UCAGenomiX related publications

Du to our strong expertise in "omics" experiments and in microRNAs topics we decided to separate into 3 categories the related publications into which the Functional genomics Platform of Nice-Sophia-Antipolis is involved :
  1. Expression studies (DNA microarrays and high-throughput sequencing experiments)
  2. MicroRNA studies
  3. Miscellaneous

Arguel Marie-Jeanne

 04 93 95 77 90
 660 route des lucioles 06560 Valbonne - Sophia-Antipolis

5 publications found

1. CD4+ T Cells Have a Permissive Effect on Enriched Environment-Induced Hippocampus Synaptic Plasticity.
Front Synaptic Neurosci. 2018 Jun 13;10:14. doi: 10.3389/fnsyn.2018.00014. eCollection 2018.
Zarif H, Hosseiny S, Paquet A, Lebrigand K, Arguel MJ, Cazareth J, Lazzari A, Heurteaux C, Glaichenhaus N, Chabry J, Guyon A, Petit-Paitel A
Université Côte d'Azur, CNRS, IPMC, Nice, France. Université Côte d'Azur, INSERM, IPMC, Nice, France. Université Côte d'Azur, INSERM, C3M, IPMC, Nice, France.

Living in an enriched environment (EE) benefits health by acting synergistically on various biological systems including the immune and the central nervous systems. The dialog between the brain and the immune cells has recently gained interest and is thought to play a pivotal role in beneficial effects of EE. Recent studies show that T lymphocytes have an important role in hippocampal plasticity, learning, and memory, although the precise mechanisms by which they act on the brain remain elusive. Using a mouse model of EE, we show here that CD4+ T cells are essential for spinogenesis and glutamatergic synaptic function in the CA of the hippocampus. However, CD4+ lymphocytes do not influence EE-induced neurogenesis in the DG of the hippocampus, by contrast to what we previously demonstrated for CD8+ T cells. Importantly, CD4+ T cells located in the choroid plexus have a specific transcriptomic signature as a function of the living environment. Our study highlights the contribution of CD4+ T cells in the brain plasticity and function.
Pubmed link : 29950983

2. CD8+ T cells are essential for the effects of enriched environment on hippocampus-dependent behavior, hippocampal neurogenesis and synaptic plasticity.
Brain Behav Immun. 2017 Nov 22. pii: S0889-1591(17)30517-2. doi: 10.1016/j.bbi.2017.11.016.
Zarif H, Nicolas S, Guyot M, Hosseiny S, Lazzari A, Canali MM, Cazareth J, Brau F, Golzne V, Dourneau E, Maillaut M, Luci C, Paquet A, Lebrigand K, Arguel MJ, Daoudlarian D, Heurteaux C, Glaichenhaus N, Chabry J, Guyon A, Petit-Paitel A
Université Côte d'Azur, CNRS, IPMC, France. Université Côte d'Azur, INSERM, CNRS, IPMC, France. Université Côte d'Azur, C3M, INSERM U 1065, France. Université Côte d'Azur, INSERM, CNRS, IPMC, France. Electronic address: joelle.chabry@ipmc.cnrs.fr. Université Côte d'Azur, CNRS, IPMC, France. Electronic address: alice.guyon@ipmc.cnrs.fr.

Enriched environment (EE) induces plasticity changes in the brain. Recently, CD4+ T cells have been shown to be involved in brain plasticity processes. Here, we show that CD8+ T cells are required for EE-induced brain plasticity in mice, as revealed by measurements of hippocampal volume, neurogenesis in the DG of the hippocampus, spinogenesis and glutamatergic synaptic function in the CA of the hippocampus. As a consequence, EE-induced behavioral benefits depend, at least in part, on CD8+ T cells. In addition, we show that spleen CD8+ T cells from mice housed in standard environment (SE) and EE have different properties in terms of 1) TNFα release after in vitro CD3/CD28 or PMA/Iono stimulation 2) in vitro proliferation properties 3) CD8+ CD44+ CD62Llow and CD62Lhi T cells repartition 4) transcriptomic signature as revealed by RNA sequencing. CD8+ T cells purified from the choroid plexus of SE and EE mice also exhibit different transcriptomic profiles as highlighted by single-cell mRNA sequencing. We show that CD8+ T cells are essential mediators of beneficial EE effects on brain plasticity and cognition. Additionally, we propose that EE differentially primes CD8+ T cells leading to behavioral improvement.
Pubmed link : 29175168

3. A cost effective 5' selective single cell transcriptome profiling approach with improved UMI design
Nucleic Acids Res. 2016 Dec 9. pii: gkw1242.
Arguel MJ, Lebrigand K, Paquet A, Ruiz Garcia S, Zaragosi LE, Barbry P, Waldmann R
Université Côte d'Azur, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, F06560 Sophia Antipolis, France. Université Côte d'Azur, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, F06560 Sophia Antipolis, France

Single cell RNA sequencing approaches are instrumental in studies of cell-to-cell variability. 5' selective transcriptome profiling approaches allow simultaneous definition of the transcription start size and have advantages over 3' selective approaches which just provide internal sequences close to the 3' end. The only currently existing 5' selective approach requires costly and labor intensive fragmentation and cell barcoding after cDNA amplification. We developed an optimized 5' selective workflow where all the cell indexing is done prior to fragmentation. With our protocol, cell indexing can be performed in the Fluidigm C1 microfluidic device, resulting in a significant reduction of cost and labor. We also designed optimized unique molecular identifiers that show less sequence bias and vulnerability towards sequencing errors resulting in an improved accuracy of molecule counting. We provide comprehensive experimental workflows for Illumina and Ion Proton sequencers that allow single cell sequencing in a cost range comparable to qPCR assays.
Pubmed link : 27940562

4. Comparative Genomic Analysis of Drechmeria coniospora Reveals Core and Specific Genetic Requirements for Fungal Endoparasitism of Nematodes.
PLoS Genet. 2016 May 6;12(5):e1006017. doi: 10.1371/journal.pgen.1006017. eCollection 2016.
Lebrigand K, He le D, Thakur N, Arguel MJ, Polanowska J, Henrissat B, Record E, Magdelenat G, Barbe V, Raffaele S, Barbry P, Ewbank JJ
CNRS and University Nice Sophia Antipolis, Institute of Molecular and Cellular Pharmacology, Sophia Antipolis, France. Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université UM2, Inserm, U1104, CNRS UMR7280, Marseille, France. CNRS UMR 7257, Aix-Marseille University, Marseille, France. INRA, USC 1408 AFMB, Marseille, France. Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia. INRA, UMR1163 Biodiversité et Biotechnologie Fongiques, Aix-Marseille Université, Polytech Marseille, CP 925, Marseille, France. Aix-Marseille Université, UMR1163 Biodiversité et Biotechnologie Fongiques, Faculté des Sciences de Luminy-Polytech, CP 925, Marseille, France. Commissariat à l'Energie Atomique, Institut de Génomique, Génoscope, Laboratoire de Biologie Moleculaire pour l'Etude des Génomes (LBioMEG), Evry, France. INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, Castanet Tolosan, France. CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, Castanet Tolosan, France.

Drechmeria coniospora is an obligate fungal pathogen that infects nematodes via the adhesion of specialized spores to the host cuticle. D. coniospora is frequently found associated with Caenorhabditis elegans in environmental samples. It is used in the study of the nematode's response to fungal infection. Full understanding of this bi-partite interaction requires knowledge of the pathogen's genome, analysis of its gene expression program and a capacity for genetic engineering. The acquisition of all three is reported here. A phylogenetic analysis placed D. coniospora close to the truffle parasite Tolypocladium ophioglossoides, and Hirsutella minnesotensis, another nematophagous fungus. Ascomycete nematopathogenicity is polyphyletic; D. coniospora represents a branch that has not been molecularly characterized. A detailed in silico functional analysis, comparing D. coniospora to 11 fungal species, revealed genes and gene families potentially involved in virulence and showed it to be a highly specialized pathogen. A targeted comparison with nematophagous fungi highlighted D. coniospora-specific genes and a core set of genes associated with nematode parasitism. A comparative gene expression analysis of samples from fungal spores and mycelia, and infected C. elegans, gave a molecular view of the different stages of the D. coniospora lifecycle. Transformation of D. coniospora allowed targeted gene knock-out and the production of fungus that expresses fluorescent reporter genes. It also permitted the initial characterisation of a potential fungal counter-defensive strategy, involving interference with a host antimicrobial mechanism. This high-quality annotated genome for D. coniospora gives insights into the evolution and virulence of nematode-destroying fungi. Coupled with genetic transformation, it opens the way for molecular dissection of D. coniospora physiology, and will allow both sides of the interaction between D. coniospora and C. elegans, as well as the evolutionary arms race that exists between pathogen and host, to be studied.
Pubmed link : 27153332

5. Identification of novel target genes for safer and more specific control of root-knot nematodes from a pan-genome mining.
PLoS Pathog. 2013 Oct;9(10):e1003745. doi: 10.1371/journal.ppat.1003745. Epub 2013 Oct 31.
Danchin EG, Arguel MJ, Campan-Fournier A, Perfus-Barbeoch L, Magliano M, Rosso MN, Da Rocha M, Da Silva C, Nottet N, Labadie K, Guy J, Artiguenave F, Abad P
INRA, UMR 1355 ISA, Institut Sophia Agrobiotech, Sophia-Antipolis, France ; CNRS, UMR 7254 ISA, Institut Sophia Agrobiotech, Sophia-Antipolis, France ; Université de Nice Sophia-Antipolis, UMR ISA, Institut Sophia Agrobiotech, Sophia-Antipolis, France.

Root-knot nematodes are globally the most aggressive and damaging plant-parasitic nematodes. Chemical nematicides have so far constituted the most efficient control measures against these agricultural pests. Because of their toxicity for the environment and danger for human health, these nematicides have now been banned from use. Consequently, new and more specific control means, safe for the environment and human health, are urgently needed to avoid worldwide proliferation of these devastating plant-parasites. Mining the genomes of root-knot nematodes through an evolutionary and comparative genomics approach, we identified and analyzed 15,952 nematode genes conserved in genomes of plant-damaging species but absent from non target genomes of chordates, plants, annelids, insect pollinators and mollusks. Functional annotation of the corresponding proteins revealed a relative abundance of putative transcription factors in this parasite-specific set compared to whole proteomes of root-knot nematodes. This may point to important and specific regulators of genes involved in parasitism. Because these nematodes are known to secrete effector proteins in planta, essential for parasitism, we searched and identified 993 such effector-like proteins absent from non-target species. Aiming at identifying novel targets for the development of future control methods, we biologically tested the effect of inactivation of the corresponding genes through RNA interference. A total of 15 novel effector-like proteins and one putative transcription factor compatible with the design of siRNAs were present as non-redundant genes and had transcriptional support in the model root-knot nematode Meloidogyne incognita. Infestation assays with siRNA-treated M. incognita on tomato plants showed significant and reproducible reduction of the infestation for 12 of the 16 tested genes compared to control nematodes. These 12 novel genes, showing efficient reduction of parasitism when silenced, constitute promising targets for the development of more specific and safer control means.
Pubmed link : 24204279