired relapses. To validate the DDR functional inhibition, we used 3 patient-derived cell lines bearing H3.3K27M mutations. A finalized signature of 28 genes involved in DNA repair and cell cycle machineries was used to cluster in two groups the pHGG cohorts. The differential protein expression of PARP1, XRCC1, p53 and stem cell markers was linked significantly to the more resistant pHGGs and the rapid progressions after radiotherapy. Those DDR makers might be used as theranostic and therapeutic targets, which were screened in PDCLs with promising results.

Published
2021

14. Histone hypoacetylation contributes to CXCL12 downregulation in colon cancer: impact on tumor growth and cell migration

Author

Radhia Benbrika-Nehmar, Cyril Bour, Michèle Legrain, Jean-Noël Freund, Isabelle Duluc, Erwan Pencreach, Dominique Guenot, Laetitia Poidevin, Laetitia Marisa, Attila Oravecz, Viviane Lobstein, Benoit Romain, Progression tumorale et microenvironnement. Approches translationnelles et épidémiologie, Université de Strasbourg (UNISTRA)-CHU Strasbourg-Les Hôpitaux Universitaires de Strasbourg (HUS)-Institut Régional du Cancer-Centre Paul Strauss : Centre Régional de Lutte contre le Cancer (CRLCC), Service de Chirurgie Générale et Digestive [Strasbourg], Les Hôpitaux Universitaires de Strasbourg (HUS), Programme 'Cartes d'Identité des Tumeurs' [Paris] (CIT), Ligue Nationale Contre le Cancer, Laboratoire de Biochimie et de Biologie Moléculaire, CHU Strasbourg-Hôpital de Hautepierre [Strasbourg], Laboratoire des sciences de l'ingénieur, de l'informatique et de l'imagerie (ICube), Institut National des Sciences Appliquées - Strasbourg (INSA Strasbourg), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-École Nationale du Génie de l'Eau et de l'Environnement de Strasbourg (ENGEES)-Réseau nanophotonique et optique, Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Centre National de la Recherche Scientifique (CNRS)-Matériaux et nanosciences d'Alsace, Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM), Equipe 1 'Emergence des Cellules Souches & Initiation Tumorale' (Groupe 1 : Identité intestinale : des Cellules Souches aux Pathologies) (SMART - Inserm U1113), Interface de Recherche Fondamentale et Appliquée en Cancérologie (IRFAC - Inserm U1113), Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre Paul Strauss : Centre Régional de Lutte contre le Cancer (CRLCC)-Fédération de Médecine Translationelle de Strasbourg (FMTS)-Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre Paul Strauss : Centre Régional de Lutte contre le Cancer (CRLCC)-Fédération de Médecine Translationelle de Strasbourg (FMTS), Centre de Ressources Biologiques, Département de Pathologie [Strasbourg], This work was supported by the Université deStrasbourg (Idex Attractivité program), Ligue Contre lecancer, a non-governmental charity organization, throughthe Cartes d’Identité des tumeurs program (CIT) and theHôpitaux Universitaires de Strasbourg., (le programme) Cartes d'identité des tumeurs (CIT), Ligue Nationales Contre le Cancer (LNCC), École Nationale du Génie de l'Eau et de l'Environnement de Strasbourg (ENGEES)-Université de Strasbourg (UNISTRA)-Institut National des Sciences Appliquées - Strasbourg (INSA Strasbourg), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Matériaux et nanosciences d'Alsace (FMNGE), Institut de Chimie du CNRS (INC)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Réseau nanophotonique et optique, Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Les Hôpitaux Universitaires de Strasbourg (HUS)-Centre National de la Recherche Scientifique (CNRS)-Matériaux et Nanosciences Grand-Est (MNGE), Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Réseau nanophotonique et optique, Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), and Freund, Jean-Noël

Subjects
0301 basic medicine, Male, Colorectal cancer, Metastasis, Histones, Mice, 0302 clinical medicine, Cell Movement, [SDV.MHEP] Life Sciences [q-bio]/Human health and pathology, biology, Middle Aged, 3. Good health, Gene Expression Regulation, Neoplastic, Histone, Oncology, PCAF, 030220 oncology & carcinogenesis, DNA methylation, Colonic Neoplasms, embryonic structures, valproate, Heterografts, Female, biological phenomena, cell phenomena, and immunity, Research Paper, Adenoma, Adult, Colon Adenoma, Down-Regulation, Adenocarcinoma, 03 medical and health sciences, Histone H3, Cell Line, Tumor, medicine, Animals, Humans, Aged, Cell Proliferation, acetylation, business.industry, chemokine, Cancer, [SDV.MHEP.HEG]Life Sciences [q-bio]/Human health and pathology/Hépatology and Gastroenterology, DNA Methylation, medicine.disease, butyrate, [SDV.MHEP.HEG] Life Sciences [q-bio]/Human health and pathology/Hépatology and Gastroenterology, Chemokine CXCL12, Mice, Mutant Strains, biological factors, 030104 developmental biology, Immunology, biology.protein, Cancer research, business, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology
Abstract

// Benoit Romain 1, 2 , Radhia Benbrika-Nehmar 1 , Laetitia Marisa 3 , Michele Legrain 4 , Viviane Lobstein 1 , Attila Oravecz 5 , Laetitia Poidevin 5 , Cyril Bour 1 , Jean-Noel Freund 6 , Isabelle Duluc 6 , Dominique Guenot 1 , Erwan Pencreach 1, 4, 7 1 Universite de Strasbourg, Progression Tumorale et Microenvironnement, Approches Translationnelles et Epidemiologie, Strasbourg, France 2 Hopitaux Universitaires de Strasbourg, Service de Chirurgie Generale et Digestive, Strasbourg, France 3 Cartes d’Identite des Tumeurs Program, Ligue Nationale Contre le Cancer, Paris, France 4 Hopitaux Universitaires de Strasbourg, Laboratoire de Biochimie et Biologie Moleculaire, Strasbourg, France 5 Universite de Strasbourg, CNRS, Department of Computer Science, ICube, Strasbourg, France 6 Universite de Strasbourg, INSERM Unit 1113, Strasbourg, France 7 Hopitaux Universitaires de Strasbourg, Centre de Ressources Biologiques, Departement de Pathologie, Strasbourg, France Correspondence to: Dominique Guenot, email: dominique.guenot@inserm.u-strasbg.fr Keywords: chemokine, valproate, butyrate, PCAF, acetylation Received: March 17, 2016 Accepted: February 27, 2017 Published: March 17, 2017 ABSTRACT CXCL12 has been shown to be involved in colon cancer metastasis, but its expression level and molecular mechanisms regulating its expression remain controversial. We thus evaluated CXCL12 expression in a large cohort of colon adenomas and carcinomas, investigated for an epigenetic mechanism controlling its expression and evaluated the impact of CXCL12 levels on cell migration and tumor growth. CXCL12 expression was measured in human colon adenomas and carcinomas with transcriptome array and RT-qPCR. The promoter methylation was analyzed with whole-genome DNA methylation chips and protein expression by immunohistochemistry. We confirm a reduced expression of CXCL12 in 75% of MSS carcinomas and show that the decrease is an early event as already present in adenomas. The methylome analysis shows that the CXCL12 promoter is methylated in only 30% of microsatellite-stable tumors. In vitro , treatments with HDAC inhibitors, butyrate and valproate restored CXCL12 expression in three colon cell lines, increased acetylation of histone H3 within the CXCL12 promoter and inhibited cell migration. In vivo , valproate diminished (65%) the number of intestinal tumors in APC mutant mice, slowed down xenograft tumor growth concomitant to restored CXCL12 expression. Finally we identified loss of PCAF expression in tumor samples and showed that forced expression of PCAF in colon cancer cell lines restored CXCL12 expression. Thus, reduced PCAF expression may participate to CXCL12 promoter hypoacetylation and its subsequent loss of expression. Our study is of potential clinical interest because agents that promote or maintain histone acetylation through HDAC inhibition and/or HAT stimulation, may help to lower colon adenoma/carcinoma incidence, especially in high-risk families, or could be included in therapeutic protocols to treat advanced colon cancer.

Published
2017
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15. Comparative analyses of Podospora anserina secretomes reveal a large array of lignocellulose-active enzymes

Author

Laetitia Poidevin, Senta Heiss-Blanquet, Pedro M. Coutinho, Bernard Henrissat, Anthony Levasseur, Jean-Guy Berrin, Eric Record, Didier Chevret, Chloé Bennati-Granier, Isabelle Herpoël-Gimbert, Biodiversité et Biotechnologie Fongiques (BBF), Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-École Centrale de Marseille (ECM), MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Architecture et fonction des macromolécules biologiques (AFMB), Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), IFP Energies nouvelles (IFPEN), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), and École Centrale de Marseille (ECM)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA)

Subjects
Arabinose, Proteome, Auxiliary activities, Hydrolases, Cellobiose, Cellulase, Xylose, Lignin, Applied Microbiology and Biotechnology, Podospora anserina, 03 medical and health sciences, chemistry.chemical_compound, Podospora, Lignocellulose degradation, Pectinase, Triticum, Trichoderma reesei, 030304 developmental biology, Secretome, 2. Zero hunger, 0303 health sciences, Coprophilous fungi, Plant Stems, biology, 030306 microbiology, [CHIM.ORGA]Chemical Sciences/Organic chemistry, food and beverages, General Medicine, biology.organism_classification, chemistry, Biochemistry, biology.protein, Xylanase, Carbohydrate-active enzymes, Biotechnology
Abstract

The genome of the coprophilous fungus Podospora anserina harbors a large and highly diverse set of putative lignocellulose-acting enzymes. In this study, we investigated the enzymatic diversity of a broad range of P. anserina secretomes induced by various carbon sources (dextrin, glucose, xylose, arabinose, lactose, cellobiose, saccharose, Avicel, Solka-floc, birchwood xylan, wheat straw, maize bran, and sugar beet pulp (SBP)). Compared with the Trichoderma reesei enzymatic cocktail, P. anserina secretomes displayed similar cellulase, xylanase, and pectinase activities and greater arabinofuranosidase, arabinanase, and galactanase activities. The secretomes were further tested for their capacity to supplement a T. reesei cocktail. Four of them improved significantly the saccharification yield of steam-exploded wheat straw up to 48 %. Fine analysis of the P. anserina secretomes produced with Avicel and SBP using proteomics revealed a large array of CAZymes with a high number of GH6 and GH7 cellulases, CE1 esterases, GH43 arabinofuranosidases, and AA1 laccase-like multicopper oxidases. Moreover, a preponderance of AA9 (formerly GH61) was exclusively produced in the SBP condition. This study brings additional insights into the P. anserina enzymatic machinery and will facilitate the selection of promising targets for the development of future biorefineries.

Published
2014
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16. Insights into Exo- and Endoglucanase Activities of Family 6 Glycoside Hydrolases from Podospora anserina

Author

Jean-Guy Berrin, Mathieu Bey, Bernard Henrissat, Annick Doan, Senta Heiss-Blanquet, Julia Feliu, Laetitia Poidevin, Eric Record, Pedro M. Coutinho, Biodiversité et Biotechnologie Fongiques (BBF), École Centrale de Marseille (ECM)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), IFP Energies nouvelles (IFPEN), Architecture et fonction des macromolécules biologiques (AFMB), Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), French National Research Agency (ANR): E-TRICEL ANR-07-BIOE-006, Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-École Centrale de Marseille (ECM), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), and Poidevin, Laetitia

Subjects
0106 biological sciences, hydroxyethylcellulose, dégradation de la biomasse, arabinane, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, glucanase, ph, 01 natural sciences, Applied Microbiology and Biotechnology, Polymerase Chain Reaction, Podospora anserina, xylane, arabinoxylane, chemistry.chemical_compound, Glycoside hydrolase, glycoside hydrolase, galactomannane, Cloning, Molecular, DNA, Fungal, Trichoderma reesei, chemistry.chemical_classification, 0303 health sciences, Podospora, Ecology, biology, excrément, Microbiology and Parasitology, incubation, Microbiologie et Parasitologie, Xyloglucan, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Biochemistry, xyloglucane, champignon ascomycete, substrat, mannane, cellulose cristalline, Biotechnology, DNA, Complementary, Glycoside Hydrolases, Molecular Sequence Data, herbivore, Cellulase, Biotechnologies, Pichia pastoris, 03 medical and health sciences, podospora anserina, 010608 biotechnology, température, Amino Acid Sequence, endoglucanase, Enzymology and Protein Engineering, coprophilie, 030304 developmental biology, pectine, pichia pastoris, trichoderma reesei, ascomycète, carboxyméthylcellulose, 15. Life on land, biology.organism_classification, exoglucanase, glucide, enzyme, Enzyme, chemistry, biology.protein, incubation en conditions contrôlees, Sequence Alignment, Food Science
Abstract

The ascomycete Podospora anserina is a coprophilous fungus that grows at late stages on droppings of herbivores. Its genome encodes a large diversity of carbohydrate-active enzymes. Among them, four genes encode glycoside hydrolases from family 6 (GH6), the members of which comprise putative endoglucanases and exoglucanases, some of them exerting important functions for biomass degradation in fungi. Therefore, this family was selected for functional analysis. Three of the enzymes, P. anserina Cel6A ( Pa Cel6A), Pa Cel6B, and Pa Cel6C, were functionally expressed in the yeast Pichia pastoris . All three GH6 enzymes hydrolyzed crystalline and amorphous cellulose but were inactive on hydroxyethyl cellulose, mannan, galactomannan, xyloglucan, arabinoxylan, arabinan, xylan, and pectin. Pa Cel6A had a catalytic efficiency on cellotetraose comparable to that of Trichoderma reesei Cel6A ( Tr Cel6A), but Pa Cel6B and Pa Cel6C were clearly less efficient. Pa Cel6A was the enzyme with the highest stability at 45�C, while Pa Cel6C was the least stable enzyme, losing more than 50% of its activity after incubation at temperatures above 30�C for 24 h. In contrast to Tr Cel6A, all three studied P. anserina GH6 cellulases were stable over a wide range of pHs and conserved high activity at pH values of up to 9. Each enzyme displayed a distinct substrate and product profile, highlighting different modes of action, with Pa Cel6A being the enzyme most similar to Tr Cel6A. Pa Cel6B was the only enzyme with higher specific activity on carboxymethylcellulose (CMC) than on Avicel and showed lower processivity than the others. Structural modeling predicts an open catalytic cleft, suggesting that Pa Cel6B is an endoglucanase.

Published
2013
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17. Cello-oligosaccharide oxidation reveals differences between two lytic polysaccharide monooxygenases (family GH61) from Podospora anserina

Author

Bernard Henrissat, Jean-Claude Sigoillot, Laetitia Poidevin, Pedro M. Coutinho, Mathieu Bey, Simeng Zhou, Jean-Guy Berrin, Biodiversité et Biotechnologie Fongiques (BBF), Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-École Centrale de Marseille (ECM), Aix Marseille Université (AMU), OSEO projet FUTUROL, and École Centrale de Marseille (ECM)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA)

Subjects
Cellobiose dehydrogenase, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, Gene Expression, Oligosaccharides, Applied Microbiology and Biotechnology, Mass Spectrometry, Pichia, Podospora anserina, Mixed Function Oxygenases, Pichia pastoris, 03 medical and health sciences, Podospora, Glycoside hydrolase, Cloning, Molecular, Enzymology and Protein Engineering, Cellulose, 030304 developmental biology, 0303 health sciences, Ecology, biology, 030306 microbiology, Pycnoporus cinnabarinus, Monooxygenase, biology.organism_classification, Recombinant Proteins, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Biochemistry, Carbohydrate Dehydrogenases, Carbohydrate-binding module, Oxidation-Reduction, Food Science, Biotechnology
Abstract

The genome of the coprophilic ascomycete Podospora anserina encodes 33 different genes encoding copper-dependent lytic polysaccharide monooxygenases (LPMOs) from glycoside hydrolase family 61 (GH61). In this study, two of these enzymes ( P. anserina GH61A [ Pa GH61A] and Pa GH61B), which both harbored a family 1 carbohydrate binding module, were successfully produced in Pichia pastoris . Synergistic cooperation between Pa GH61A or Pa GH61B with the cellobiose dehydrogenase (CDH) of Pycnoporus cinnabarinus on cellulose resulted in the formation of oxidized and nonoxidized cello-oligosaccharides. A striking difference between Pa GH61A and Pa GH61B was observed through the identification of the products, among which were doubly and triply oxidized cellodextrins, which were released only by the combination of Pa GH61B with CDH. The mass spectrometry fragmentation patterns of these oxidized products could be consistent with oxidation at the C-6 position with a geminal diol group. The different properties of Pa GH61A and Pa GH61B and their effect on the interaction with CDH are discussed in regard to the proposed in vivo function of the CDH/GH61 enzyme system in oxidative cellulose hydrolysis.

Published
2013
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18. KD4v: comprehensible knowledge discovery system for missense variant

Author

Olivier Poch, Hoan Nguyen, Tien-Dao Luu, Wolfgang Raffelsberger, Vincent Walter, Nicolas Wicker, Odile Lecompte, Jean Muller, Raymond Ripp, Luc Moulinier, Laetitia Poidevin, Julie D. Thompson, Benjamin Linard, Alin Rusu, Franche-Comté Électronique Mécanique, Thermique et Optique - Sciences et Technologies (UMR 6174) (FEMTO-ST), Université de Franche-Comté (UFC)-Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Supérieure de Mécanique et des Microtechniques (ENSMM)-Université de Technologie de Belfort-Montbeliard (UTBM), Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Biodiversité et Biotechnologie Fongiques (BBF), École Centrale de Marseille (ECM)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), Université de Technologie de Belfort-Montbeliard (UTBM)-Ecole Nationale Supérieure de Mécanique et des Microtechniques (ENSMM)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-École Centrale de Marseille (ECM), Université de Technologie de Belfort-Montbeliard (UTBM)-Ecole Nationale Supérieure de Mécanique et des Microtechniques (ENSMM)-Centre National de la Recherche Scientifique (CNRS)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC), and linard, benjamin

Subjects
Knowledge Bases, education, Mutation, Missense, Biology, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Polymorphism, Single Nucleotide, Genome, Set (abstract data type), 03 medical and health sciences, 0302 clinical medicine, Knowledge extraction, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], [SDV.BID.SPT] Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Genetics, Humans, Missense mutation, Disease, Gene, Genetic Association Studies, Logic programming, [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM], 030304 developmental biology, Structure (mathematical logic), Internet, 0303 health sciences, Proteins, Articles, [SDE.BE] Environmental Sciences/Biodiversity and Ecology, Phenotype, 030220 oncology & carcinogenesis, Mutation (genetic algorithm), [SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], [SDE.BE]Environmental Sciences/Biodiversity and Ecology, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Software
Abstract

International audience; A major challenge in the post-genomic era is a better understanding of how human genetic alterations involved in disease affect the gene products. The KD4v (Comprehensible Knowledge Discovery System for Missense Variant) server allows to characterize and predict the phenotypic effects (deleteri-ous/neutral) of missense variants. The server provides a set of rules learned by Induction Logic Programming (ILP) on a set of missense variants described by conservation, physico-chemical, functional and 3D structure predicates. These rules are interpretable by non-expert humans and are used to accurately predict the deleterious/neutral status of an unknown mutation. The web server is available at http://decrypthon.igbmc.fr/kd4v.

Published
2012
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19. Heterologous expression of Pycnoporus cinnabarinus cellobiose dehydrogenase in Pichia pastoris and involvement in saccharification processes

Author

Jean Claude Sigoillot, Mathieu Bey, Laetitia Poidevin, Jean-Guy Berrin, Unité mixte de recherche de biotechnologie des champignons filamenteux, Université de Provence - Aix-Marseille 1-Institut National de la Recherche Agronomique (INRA)-Université de la Méditerranée - Aix-Marseille 2, Institut Français du Pétrole, This work was supported by the Futurol project. We thank Siemeng Zhou for technical assistance in bioreactor culture, CIRM Marseille for supplying Pycnoporus cinnabarinus strain BRFM 137, and Sacha Grisel for sugar analysis, and Bey, Mathieu

Subjects
Cellobiose dehydrogenase, [SDV]Life Sciences [q-bio], lcsh:QR1-502, Lignocellulosic biomass, Bioengineering, Lignin, Applied Microbiology and Biotechnology, white-rot fungi, lcsh:Microbiology, Pichia, Microbiology, Pichia pastoris, Fungal Proteins, 03 medical and health sciences, lignocellulose, expression hétérologue, processus, [SDV.IDA]Life Sciences [q-bio]/Food engineering, gluconic acid, [SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering, cdh, saccharification, biomass, biotechnology and applied microbiology, 030304 developmental biology, 0303 health sciences, Fungal protein, biology, 030306 microbiology, Research, Pycnoporus cinnabarinus, biology.organism_classification, Pycnoporus, Recombinant Proteins, Biochemistry, cellobiose déshydrogénase, Carbohydrate Dehydrogenases, Electrophoresis, Polyacrylamide Gel, Heterologous expression, Biotechnology
Abstract

Background Cellobiose dehydrogenase (CDH) is an extracellular hemoflavoenzyme produced by lignocellulose-degrading fungi including Pycnoporus cinnabarinus. We investigated the cellulolytic system of P. cinnabarinus, focusing on the involvement of CDH in the deconstruction of lignocellulosic biomass. Results First, P. cinnabarinus growth conditions were optimized for CDH production. Following growth under cellulolytic conditions, the main components secreted were cellulases, xylanases and CDH. To investigate the contribution of P. cinnabarinus secretome in saccharification processes, the Trichoderma reesei enzymatic cocktail was supplemented with the P. cinnabarinus secretome. A significant enhancement of the degradation of wheat straw was observed with (i) the production of a large amount of gluconic acid, (ii) increased hemicellulose degradation, and (iii) increased overall degradation of the lignocellulosic material. P. cinnabarinus CDH was heterologously expressed in Pichia pastoris to obtain large amounts of pure enzyme. In a bioreactor, the recombinant CDH (rCDH) expression level reached 7800 U/L. rCDH exhibited values of biochemical parameters similar to those of the natural enzyme, and was able to bind cellulose despite the absence of a carbohydrate-binding module (CBM). Following supplementation of purified rCDH to T. reesei enzymatic cocktail, formation of gluconic acid and increased hemicellulose degradation were observed, thus confirming the previous results observed with P. cinnabarinus secretome. Conclusions We demonstrate that CDH offers an attractive tool for saccharification process enhancement due to gluconic acid production from raw lignocellulosic material.

Published
2011
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20. The thioredoxin-like protein rod-derived cone viability factor (RdCVFL) interacts with TAU and inhibits its phosphorylation in the retina

Author

François Delalande, Olivier Poch, Therese Cronin, Géraldine Millet-Puel, Ram Fridlich, Alain Van Dorsselaer, Arne Holmgren, Céline Jaillard, Jun Lu, Ludivine Perrocheau, Thierry Léveillard, José-Alain Sahel, Marie-Laure Niepon, Laetitia Poidevin, Laboratoire de Physiopathologie Cellulaire et Moleculaire de la Retine, Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Pluridisciplinaire Hubert Curien (IPHC), Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Department of Medical Biochemistry and Biophysics, karolinska institute-Medical Nobel Institute for Biochemistry, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut de la Vision, Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Pierre et Marie Curie - Paris 6 (UPMC), Peney, Maité, and Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Retinal degeneration, MESH: Protein Isoforms, Biochemistry, MESH: Mice, Knockout, Analytical Chemistry, Mice, Thioredoxins, 0302 clinical medicine, MESH: Thioredoxins, MESH: Eye Proteins, Tandem Mass Spectrometry, Protein Isoforms, MESH: Animals, Phosphorylation, Mice, Knockout, Mice, Inbred BALB C, 0303 health sciences, MESH: Oxidative Stress, biology, MESH: Retina, 3. Good health, MESH: tau Proteins, Signal transduction, Thioredoxin, Protein Binding, Programmed cell death, Tau protein, MESH: Mice, Inbred BALB C, tau Proteins, Retina, Cell Line, 03 medical and health sciences, Retinitis pigmentosa, medicine, Animals, Humans, MESH: Protein Binding, Eye Proteins, Molecular Biology, MESH: Mice, 030304 developmental biology, MESH: Humans, MESH: Phosphorylation, Research, Alternative splicing, MESH: Tandem Mass Spectrometry, medicine.disease, Molecular biology, MESH: Cell Line, Oxidative Stress, biology.protein, sense organs, MESH: Chromatography, Liquid, 030217 neurology & neurosurgery, Chromatography, Liquid
Abstract

International audience; Rod-derived cone viability factor (RdCVF) is produced by the Nxnl1 gene that codes for a second polypeptide, RdCVFL, by alternative splicing. Although the role of RdCVF in promoting cone survival has been described, the implication of RdCVFL, a putative thioredoxin enzyme, in the protection of photoreceptors is presently unknown. Using a proteomics approach we identified 90 proteins interacting with RdCVFL including the microtubule-binding protein TAU. We demonstrate that the level of phosphorylation of TAU is increased in the retina of the Nxnl1(-/-) mice as it is hyperphosphorylated in the brain of patients suffering from Alzheimer disease, presumably in some cases through oxidative stress. Using a cell-based assay, we show that RdCVFL inhibits TAU phosphorylation. In vitro, RdCVFL protects TAU from oxidative damage. Photooxidative stress is implicated in retinal degeneration, particularly in retinitis pigmentosa, where it is considered to be a contributor to secondary cone death. The functional interaction between RdCVFL and TAU described here is the first characterization of the RdCVFL signaling pathway involved in neuronal cell death mediated by oxidative stress.

Published
2009
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21. RETINOBASE: a web database, data mining and analysis platform for gene expression data on retina

Author

Olivier Poch, Wolfgang Raffelsberger, Laetitia Poidevin, Raymond Ripp, Guillaume Berthommier, Thierry Léveillard, Nicolas Gagnière, Ravi Kiran Reddy Kalathur, Institut de génétique et biologie moléculaire et cellulaire (IGBMC), Université Louis Pasteur - Strasbourg I-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Physiopathologie Cellulaire et Moleculaire de la Retine, and Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)

Subjects
lcsh:QH426-470, Relational database, lcsh:Biotechnology, Gene regulatory network, Information Storage and Retrieval, Context (language use), Biology, computer.software_genre, Retina, Database, 03 medical and health sciences, 0302 clinical medicine, lcsh:TP248.13-248.65, Databases, Genetic, Genetics, medicine, Microarray databases, 030304 developmental biology, Internet, 0303 health sciences, Gene Expression Profiling, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Gene expression profiling, lcsh:Genetics, medicine.anatomical_structure, Gene chip analysis, Database Management Systems, DNA microarray, computer, 030217 neurology & neurosurgery, Biotechnology
Abstract

Background The retina is a multi-layered sensory tissue that lines the back of the eye and acts at the interface of input light and visual perception. Its main function is to capture photons and convert them into electrical impulses that travel along the optic nerve to the brain where they are turned into images. It consists of neurons, nourishing blood vessels and different cell types, of which neural cells predominate. Defects in any of these cells can lead to a variety of retinal diseases, including age-related macular degeneration, retinitis pigmentosa, Leber congenital amaurosis and glaucoma. Recent progress in genomics and microarray technology provides extensive opportunities to examine alterations in retinal gene expression profiles during development and diseases. However, there is no specific database that deals with retinal gene expression profiling. In this context we have built RETINOBASE, a dedicated microarray database for retina. Description RETINOBASE is a microarray relational database, analysis and visualization system that allows simple yet powerful queries to retrieve information about gene expression in retina. It provides access to gene expression meta-data and offers significant insights into gene networks in retina, resulting in better hypothesis framing for biological problems that can subsequently be tested in the laboratory. Public and proprietary data are automatically analyzed with 3 distinct methods, RMA, dChip and MAS5, then clustered using 2 different K-means and 1 mixture models method. Thus, RETINOBASE provides a framework to compare these methods and to optimize the retinal data analysis. RETINOBASE has three different modules, "Gene Information", "Raw Data System Analysis" and "Fold change system Analysis" that are interconnected in a relational schema, allowing efficient retrieval and cross comparison of data. Currently, RETINOBASE contains datasets from 28 different microarray experiments performed in 5 different model systems: drosophila, zebrafish, rat, mouse and human. The database is supported by a platform that is designed to easily integrate new functionalities and is also frequently updated. Conclusion The results obtained from various biological scenarios can be visualized, compared and downloaded. The results of a case study are presented that highlight the utility of RETINOBASE. Overall, RETINOBASE provides efficient access to the global expression profiling of retinal genes from different organisms under various conditions.

Published
2008
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22. Cello-Oligosaccharide Oxidation Reveals Differences between Two Lytic Polysaccharide Monooxygenases (Family GH61) from Podospora anserina.

Author

Mathieu Bey, Simeng Zhou, Laetitia Poidevin, Bernard Henrissat, Coutinho, Pedro M., Berrin, Jean-Guy, and Sigoillot, Jean-Claude

Subjects
*OLIGOSACCHARIDES, *LYSINS, *POLYSACCHARIDES, *MONOOXYGENASES, *PODOSPORA anserina, *CELLOBIOSE
Abstract

The genome of the coprophilic ascomycete Podospora anserina encodes 33 different genes encoding copper-dependent lytic polysaccharide monooxygenases (LPMOs) from glycoside hydrolase family 61 (GH61). In this study, two of these enzymes (P. anserina GH61A [PaGH61A] and PaGH61B), which both harbored a family 1 carbohydrate binding module, were successfully produced in Pichiapastoris. Synergistic cooperation between PaGH61A or PaGH61B with the cellobiose dehydrogenase (CDH) of Pycnoporus cinnabarinus on cellulose resulted in the formation of oxidized and nonoxidized cello-oligosaccharides. A strik- ing difference between PaGH61A and PaGH61B was observed through the identification of the products, among which were doubly and triply oxidized cellodextrins, which were released only by the combination of PaGH61B with CDH. The mass spectrometry fragmentation patterns of these oxidized products could be consistent with oxidation at the C-6 position with a gemial diol group. The different properties of PaGH6IA and PaGH6IB and their effect on the interaction with CDH are discussed in regard to the proposed in vivo function of the CDH/GH61 enzyme system in oxidative cellulose hydrolysis. [ABSTRACT FROM AUTHOR]

Published
2013
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