Immunome differences between porcine ileal and jejunal Peyer\u2019s patches revealed by global transcriptome sequencing of gut-associated lymphoid tissues

T Maroilley,J L Coville,M J Mercat,J J Leplat,C Rogel-Gaillard,F Meurens,S Mélo,G Lemonnier,C Chevaleyre,B Bed’Hom,J Estellé,S Vincent-Naulleau,Y Billon,M Berri,A Rau,P Lepage,D Esquerré

doi:10.1038/s41598-018-27019-7

Abstract

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 FOXP3, GATA3, STAT4, TBX21 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.

Highlights

The digestive tract provides nutrients and energy from food to the organism, and it is a major potential entry site for pathogens
Swine Peyer’s patches (PPs) are an exception to this rule because, as in ruminants and rabbits, they have the particularity of forming a continuous structure in the ileum, while in humans they constitute independent follicles in all intestinal segments as in the pig jejunum[31,30,32]
We report here a comparative analysis of the transcriptomic profiles of gut-associated lymphoid tissues (GALT) in pigs including ileal PPs (IPPs), jejunal PPs (JPPs) and mesenteric lymph nodes (MLNs), and peripheral blood (PB) as non-GALT reference immune tissue

Summary

Introduction

The digestive tract provides nutrients and energy from food to the organism, and it is a major potential entry site for pathogens. MLNs are induction sites of immune responses, as they initiate peptide presentation to lymphocytes by antigen presenting cells arriving from the intestine[2]. In a targeted gene expression approach, Levast et al.[10] showed differential expression of 29 immune genes between IPPs and JPPs and observed a more diverse IgA repertoire in IPPs. Gourbeyre et al.[11] focused on pattern recognition receptors involved in innate immunity and observed differential expression for TLR2, 6, 7, 9, 10 and NLRP3 between IPPs and JPPs. The existing published results strongly suggest shared but subtle differences between the functionalities of IPPs and JPPs. The existing published results strongly suggest shared but subtle differences between the functionalities of IPPs and JPPs To further explore this question, we are presenting in this work a study focusing on transcriptome profiles in pigs with no clinical signs of infection, by stranded RNA-sequencing of IPPs, JPPs, MLNs and peripheral blood as a complementary non-GALT immune tissue. We report the differential gene expression between PPs and MLNs, and between IPPs and JPPs, together with the analysis of antisense transcription and allele-specific expression (ASE) in the four tissues

Methods

Results

Conclusion