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Identification of differential duodenal gene expression levels correlated with differences in energy utilization in chickens

ABSTRACT: The amount of energy that can be extracted from a diet varies between individuals. Apparent Metabolizable Energy (AME) is a measure of energy utilization efficiency and represents the difference between the energy consumed and the energy lost via the excreta. There are significant differences in the energy utilization capability of individual birds that have a similar genetic background and are raised under identical conditions. We analyzed duodenal gene expression and microbiota differences between birds with different efficiencies in food to energy conversion using microarrays and sequencing of 16s rRNA genes. Differences were found in duodenal gene expression between high and low AME birds, they were however mostly related to genes of unknown function.

ORGANISM(S): Gallus gallus

PROVIDER: GSE47213 | GEO | 2013/06/01

SECONDARY ACCESSION(S): PRJNA205148

REPOSITORIES: GEO

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Identification of differential duodenal gene expression levels correlated with differences in energy utilization in chickens

Project description:The amount of energy that can be extracted from a diet varies between individuals. Apparent Metabolizable Energy (AME) is a measure of energy utilization efficiency and represents the difference between the energy consumed and the energy lost via the excreta. There are significant differences in the energy utilization capability of individual birds that have a similar genetic background and are raised under identical conditions. We analyzed duodenal gene expression and microbiota differences between birds with different efficiencies in food to energy conversion using microarrays and sequencing of 16s rRNA genes. Differences were found in duodenal gene expression between high and low AME birds, they were however mostly related to genes of unknown function. The flock of 96 chickens was used to study ability of the bird to utilise the energy from feed. We measured energy content in feed and in excreta of individually housed birds. The microarrays were used to compare expression between the best and worst energy utilisers.

2013-06-01 | E-GEOD-47213 | biostudies-arrayexpress

Duodenal adenoma/adenocarcinomas vs matched normal mucosa

Project description:Background: Duodenal adenoma/adenocarcinomas are rare, and the global gene expression changes associated with the initial stages of carcinogenesis of these neoplasms have not been elucidated. Results: To comprehensively analyze genetic markers and pathways specific to early-stage duodenal adenoma/adenocarcinomas, transcriptional profiles of 4 fresh-frozen non-ampullary duodenal adenoma/adenocarcinomas and surrounding duodenal normal mucosa were compared. Key features of gene expression analysis demonstrated a strong correlation between these tumors and colorectal adenomas, as well as the Wnt/β-catenin pathway. These results shed new light on the transcriptional changes that occur during the early stages of duodenal tumorigenesis. All samples were obtained prior to treatment in order to minimize effects of cauterization, and immediately fresh-frozen.

2018-08-06 | GSE102208 | GEO

Gallus gallus

Project description:Identification of differential duodenal gene expression levels correlated with differences in energy utilization in chickens

| PRJNA205148 | ENA

Chicken family BC1 1940: transcriptome profiling used for QTL/eQTL detection

Project description:The family concerns 46 offspring of the sire BC1 n°1940 (produced from an F1 male obtained by-intercrossing two fat (FL) and lean (LL) meat-type chicken lines that divergently selected on fatness [Leclercq et al. 1980]) mated with 8 LL females. Hepatic transcriptomic profiles were obtained using the chicken 20K oligochip (ARK-genomics). The 46 chickens were fed ad libitum using a conventional starter diet (0-3 weeks: 12.8 MJ of metabolizable energy) and then a growing broiler diet (4-9 weeks: 13.0 Mj of metabolizable energy). Light/dark periods were 24h light for the first 2 days, then 14h light/10h night up to slaughtering. At 4 weeks of age, blood samples were collected for DNA extraction and genotyping. At 9 weeks of age, the birds were fed ad libitum for 4 hours minimum after overnight fasting and then weighed and sacrificed by electrical stunning in the experimental processing plant (Station de Recherches Avicoles, Inra, Nouzilly, France). Following sacrifice, livers were collected, quickly frozen in liquid nitrogen and stored at −80°C until RNA extraction for transcriptome analyses.

2008-09-20 | GSE12319 | GEO

Chicken family BC1 1998: transcriptome profiling used for QTL/eQTL detection

Project description:The family concerns 44 offspring of the sire BC1 n°1998 (produced from a F1 male obtained by-intercrossing two fat (FL) and lean (LL) meat-type chicken lines that divergently selected on fatness [Leclercq et al 1980] mated with 8 LL females. Hepatic transcriptomic profiles were obtained using a chicken 20K oligochips (ARK-genomics). The 44 chickens were fed ad libitum using a conventional starter diet (0-3 weeks: 12.8 MJ of metabolizable energy) and then a growing broiler diet (4-9 weeks: 13.0 Mj of metabolizable energy). Light/dark periods were 24h light for the first 2 days, then 14h light/10h night up to slaughtering. At 4 weeks of age, blood samples were collected for DNA extraction and genotyping. At 9 weeks of age, the birds were fed ad libitum for 4 hours minimum after overnight fasting and then weighed and sacrificed by electrical stunning in the experimental processing plant (Station de Recherches Avicoles, Inra, Nouzilly, France). Following sacrifice, livers were collected, quickly frozen in liquid nitrogen and stored at −80°C until RNA extraction for transcriptome analyses

2014-12-22 | GSE16781 | GEO

Mouse duodenal enteroendocrine transcriptome

Project description:Mouse duodenal enteroendocrine transcriptome

| PRJNA473085 | ENA

PIGA mutation and glycosylphosphatidylinositol anchor dysregulation in polyposis-associated duodenal tumorigenesis

Project description:Progression of duodenal polyposis into cancer is an important cause of morbidity and mortality in the inherited tumour syndromes Familial Adenomatous Polyposis (FAP) and MUTYH-associated Polyposis (MAP), yet this process remains poorly understood. This study aimed to identify genes that are mutated in FAP and MAP duodenal adenomas and to characterise the cellular consequences for duodenal tumorigenesis.

2023-08-07 | GSE189035 | GEO

Duodenal inflammation in Common variable immunodeficiency has altered transcriptional response to viruses

Project description:To elucidate the role of duodenal microenvironment in Common variable immunodeficiency pathogenesis (CVID), we sought to explore the transcriptome regulation in duodenal biopsies.

2022-11-03 | GSE207243 | GEO

Mouse duodenal enteroendocrine transcriptome

Project description:Using genetically modifed mice to express fluorescent reporter in proglucagon expressing cells (GluVenus) or in all enteroendocrine cells (NeuroD1), we purifed positive and negative cells by FACS from duodenal epithelial cells and identified transcripts enriched in positive populations

2018-12-31 | GSE114913 | GEO

Single-cell analysis of CD45+ cells from duodenal RCDII tissue

Project description:Refractory Celiac Disease type II (RCDII) is a rare lymphoma in the small intestine characterized by a clonally expanded intra-epithelial iCD3+sCD3-CD7+CD56- aberrant cell population. However, RCDII pathogenesis is ill-defined. Here, we aimed at single-cell characterization of the innate and adaptive immune system in RCDII. Paired small intestinal and blood samples from 12 RCDII patients and 6 healthy controls were assessed by single-cell mass cytometry with a 39 cell surface marker antibody panel, designed to capture heterogeneity of the innate and adaptive immune system. A second single-cell mass cytometry panel which included transcription factors and immune checkpoints was used for analysis of paired samples from 5 RCDII patients. Single-cell RNA sequencing analysis was performed on duodenal samples from 2 RCDII patients. Finally, we developed a 40-marker imaging mass cytometry antibody panel to evaluate cell-cell interactions in duodenal biopsies of RCDII patients. We provide evidence for inter- and intra-tumoral cell heterogeneity within the duodenal and peripheral aberrant cell population present in RCDII. We observed that part of the aberrant cell population proliferated and observed co-localization of aberrant cells with CD163+ APCs in situ. Additionally, we observed phenotypic discrepancy between peripheral and duodenal aberrant cells. Novel high-dimensional technologies reveal substantial inter- and intra-tumoral heterogeneity in the aberrant cell population in RCDII. This may underlie variability in refractory disease status between patients and responsiveness to therapy, pointing to the need for personalized therapy in RCDII based on patient-specific immune profiles.

2022-04-30 | GSE195780 | GEO

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