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Immunome differences between porcine ileal and jejunal Peyer’s patches revealed by global transcriptome sequencing of gut-associated lymphoid tissues

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T. Maroilley et al., Scientific Reports, 2018, volume 8, n° 1, 13 juin, 12 pages

The epithelium of the intestinal mucosa and the gut-associated lymphoid tissues (GALT) constitute an essential physical and immunological barrier against pathogens. In order to study the specificities of the GALT transcriptome in pigs, we compared the transcriptome profiles of jejunal and ileal Peyer’s patches (PPs), mesenteric lymph nodes (MLNs) and peripheral blood (PB) of four male piglets by RNA-Seq. We identified 1,103 differentially expressed (DE) genes between ileal PPs (IPPs) and jejunal PPs (JPPs), and six times more DE genes between PPs and MLNs. The master regulator genes FOXP3GATA3STAT4TBX21 and RORC were less expressed in IPPs compared to JPPs, whereas the transcription factor BCL6 was found more expressed in IPPs. In comparison between IPPs and JPPs, our analyses revealed predominant differential expression related to the differentiation of T cells into Th1, Th2, Th17 and iTreg in JPPs. Our results were consistent with previous reports regarding a higher T/B cells ratio in JPPs compared to IPPs. We found antisense transcription for respectively 24%, 22% and 14% of the transcripts detected in MLNs, PPs and PB, and significant positive correlations between PB and GALT transcriptomes. Allele-specific expression analyses revealed both shared and tissue-specific cis-genetic control of gene expression.

2018

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

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T. Maroilley et al., BMC Genomics, 2017, 13 décembre, volume 18, n° 1, 13 décembre,19 pages

Abstract

BACKGROUND:

Efforts 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.

RESULTS:

The 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.

CONCLUSIONS:

This 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.

2017

Exploring transcriptomic diversity in muscle revealed that cellular signaling pathways mainly differentiate five Western porcine breeds

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Background

Among transcriptomic studies, those comparing species or populations can increase our understanding of the impact of the evolutionary forces on the differentiation of populations. A particular situation is the one of short evolution time with breeds of a domesticated species that underwent strong selective pressures. In this study, the gene expression diversity across five pig breeds has been explored in muscle. Samples came from: 24 Duroc, 33 Landrace, 41 Large White dam line, 10 Large White sire line and 39 Piétrain. From these animals, 147 muscle samples obtained at slaughter were analyzed using the porcine Agilent 44 K v1 microarray.

Results

A total of 12,358 genes were identified as expressed in muscle after normalization and 1,703 genes were declared differential for at least one breed (FDR < 0.001). The functional analysis highlighted that gene expression diversity is mainly linked to cellular signaling pathways such as the PI3K (phosphoinositide 3-kinase) pathway. The PI3K pathway is known to be involved in the control of development of the skeletal muscle mass by affecting extracellular matrix - receptor interactions, regulation of actin cytoskeleton pathways and some metabolic functions. This study also highlighted 228 spots (171 unique genes) that differentiate the breeds from each other. A common subgroup of 15 genes selected by three statistical methods was able to differentiate Duroc, Large White and Piétrain breeds.

Conclusions

This study on transcriptomic differentiation across Western pig breeds highlighted a global picture: mainly signaling pathways were affected. This result is consistent with the selection objective of increasing muscle mass. These transcriptional changes may indicate selection pressure or simply breed differences which may be driven by human selection. Further work aiming at comparing genetic and transcriptomic diversities would further increase our understanding of the consequences of human impact on livestock species.

2015

Deciphering the genetic control of innate and adaptive immune responses in pig: a combined genetic and genomic study

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Improving animal robustness and resistance to pathogens by adding health criteria in selection schemes is one of the challenging objectives of the next decade. In order to better understand the genetic control of immunity in French Large White pigs, we have launched a program combining genetic and genomic studies not focussing on any particular pathogen.
PDF icon Deciphering the genetic control of innate and adaptive immune responses in pig: a combined genetic and genomic study
2011

Décryptage du contrôle génétique des réponses immunitaires innées et adaptatives chez le porc Large White : une étude combinant des approches génétiques et fonctionnelles

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Un programme d'analyse fine du contrôle génétique de la réponse immunitaire (RI) combinant des approches génétiques et fonctionnelles a été développé. Plus de 400 animaux de race Large White mesurés pour des caractères de production ont été caractérisés pour un large éventail de paramètres de l'immunité trois semaines après vaccination contre Mycoplasma hyopneumoniae.
PDF icon Décryptage du contrôle génétique des réponses immunitaires innées et adaptatives chez le porc Large White : une étude combinant des approches génétiques et fonctionnelles
2011

Deciphering the genetic control of innate and adaptive immune responses in pig: a combined genetic and genomic study

Consulter le resumé

Improving animal robustness and resistance to pathogens by adding health criteria in selection schemes is one of the challenging objectives of the next decade. In order to better understand the genetic control of immunity in French Large White pigs, we have launched a program combining genetic and genomic studies not focussing on any particular pathogen.
2010

A genetic and functional analysis of innate and adaptive immunity in pigs

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PDF icon A genetic and functional analysis of innate and adaptive immunity in pigs
2010

Transcriptome épididymaire et testiculaire chez le verrat - Approche génomique et protéomique des mécanismes intervenant dans le contrôle de la fertilité du gamète mâle

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La qualité des spermatozoïdes (mobilité et les différentes étapes de reconnaissance ovocytaire) est liée à leur différenciation post-testiculaire lors de leur transit dans l’épididyme. La connaissance de la génomique fonctionnelle de cet organe et l'identification des facteurs contrôlant son activité sont primordiales pour comprendre les mécanismes d’acquisition de la fécondance des gamètes mâles.
PDF icon Transcriptome épididymaire et testiculaire chez le verrat - Approche génomique et protéomique des mécanismes intervenant dans le contrôle de la fertilité du gamète mâle
2009

Etude de la réponse immunitaire des porcs français de race Large White et analyse conjointe du transcriptome des leucocytes du sang périphérique

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Depuis plus de 25 ans maintenant, un programme de sélection génétique ciblant des caractères de production a été poursuivi en France dans l’espèce porcine. Associé à l’application de mesures sanitaires et médicales strictes, il a permis une nette amélioration des performances zootechniques des animaux. Cependant, la législation européenne, de plus en plus préoccupée par le bien-être animal et la sécurité du consommateur, a récemment interdit l’utilisation d’antibiotiques comme facteurs régulateurs de croissance et tend à réduire de manière générale les mesures prophylactiques médicamenteuses.
PDF icon Etude de la réponse immunitaire des porcs français de race Large White et analyse conjointe du transcriptome des leucocytes du sang périphérique
2009

Transcriptome épididymaire et testiculaire chez le verrat.<br /><br />The adult boar testicular and epididymal transcriptomes.

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Background
2009

Etude de la réponse immunitaire des porcs français de race Large White et analyse conjointe du transcriptome des leucocytes du sang périphérique

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L’espèce porcine a bénéficié depuis 20 ans d’un programme de sélection génétique qui a ciblé des caractères de production et cette sélection, accompagnée du respect de règles sanitaires strictes incluant vaccination et antibiothérapie préventive, a permis une nette amélioration des performances zootechniques. Or, dans une perspective de respect accru du bien-être animal et de la sécurité du consommateur, les normes européennes visent une réduction des mesures prophylactiques médicamenteuses.
PDF icon Etude de la réponse immunitaire des porcs français de race Large White et analyse conjointe du transcriptome des leucocytes du sang périphérique
2008

Transcriptome épididymaire et testiculaire chez le verrat. <br /><br />The adult boar testicular and epididymal transcriptome.

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Our laboratory has established the cartography of secreted proteins(secretomes) and proteins present (proteomes) in the epididymalfluid of different mammals and has demonstrated their regionalvariations along the epididymis. To extend the understanding of epididymal function in large mammals, we undertook a transcriptomic study of differentially expressed genes along the boar epididymis using the testis as organ of comparison. Our analysis focusedon genes considered to be markers of a single organ or a transcriptomic region and over-expressed mainly in this organ or region.
PDF icon Transcriptome épididymaire et testiculaire chez le verrat. <br /><br />The adult boar testicular and epididymal transcriptome.
2008

Transcriptome épididymaire et testiculaire chez le verrat.<br /><br />The adult boar testicular and epididymal transcriptome.

Consulter le resumé

Our laboratory has established the cartography of secreted proteins(secretomes) and proteins present (proteomes) in the epididymalfluid of different mammals and has demonstrated their regionalvariations along the epididymis. To extend the understandingof epididymal function in large mammals, we undertook a transcriptomicstudy of differentially expressed genes along the boar epididymisusing the testis as organ of comparison. Our analysis focusedon genes considered to be markers of a single organ or a transcriptomicregion and over-expressed mainly in this organ or region.
2008

Le transcriptome épididymaire du verrat: étude de la régionalisation

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Chez les mammifères, les spermatozoïdes acquièrent leur pouvoir fécondant au cours du passage dans l’épididyme, organe constitué d'un tube pelotonné et relié au testicule par le canal efférent. L'épididyme est divisé en 3 régions morphologiques (tête, corps, queue) subdivisées en 10 zones.
PDF icon Le transcriptome épididymaire du verrat: étude de la régionalisation
2008

Recherche et identification des gènes différentiellement exprimés dans l'épididyme de verrat par une approche transcriptomique

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Chez les Mammifères, la production de spermatozoïdes fécondants fait intervenir deux organes : le testicule et l’épididyme.

Le testicule est le lieu de production et a donc un rôle sur la quantité de gamètes produits. À la sortie du

testicule, les spermatozoïdes bien que morphologiquement formés sont immobiles et incapables de féconder un ovocyte. C’est au cours de leur transit dans l’épididyme, tube pelotonné d’environ 70 m de long chez le verrat, que les spermatozoïdes vont acquérir leur mobilité et leur pouvoir fécondant.
PDF icon Recherche et identification des gènes différentiellement exprimés dans l'épididyme de verrat par une approche transcriptomique
2007