Exploring Differential Transcriptome between Jejunal and Cecal Tissue of Broiler Chickens.

Micol Bertocchi,Federico Sirri,Paolo Trevisi,Diana Luise,Giuseppe Maiorano,Orazio Palumbo,Paolo Bosi

doi:10.3390/ani9050221

Abstract

Simple SummaryIntestinal main functions and different gut tract peculiarities in poultry are known. However, a wider view at the molecular level in terms of functional genes may contribute to deepening knowledge on less considered biological aspects, with possible differentiation in gene expression and functionality between gut tracts. This experiment aimed to extend the exploration of chicken gut functional aspects by scouting differential gene expression in the jejunum and cecum, which may help in the detection of new interesting functions from a biological point of view. The work identified key aspects linked to gut biological processes that may be worthy of further investigations in experimental studies considering factors which may specifically address peculiarities of the different chicken gut tracts at the molecular level.The study proposed an exploratory functional analysis on differential gene expression of the jejunum and of cecum in chickens. For this study, 150 Ross 308 male chickens were randomly allotted in six pens (25 birds/pen) and fed the same commercial diet. From 19 birds of 42 days of age, jejunum and cecum mucosae were collected for RNA extraction for transcriptome microarray analysis. Differentially expressed genes (DEGs) submitted to DAVID (Database for Annotation, Visualization, and Integrated Discovery) and Gene Set Enrichment Analysis (GSEA) software evidenced enriched gene clusters for biological functions differentiated in the tissues. DAVID analysis in the jejunum showed enriched annotations for cell membrane integral components, PPAR (peroxisome proliferator-activated receptor) signaling pathway, and peroxisome and lipid metabolism, and showed DEGs for gluconeogenesis, not previously reported in chicken jejunum. The cecum showed enriched annotations for disulfide bond category, cysteine and methionine metabolism, glycoprotein category, cell cycle, and extracellular matrix (ECM). GSEA analysis in the jejunum showed peroxisome and PPAR signaling pathway-related gene sets, as found with DAVID, and gene sets for immune regulation, tryptophan and histidine metabolism, and renin–angiotensin system, like in mammals. The cecum showed cell cycle and regulation processes, as well as ECM receptor interaction and focal adhesion-related gene sets. Typical intestinal functions specific for the gut site and interesting functional genes groups emerged, revealing tissue-related key aspects which future studies might take advantage of.

Highlights

Primary functional specificities of the small and large intestine, which are important for the proper activities of the gut, are considered well known and were explored for several decades
671 and 681 differentially expressed transcripts (DETs) were found in the jejunum and cecum; of them, 524 and 608 were defined as Differentially expressed genes (DEGs)
The lists of the first 20 DETs in the jejunum and cecum, ranked by fold change ratio (FCR), are presented in Tables 1 and 2, respectively, while the full lists for DETs are reported in Tables S2 and S3

Summary

Introduction

Primary functional specificities of the small and large intestine, which are important for the proper activities of the gut, are considered well known and were explored for several decades. A more in-depth exploration of gut functional aspects may be interesting in order to provide hints for action (e.g., dietary strategies) to favor gut homeostasis [3], given the important role of the intestine in the development of possible metabolic diseases. The gene expression in different tissues is currently collected by some portals developed by medical projects, such as GTEX (gtexportal.org, The Broad Institute of MIT and Harvard, Cambridge, MA, USA) or BioGPS (biogps.org, The Scripps Research Institute, La Jolla, CA, USA); differential gene expression between different gut tracts was explored and discussed in mice (from the stomach to the colon [4]) and in pigs (among different gastric mucosae [5], and along the small intestine [6]), while a lack of such a survey was detected in chickens. While in other species the cecum is not considered a key intestinal tract, in chicken, it has a key role for the digesta fermentation, and further information on its molecular functionality may be important

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