Gene expression profiling of jejunal Peyer’s patches in juvenile and adult pigs

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

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.

Weaning Markedly Affects Transcriptome Profiles and Peyer's Patch Development in Piglet Ileum

Transcriptome analyses were conducted on the ileal mucosa of 14- to 35-day-old piglets to investigate postnatal gut development during suckling and postweaning. The transcriptome profiles of 14-day-old suckling piglets showed a considerably higher number of differentially expressed genes than did those of 21-, 28-, and 35-day olds, indicating an intensive gut development during the first 14–21 postnatal days. In addition, the analysis of biological pathways indicated that Chemotaxis Leucocyte chemotaxis was the most significantly affected pathway in suckling piglets between 14 and 21 days of age. Weaning negatively affected pathways associated with acquired immunity, but positively affected those associated with innate immunity. Interestingly, pathway Chemotaxis Leucocyte chemotaxis was found positively affected when comparing 14- and 21-day-old suckling piglets, but negatively affected in 28-day-old piglets weaned at 21 days of age, when compared with 28-day-old suckling piglets. Genes CXCL13, SLA-DOA (MHC class II), ICAM1, VAV1, and VCAM1 were involved in the pathway Chemotaxis Leukocyte chemotaxis and they were found to significantly change between 14- and 21-day-old suckling piglets and between groups of suckling and weaned piglets. The expression of these genes significantly declined after weaning at 14, 21, and 28 days of age. This decline indicated that CXCL13, SLA-DOA, ICAM1, VAV1, and VCAM1 may be involved in the development of Peyer’s patches (PP) because lower gene expression clearly corresponded with smaller areas of PP in the ileal mucosa of piglets. Moreover, weaning piglets prior to a period of intensive gut development, i.e., 14 days of age, caused significant adverse effects on the size of PP, which were not reverted even 14 days postweaning.

Extensive expression differences along porcine small intestine evidenced by transcriptome sequencing

The aim of this study was to analyse gene expression along the small intestine (duodenum, jejunum, ileum) and in the ileal Peyer's patches in four young pigs with no clinical signs of disease by transcriptome sequencing. Multidimensional scaling evidenced that samples clustered by tissue type rather than by individual, thus prefiguring a relevant scenario to draw tissue-specific gene expression profiles. Accordingly, 1,349 genes were found differentially expressed between duodenum and jejunum, and up to 3,455 genes between duodenum and ileum. Additionally, a considerable number of differentially expressed genes were found by comparing duodenum (7,027 genes), jejunum (6,122 genes), and ileum (6,991 genes) with ileal Peyer's patches tissue. Functional analyses revealed that most of the significant differentially expressed genes along small intestinal tissues were involved in the regulation of general biological processes such as cell development, signalling, growth and proliferation, death and survival or cell function and maintenance. These results suggest that the intrinsic large turnover of intestinal tissues would have local specificities at duodenum, ileum and jejunum. In addition, in concordance with their biological function, enteric innate immune pathways were overrepresented in ileal Peyer's patches. The reported data provide an expression map of the cell pathway variation in the different small intestinal tissues. Furthermore, expression levels measured in healthy individuals could help to understand changes in gene expression that occur in dysbiosis or pathological states.

Expression patterns of porcine Toll-like receptors family set of genes (TLR1-10) in gut-associated lymphoid tissues alter with age

The aim was to study the expression pattern of the porcine TLR family (TLR1-10) genes in gut-associated lymphoid tissues (GALT) of varying ages. A total of nine clinically healthy pigs of three ages group (1 day, 2 months and 5 months old) were selected for this experiment (three pigs in each group). Tissues from intestinal mucosa in stomach, duodenum, jejunum and ileum and mesenteric lymph node (MLN) were used. mRNA expression of TLRs (1-10) was detectable in all tissues and TLR3 showed the highest mRNA abundance among TLRs. TLR3 expression in stomach, and TLR1 and TLR6 expression in MLN were higher in adult than newborn pigs. The western blot results of TLR2, 3 and 9 in some cases, did not coincide with the mRNA expression results. The protein localization of TLR2, 3 and 9 showed that TLR expressing cells were abundant in the lamina propria, Peyer's patches in intestine, and around and within the lymphoid follicles in the MLN. This expressions study sheds the first light on the expression patterns of all TLR genes in GALT at different ages of pigs.

Differences in transcriptomic profile and IgA repertoire between jejunal and ileal Peyer's patches

In many species such as sheep and pig, there are two types of Peyer's patches (PP): several discrete patches in the jejunum and a long and continuous patch in the ileum. Most of the immunoglobulin A in the gut is generated by B-cells in the PP germinal centers. Moreover, swine like ovine ileal PP might be important for antigen independent B-cell repertoire diversification. We examined, by quantitative real-time PCR, the expression of 36 transcripts of antimicrobial peptides, chemokines, interleukines, Toll-like receptors and transcription factors from both PP and we highlighted the differences by a principal component analysis. Ileal PP was characterized by a higher mRNA expression of CCL28, IL5, IL10, TLR2 and TLR4 while jejunal PP showed higher mRNA expression of antimicrobial peptides, CCL25, FOXP3, IL4, T-Bet, TSLP and SOCS2. Then, we analyzed some VDJ rearrangements to assess immunoglobulin repertoire diversity in jejunal and ileal PP from weaned piglets. The IgA and IgM repertoires were more diverse in ileal than in jejunal piglet PP. All these results could be related to the rarefaction of interfollicular T-cell zone and the presence in ileal versus jejunal lumen of a more diversified microflora. These findings shed a light on the functional differences between both PP.

Effects of Lactobacillus plant arum on genes expression pattern in mice jejunal Peyer's patches

Jejunal Peyer's patches contain specialized epithelial M cells that take up ingested microorganisms from the lumen of the gut by transcytosis. Using DNA-micro array, we analyzed the gene expression patterns of jejunal Peyer's patches in order to gain insight into the molecular mechanism by which Lp6 interacted with the host organism in a gnotobiotic environment v. in the gut normal microflora. The micro array data revealed that, among approximately 14,000 genes, 420 were expressed in Lp6 administration group at twofold or higher levels compared to the control group. These included genes involved in immune response, and cell differentiation, cell-cell signaling, cell adhesion, signal transcription, and transduction. Real-time PCR confirmed the reliability of the analysis. These data indicated that administration of Lactobacillus Lp6 was associated with a complex genetic response in the jejunal Peyer's patches.

The mucosal immune system: recent developments and future directions in the pig

In most animals, the mucosal immune system effectively controls expression of active immune responses to pathogen and tolerance to harmless antigens. Our understanding of the function and control of the mucosal immune system has advanced as a result of studies in rodents and humans. The discoveries of regulatory T-cells and T-helper-17 cells, and studies on the interactions between epithelial and dendritic cells, demonstrate its complexity. In pigs, some of the systems and reagents for determining the relevance of these mechanisms are present, and indicate lines for future work. However, many empirical studies of the effect of manipulation of the mucosal immune system in the pig by prebiotics, probiotics and feed additives have been carried out. Interpretation of these results needs to be made with care, since manipulation of the mucosal immune system may improve its efficiency under a specific set of environmental and husbandry conditions, but impair it under others.

A pig multi-tissue normalised cDNA library: large-scale sequencing, cluster analysis and 9K micro-array resource generation

Background

Domestic animal breeding and product quality improvement require the control of reproduction, nutrition, health and welfare in these animals. It is thus necessary to improve our knowledge of the major physiological functions and their interactions. This would be greatly enhanced by the availability of expressed gene sequences in the databases and by cDNA arrays allowing the transcriptome analysis of any function.

The objective within the AGENAE French program was to initiate a high-throughput cDNA sequencing program of a 38-tissue normalised library and generate a diverse microarray for transcriptome analysis in pig species.

Results

We constructed a multi-tissue cDNA library, which was normalised and subtracted to reduce the redundancy of the clones. Expressed Sequence Tags were produced and 24449 high-quality sequences were released in EMBL database. The assembly of all the public ESTs (available through SIGENAE website) resulted in 40786 contigs and 54653 singletons. At least one Agenae sequence is present in 11969 contigs (12.5%) and in 9291 of the deeper-than-one-contigs (22.8%). Sequence analysis showed that both normalisation and subtraction processes were successful and that the initial tissue complexity was maintained in the final libraries. A 9K nylon cDNA microarray was produced and is available through CRB-GADIE. It will allow high sensitivity transcriptome analyses in pigs.

Conclusion

In the present work, a pig multi-tissue cDNA library was constructed and a 9K cDNA microarray designed. It contributes to the Expressed Sequence Tags pig data, and offers a valuable tool for transcriptome analysis.

Development of a microarray for studying porcine cytokine production in blood mononuclear cells and intestinal biopsies

A microarray for demonstration of a limited number of porcine cytokines was initiated. Polymerase chain reaction (PCR) products were synthesized for four house-keeping genes, cyclophilin, beta-actin, hypoxanthine phosphoribosyltransferase (HPRT) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH), and the following cytokines: interleukin (IL)-1beta, IL-4, IL-6, IL-8, IL-10, IL-12 p35, IL-12 p40, IL-18, interferon (IFN)-alpha, IFN-beta, IFN-gamma, tumour necrosis factor (TNF)-alpha, macrophage inhibition factor (MIF) and granulocyte/macrophage colony-stimulating factor (GM-CSF). Cytokine production was induced by incubation of porcine peripheral blood mononuclear cells (PBMC) with Concanavalin A (ConA) or oligodeoxynucleotide (ODN) 2216. RNA was isolated after 6 or 24 h from stimulated cells or unstimulated control cells and from intestinal biopsies. Cytokine expression was analysed using a 3-DNA Array 350(TM) labelling kit from Genisphere. Data were normalized using external control genes and analysed with the genepix pro 5.0 software. All the cytokines could be induced in PBMC and expressed on the array and the cytokines IL-6 and IFN-alpha were also analysed at protein level. All but one cytokine were expressed in samples from intestinal biopsies. Densitometric analyses of PCR products of the house-keeping genes were performed to validate the results from the microarray. Thus, this microarray will enable analyses of the cytokine profile during local and systemic infections in the pig.

Advances in swine transcriptomics

The past five years have seen a tremendous rise in porcine transcriptomic data. Available porcine Expressed Sequence Tags (ESTs) have expanded greatly, with over 623,000 ESTs deposited in Genbank. ESTs have been used to expand the pig-human comparative maps, but such data has also been used in many ways to understand pig gene expression. Several methods have been used to identify genes differentially expressed (DE) in specific tissues or cell types under different treatments. These include open screening methods such as suppression subtractive hybridization, differential display, serial analysis of gene expression, and EST sequence frequency, as well as closed methods that measure expression of a defined set of sequences such as hybridization to membrane arrays and microarrays. The use of microarrays to begin large-scale transcriptome analysis has been recently reported, using either specialized or broad-coverage arrays. This review covers published results using the above techniques in the pig, as well as unpublished data provided by the research community, and reports on unpublished Affymetrix data from our group. Published and unpublished bioinformatics efforts are discussed, including recent work by our group to integrate two broad-coverage microarray platforms. We conclude by predicting experiments that will become possible with new anticipated tools and data, including the porcine genome sequence. We emphasize that the need for bioinformatics infrastructure to efficiently store and analyze the expanding amounts of gene expression data is critical, and that this deficit has emerged as a limiting factor for acceleration of genomic understanding in the pig.

Genomic dissection of mucosal immunobiology in the porcine small intestine

The enteric immune system of swine protects against infectious and noninfectious environmental insults and discriminates ingested nutrients, food, and commensal microflora from pathogenic agents. The molecular and cellular elements of the immune system have been selected over evolutionary time in response to the specific environment of pigs. Thus, models of immune function based on mouse and human need to be applied cautiously in the pig. To better understand how the mucosal immune system of the small intestine accomplishes the conflicting functions of food tolerance and immunity to enteric infection, we used a genomic approach to profile gene expression in the Peyer's patch. More than 40% of mRNA enriched by differential subtraction for Peyer's patch-specific expressed sequences represented genes of unknown function or had no match in GenBank. Microarray analysis and radiation hybrid mapping validated their porcine origin and provided additional insights into putative functions. The abundance of expressed genes of unknown function indicates that a substantial fraction of the immunological and physiological processes of the Peyer's patch remains to be discovered. It further suggests that swine have evolved specialized biochemical and immunological processes in the small intestine. Further elucidation of these processes are expected to provide novel insights into swine enteric mucosal immune function.