PLoS Pathog

The low pathogenicity and replicative potential of HIV-2 are still poorly understood. We investigated whether HIV-2 reservoirs might follow the peculiar distribution reported in models of attenuated HIV-1/SIV infections, i.e. limited infection of central-memory CD4 T lymphocytes (TCM). Antiretroviral-naive HIV-2 infected individuals from the ANRS-CO5 (12 non-progressors, 2 progressors) were prospectively included. Peripheral blood mononuclear cells (PBMCs) were sorted into monocytes and resting CD4 T-cell subsets (naive [TN], central- [TCM], transitional- [TTM] and effector-memory [TEM]). Reactivation of HIV-2 was tested in 30-day cultures of CD8-depleted PBMCs. HIV-2 DNA was quantified by real-time PCR. Cell surface markers, co-receptors and restriction factors were analyzed by flow-cytometry and multiplex transcriptomic study. HIV-2 DNA was undetectable in monocytes from all individuals and was quantifiable in TTM from 4 individuals (median: 2.25 log10 copies/106 cells [IQR: 1.99-2.94]) but in TCM from only 1 individual (1.75 log10 copies/106 cells). HIV-2 DNA levels in PBMCs (median: 1.94 log10 copies/106 PBMC [IQR = 1.53-2.13]) positively correlated with those in TTM (r = 0.66, p = 0.01) but not TCM. HIV-2 reactivation was observed in the cells from only 3 individuals. The CCR5 co-receptor was distributed similarly in cell populations from individuals and donors. TCM had a lower expression of CXCR6 transcripts (p = 0.002) than TTM confirmed by FACS analysis, and a higher expression of TRIM5 transcripts (p = 0.004). Thus the low HIV-2 reservoirs differ from HIV-1 reservoirs by the lack of monocytic infection and a limited infection of TCM associated to a lower expression of a potential alternative HIV-2 co-receptor, CXCR6 and a higher expression of a restriction factor, TRIM5. These findings shed new light on the low pathogenicity of HIV-2 infection suggesting mechanisms close to those reported in other models of attenuated HIV/SIV infection models

Sequence of a complete chicken BG haplotype shows dynamic expansion and contraction of two gene lineages with particular expression patterns.

Many genes important in immunity are found as multigene families. The butyrophilin genes are members of the B7 family, playing diverse roles in co-regulation and perhaps in antigen presentation. In humans, a fixed number of butyrophilin genes are found in and around the major histocompatibility complex (MHC), and show striking association with particular autoimmune diseases. In chickens, BG genes encode homologues with somewhat different domain organisation. Only a few BG genes have been characterised, one involved in actin-myosin interaction in the intestinal brush border, and another implicated in resistance to viral diseases. We characterise all BG genes in B12 chickens, finding a multigene family organised as tandem repeats in the BG region outside the MHC, a single gene in the MHC (the BF-BL region), and another single gene on a different chromosome. There is a precise cell and tissue expression for each gene, but overall there are two kinds, those expressed by haemopoietic cells and those expressed in tissues (presumably non-haemopoietic cells), correlating with two different kinds of promoters and 5' untranslated regions (5'UTR). However, the multigene family in the BG region contains many hybrid genes, suggesting recombination and/or deletion as major evolutionary forces. We identify BG genes in the chicken whole genome shotgun sequence, as well as by comparison to other haplotypes by fibre fluorescence in situ hybridisation, confirming dynamic expansion and contraction within the BG region. Thus, the BG genes in chickens are undergoing much more rapid evolution compared to their homologues in mammals, for reasons yet to be understood.This is the final published version. It was originally published by PLOS in PLOS Genetics here: http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1004417

Etude de l'immunité du poulet et de sa résistance aux pathogènes (identification de nouveaux facteurs impliqués dans la réponse immunitaire)

Dans le cadre de l étude des interactions entre un hôte et un pathogène, le poulet est un organisme modèle qui a largement contribué à la compréhension des mécanismes impliqués dans les réponses immunitaires de l hôte. Les outils génomiques développés récemment permettent d étudier ces réponses à l échelle du génome entier. Les travaux présentés ici ont porté sur l utilisation de ce type d outils appliquée à l étude de la réponse immunitaire du poulet afin d en identifier de nouveaux facteurs ainsi que leur implication éventuelle dans le phénomène de résistance aux pathogènes. Nous avons complété la carte moléculaire du Complexe Majeur d Histocompatibilité qui est lié à la résistance du poulet à certains pathogènes. Dans cette nouvelle région, nous avons pu caractériser différents membres de la famille TRIM-B30.2, inconnus jusqu alors. Puis, l analyse du transcriptome de la bourse de Fabricius infectée par le virus IBDV a permis de mettre en évidence la précocité de la mise en place de la réponse inflammatoire chez des animaux résistants à ce virus par rapport à des animaux sensibles. De plus, cette analyse a permis de suggérer que l apoptose était impliquée dans la résistance à IBDV. Enfin une analyse bioinformatique réalisée à partir de quatre banques d ADNc a permis d identifier des clones correspondant à des ARN non codant. L étude des profils d expression de ces derniers a suggéré que certains puissent jouer un rôle dans la réponse immune chez le poulet. Nous avons donc identifié de nouveaux facteurs potentiellement impliqués dans les défenses immunitaires du poulet. Ces éléments mettent en relief la complexité du système immun du poulet en même temps qu ils permettent de mieux appréhender le phénomène de résistance à un pathogène.The chicken is an important model organism for the study of the host immune responses. The recent available genomic tools allow high-throughput analyses of the processes involved in the immune mechanisms. This work is based on the genomic analysis of the chicken immune response and aimed at identifying news elements of this response as well as their possible role in the pathogen resistance of the chicken. We extended the molecular map of the Major Histocompatibility Complex involved in the chicken resistance to pathogens. In this new region, we have characterised a cluster of previously unknown TRIM-B30.2 genes. Transcriptomic analysis of the IBDV-infected bursa of Fabricius led us to propose a model for resistance in which a more rapid inflammatory response and more-extensive p53-related induction of apoptosis in the target B-cells might limit viral replication and consequent pathology. Further, bioinformatics studies of immune-related cDNA libraries identified non coding RNAs. A fraction of these ncRNAs exhibited immune tissue-specific expression patterns and changes in expression following a viral infection, thereby suggesting that they could play an active role in the immune response. Thus, we have identified new factors potentially involved in the chicken immune defences. These new elements highlight the complexity of the chicken immune system, and give new clues into the understanding of the pathogen resistance mechanisms.ORSAY-PARIS 11-BU Sciences (914712101) / SudocSudocFranceF

Etude du transcriptome non-codant chez le poulet

Ces dernière années ont mis en lumière l'immense complexité du transcriptome eucaryote et révélé une multitude d'ARN non-codants impliqués dans un grand panel de processus biologiques. Les travaux présentés ici proposent d'explorer leur expression chez le poulet et chez l'homme et de rechercher leur implication dans différentes maladies aussi bien infectieuses que génétiques. Nous avons identifié des ARN non-codants dans des banques d'ADN complémentaires de tissus immuns activés de poulet. Et l'étude de leurs profils d'expression, au cours d'une infection virale suggèrent qu'ils pourraient réguler l'expression de gènes impliqués dans la défense de l'hôte contre les pathogènes. Ensuite, nous avons montré que la présenced'une forme mutée de la protéine CFTR, responsable de la mucoviscidose chez la plupart des patients, augmente l'expression de plusieurs microARN parmi lesquels, miR-125a dont l'une des cibles pourait êre impliquée dans la maladie. Puis, nous avons suivi l'espression des microARN, chez le poulet, après infection par des pathogènes entériques et détecté l'expression différentielle de mirocARN impliqués dans le contrôle de la réponse inflammatoire et dans l'apoptose; Enfin, nous avons découvert des microARN exprimés différentiellement suite à l'infection de cellules épithéliales par le virus influenza H1N1 sauvage ou un mutant incapable d'exprimer un des facteurs de la virulence, et avons identifié les voies de signalisation qu'ils réguleraient.In the last decade, the complexity of the transcription in the eukaryotic genomes was discovered, and revealed thousands of noncoding RNAs involved in a large range of biological processes. This work explores their expression and involvement in infectious and genetic diseases in chicken and human. First we identified noncoding RNAs from chicken immune-related cDNA libraries. Their expression profiles following a viral infection suggested that they could act as regulators of genes involved in the chicken immune defences. We showed also in an in vitro cystic fibrosis context, that several microRNAs are upregulated, including miR-125a which targets a gene that could be involved in the disease. We investigated then microRNAs expression following enteric pathogens infection in chicken and showed a diffrential expression of microRNAs reported to act as negative regulators of inflammation and inducers of cell-cycle arrest. Finally, we have revealed microRNAs differentially expresses between epithelial cells infected by a wild-type H1N1 influenza virus or an H1N1 influenza virus defective for a virulence foctor, and identified signaling pathways targeted by these micro RNAs.ORSAY-PARIS 11-BU Sciences (914712101) / SudocSudocFranceF

Concerted evolution of two Mhc class II B loci in pheasants and domestic chickens

The major histocompatibility complex (Mhc) of the ring-necked pheasant contains two polymorphic Mhc class II B genes. We show here, by screening of a cDNA library and RT-PCR from RNA, that both of these loci, Phco-DAB1 and Phco-DAB2, normally are transcribed in the spleen. They differ mainly in the 3' untranslated (UT) region, with the transcript lengths, not including the poly(A) tails, being 1,100 nt for DAB1 and 955 nt for DAB2. These two loci are orthologous to the B-LBI and B-LBII loci of the domestic chicken, respectively. DAB1 and DAB2 therefore seem to have evolved from a duplication before the split of the evolutionary lineages leading to the pheasant and the domestic chicken ca. 20 MYA. This is the first report of an orthologous relationship between avian Mhc genes. Yet, the third exons of DAB1 and DAB2 were identical in all available sequences and differed at 10 positions from the exon 3 sequences of B-LBI/B-LBII. The species-specific exon 3 suggests that DAB1 and DAB2 are subject to concerted evolution, i.e., interlocus genetic exchange. The exon 2 sequences show characteristic polymorphism, with hypervariable segments occurring in different combinations in different alleles. Given the divergence in the 3'UT region, the finding of the same exon 2 sequence at both the DAB1 and the DAB2 loci in one of the pheasant haplotypes also suggests that interlocus genetic exchange does occur. Accordingly, the exon 2 sequences tended to cluster irrespective of locus in the phylogenetic analyses. Genetic exchange simultaneously involving both exon 2 and exon 3 may be facilitated by the short length of the intervening intron (<100 bp) in pheasants and domestic chickens compared with, e.g., humans (about 3 kb)

RFP-Y-like sequences assort independently of pheasant MHC genes

Abstract is not availabl

Molecular characterization of 3 MHC class II B haplotypes in the ring-necked pheasant

We investigated the class II B genes in a free-ranging population of the ring-necked pheasant Phasianus colchicus by a combination of restriction fragment length polymorphism (RFLP), polymerase chain reaction (PCR), and DNA sequencing. Special attention was paid to the variation in the second exon, which encodes the peptide-binding beta(i)-domain. The population was introduced, but it still exhibited major histocompatibility complex polymorphism with at least three segregating class II B haplotypes and consequently six genotypes. We found two class LI B genes associated with each haplotype. The class II B genes of birds had until then only been molecularly characterized in the domestic chicken. The pheasant genes were highly variable, although one of the amplified sequences was found in two different haplotypes. Taken together, the most polymorphic positions (residues 37 and 38) were not identical in any of the predicted protein sequences, but all except one of the motifs had already been found in the domestic chicken. Structurally important features in mammalian class II B genes were generally conserved also in the pheasant sequences, but the loss of a potential salt bridge constituent (Arg(72)) in several sequences may suggest a slightly different structure of the adjacent parts of the peptide-binding groove. The pheasant genes are most closely related to the so called B-LBII family in the chicken, indicating that this represents a major line of development among avian class II B genes

Refined localization of twenty-one genes in subregion p13.1 of human chromosome 1

http://content.karger.comIn this report, we describe a refinement of the human transcript map of chromosome 1p13.1, a subregion undergoing many aberrations in various types of human cancers. Publicly available genetic linkage, radiation hybrid and physical maps, as well as cytogenetic and sequence data were used to establish the relative order and orientation of ten known intragenic markers. The complete sequence of genomic clones of the region, available at the Sanger Centre, provided the tool for further studies performed by BLAST analysis against all cDNA sequences registered in the Genexpress Index2. This allowed us to assign to subband 1p13.1 nine of the ten known genes, an additional member of the gene family of one of these genes and eleven new transcripts. The remaining known gene and one additional new transcript map at the 1p13.1 and 1p13.2 boundary. The corresponding genes may be responsible for disorders related to this region. The resulting transcript map of 1p13.1 is presented in the printed article with additional data available on a dedicated Web site at the address http://idefix.upr420.vjf.cnrs.fr/CART

Chicken MHC Class I genes in B and Rfp-Y are members of two different gene families

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Insights into the evolution of B and Rfp-Y - Two genetically independent Mhc gene clusters in the chicken

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