Genome-wide immunity studies in the rabbit: transcriptome variations in peripheral blood mononuclear cells after in vitro stimulation by LPS or PMA-Ionomycin

Jacquier, Vincent; Estellé, Jordi; Schmaltz-Panneau, Barbara; Lecardonnel, Jérôme; Moroldo, Marco; Lemonnier, Gaëtan; Turner-Maier, Jason; Duranthon, Véronique; Oswald, Isabelle P.; Gidenne, T.; Rogel–Gaillard, Claire

doi:10.1186/s12864-015-1218-9

Cited by 23 publications

(17 citation statements)

References 71 publications

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“…We used rabbit-specific gene expression microarray ( Jacquier et al., 2015 ) to analyze the expression of approximately 13,000 genes in CKF-4, CKF-8, AKF-5, AKF-20, AKSL-4, AKSL-8, AKSL-20, AKSF-19, AKSF-26, AKSgff-3, and AKSgff-62 (Gene Ontology accession number GEO: GSE79195 ). Given the inherent instability of CKL cells, they were not included in the transcriptome analysis.…”

Section: Resultsmentioning

confidence: 99%

A Panel of Embryonic Stem Cell Lines Reveals the Variety and Dynamic of Pluripotent States in Rabbits

et al. 2016

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SummaryConventional rabbit embryonic stem cell (ESC) lines are derived from the inner cell mass (ICM) of pre-implantation embryos using methods and culture conditions that are established for primate ESCs. In this study, we explored the capacity of the rabbit ICM to give rise to ESC lines using conditions similar to those utilized to generate naive ESCs in mice. On single-cell dissociation and culture in fibroblast growth factor 2 (FGF2)-free, serum-supplemented medium, rabbit ICMs gave rise to ESC lines lacking the DNA-damage checkpoint in the G1 phase like mouse ESCs, and with a pluripotency gene expression profile closer to the rabbit ICM/epiblast profiles. These cell lines can be converted to FGF2-dependent ESCs after culture in conventional conditions. They can also colonize the rabbit pre-implantation embryo. These results indicate that rabbit epiblast cells can be coaxed toward different types of pluripotent stem cells and reveal the dynamics of pluripotent states in rabbit ESCs.

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Section: Resultsmentioning

confidence: 99%

A Panel of Embryonic Stem Cell Lines Reveals the Variety and Dynamic of Pluripotent States in Rabbits

et al. 2016

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“…Total blood RNA (200 ng) was retro-transcribed, Cy3-labeled, and hybridized onto customized single-channel 8X60K Agilent Technologies arrays (platform Agilent-037880/INRA Susscrofa 60K v1), which were enriched in genes linked to immunity and muscle physiology, following the manufacturer’s instructions and a protocol described in Jacquier et al (2015) [ 46 ]. Because genomic sequencing data were not available, it was not possible to take a possible effect of within cDNA target polymorphisms on hybridization levels into account.…”

Section: Methodsmentioning

confidence: 99%

Deciphering the genetic regulation of peripheral blood transcriptome in pigs through expression genome-wide association study and allele-specific expression analysis

et al. 2017

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BackgroundEfforts to improve sustainability in livestock production systems have focused on two objectives: investigating the genetic control of immune function as it pertains to robustness and disease resistance, and finding predictive markers for use in breeding programs. In this context, the peripheral blood transcriptome represents an important source of biological information about an individual’s health and immunological status, and has been proposed for use as an intermediate phenotype to measure immune capacity. The objective of this work was to study the genetic architecture of variation in gene expression in the blood of healthy young pigs using two approaches: an expression genome-wide association study (eGWAS) and allele-specific expression (ASE) analysis.ResultsThe blood transcriptomes of 60-day-old Large White pigs were analyzed by expression microarrays for eGWAS (242 animals) and by RNA-Seq for ASE analysis (38 animals). Using eGWAS, the expression levels of 1901 genes were found to be associated with expression quantitative trait loci (eQTLs). We recovered 2839 local and 1752 distant associations (Single Nucleotide Polymorphism or SNP located less or more than 1 Mb from expression probe, respectively). ASE analyses confirmed the extensive cis-regulation of gene transcription in blood, and revealed allelic imbalance in 2286 SNPs, which affected 763 genes. eQTLs and ASE-genes were widely distributed on all chromosomes. By analyzing mutually overlapping eGWAS results, we were able to describe putative regulatory networks, which were further refined using ASE data. At the functional level, genes with genetically controlled expression that were detected by eGWAS and/or ASE analyses were significantly enriched in biological processes related to RNA processing and immune function. Indeed, numerous distant and local regulatory relationships were detected within the major histocompatibility complex region on chromosome 7, revealing ASE for most class I and II genes.ConclusionsThis study represents, to the best of our knowledge, the first genome-wide map of the genetic control of gene expression in porcine peripheral blood. These results represent an interesting resource for the identification of genetic markers and blood biomarkers associated with variations in immunity traits in pigs, as well as any other complex traits for which blood is an appropriate surrogate tissue.Electronic supplementary materialThe online version of this article (10.1186/s12864-017-4354-6) contains supplementary material, which is available to authorized users.

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“…One pHu-sample was considered an outlier after the principal component analysis and was thus removed from the analysis. All of the steps of the RNA labelling and microarray processing were performed by the CRB GADIE facility (INRA, UMR GABI, Jouy-en-Josas, France, http://crbgadie.inra.fr/) as described in Jacquier et al 45 . The microarray data were submitted to the Gene Expression Omnibus (GEO) microarray database (accession number GSE89268).…”

Section: Microarray Data Production and Statistical Analysesmentioning

confidence: 99%

Muscle transcriptome analysis reveals molecular pathways and biomarkers involved in extreme ultimate pH and meat defect occurrence in chicken

Beauclercq¹,

Hennequet-Antier²,

Praud³

et al. 2017

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The processing ability and sensory quality of chicken breast meat are highly related to its ultimate pH (pHu), which is mainly determined by the amount of glycogen in the muscle at death. To unravel the molecular mechanisms underlying glycogen and meat pHu variations and to identify predictive biomarkers of these traits, a transcriptome profiling analysis was performed using an Agilent custom chicken 8×60K microarray. The breast muscle gene expression patterns were studied in two chicken lines experimentally selected for high (pHu+) and low (pHu-) pHu values of the breast meat. Across the 1,436 differentially expressed (DE) genes found between the two lines, many were involved in biological processes related to muscle development and remodelling and carbohydrate and energy metabolism. The functional analysis showed an intensive use of carbohydrate metabolism to produce energy in the pHu-line, while alternative catabolic pathways were solicited in the muscle of the pHu+ broilers, compromising their muscle development and integrity. After a validation step on a population of 278 broilers using microfluidic RT-qPCR, 20 genes were identified by partial least squares regression as good predictors of the pHu, opening new perspectives of screening broilers likely to present meat quality defects.peer-reviewed)

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Genome-wide immunity studies in the rabbit: transcriptome variations in peripheral blood mononuclear cells after in vitro stimulation by LPS or PMA-Ionomycin

Cited by 23 publications

References 71 publications

A Panel of Embryonic Stem Cell Lines Reveals the Variety and Dynamic of Pluripotent States in Rabbits

A Panel of Embryonic Stem Cell Lines Reveals the Variety and Dynamic of Pluripotent States in Rabbits

Deciphering the genetic regulation of peripheral blood transcriptome in pigs through expression genome-wide association study and allele-specific expression analysis

Muscle transcriptome analysis reveals molecular pathways and biomarkers involved in extreme ultimate pH and meat defect occurrence in chicken

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