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Transcriptional Profiling of Ileocecal Valve of Holstein Dairy Cows Infected with Mycobacterium avium subsp. Paratuberculosis.

Hempel RJ, Bannantine JP, Stabel JR - PLoS ONE (2016)

Bottom Line: The ICV is known to be a primary site of MAP colonization and provides an ideal location to identify genes that are relevant to the progression of this disease.Interpretation of the gene expression data was performed using pathway analysis and gene ontology categories containing multiple differentially expressed genes.The results from the comparison between clinical and subclinical animals indicate recruitment of neutrophils, up regulation of lysosomal peptidases, increase in immune cell transendothelial migration, and modifications of the extracelluar matrix.

View Article: PubMed Central - PubMed

Affiliation: USDA-Agricultural Research Service (ARS), National Animal Disease Center, Ames, Iowa, United States of America.

ABSTRACT
Johne's disease is a chronic infection of the small intestine caused by Mycobacterium avium subspecies paratuberculosis (MAP), an intracellular bacterium. The events of pathogen survival within the host cell(s), chronic inflammation and the progression from asymptomatic subclinical stage to an advanced clinical stage of infection, are poorly understood. This study examines gene expression in the ileocecal valve (ICV) of Holstein dairy cows at different stages of MAP infection. The ICV is known to be a primary site of MAP colonization and provides an ideal location to identify genes that are relevant to the progression of this disease. RNA was prepared from ICV tissues and RNA-Seq was used to compare gene transcription between clinical, subclinical, and uninfected control animals. Interpretation of the gene expression data was performed using pathway analysis and gene ontology categories containing multiple differentially expressed genes. Results demonstrated that many of the pathways that had strong differential gene expression between uninfected control and clinical cows were related to the immune system, such as the T- and B-cell receptor signaling, apoptosis, NOD-like receptor signaling, and leukocyte transendothelial migration pathways. In contrast, the comparison of gene transcription between control and subclinical cows identified pathways that were primarily involved in metabolism. The results from the comparison between clinical and subclinical animals indicate recruitment of neutrophils, up regulation of lysosomal peptidases, increase in immune cell transendothelial migration, and modifications of the extracelluar matrix. This study provides important insight into how cattle respond to a natural MAP infection at the gene transcription level within a key target tissue for infection.

No MeSH data available.


Related in: MedlinePlus

Multidimensional scaling plots of samples from uninfected control, subclinical, and clinical animals based on RNA-seq data.Distance 1 and distance 2 separate all samples based on the expression values of all 12,133 genes that passed filtering criteria prior to differential gene expression analysis. A) Comparison of all 15 samples. B) Comparison of 14 samples after the removal of uninfected control animal 5 (Cow #8102).
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pone.0153932.g002: Multidimensional scaling plots of samples from uninfected control, subclinical, and clinical animals based on RNA-seq data.Distance 1 and distance 2 separate all samples based on the expression values of all 12,133 genes that passed filtering criteria prior to differential gene expression analysis. A) Comparison of all 15 samples. B) Comparison of 14 samples after the removal of uninfected control animal 5 (Cow #8102).

Mentions: HT-Seq, a program designed to process high-throughput sequencing data, was used to quantify the reads that aligned to the bovine Ensembl gene IDs. The genes were further filtered to remove genes that didn’t have at least 1 read per million mapped in seven or more animals, which yielded 12,132 genes used in downstream analyses. Prior to differential gene expression analysis using EdgeR, the normalized count data were used to generate a multidimensional scaling (MDS) plot to observe sample clustering and to identify outliers (Fig 2). One cow in the uninfected control group (#8102) did not cluster closely with any group and was removed in downstream analyses (Fig 2A). Outliers were expected since these cows were not age matched and were acquired from farms outside of our facility, where the cows were naturally infected with MAP. However, despite all the animals coming from different outside sources at different stages of disease, the samples differentiated according to their disease status (Fig 2B).


Transcriptional Profiling of Ileocecal Valve of Holstein Dairy Cows Infected with Mycobacterium avium subsp. Paratuberculosis.

Hempel RJ, Bannantine JP, Stabel JR - PLoS ONE (2016)

Multidimensional scaling plots of samples from uninfected control, subclinical, and clinical animals based on RNA-seq data.Distance 1 and distance 2 separate all samples based on the expression values of all 12,133 genes that passed filtering criteria prior to differential gene expression analysis. A) Comparison of all 15 samples. B) Comparison of 14 samples after the removal of uninfected control animal 5 (Cow #8102).
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4836751&req=5

pone.0153932.g002: Multidimensional scaling plots of samples from uninfected control, subclinical, and clinical animals based on RNA-seq data.Distance 1 and distance 2 separate all samples based on the expression values of all 12,133 genes that passed filtering criteria prior to differential gene expression analysis. A) Comparison of all 15 samples. B) Comparison of 14 samples after the removal of uninfected control animal 5 (Cow #8102).
Mentions: HT-Seq, a program designed to process high-throughput sequencing data, was used to quantify the reads that aligned to the bovine Ensembl gene IDs. The genes were further filtered to remove genes that didn’t have at least 1 read per million mapped in seven or more animals, which yielded 12,132 genes used in downstream analyses. Prior to differential gene expression analysis using EdgeR, the normalized count data were used to generate a multidimensional scaling (MDS) plot to observe sample clustering and to identify outliers (Fig 2). One cow in the uninfected control group (#8102) did not cluster closely with any group and was removed in downstream analyses (Fig 2A). Outliers were expected since these cows were not age matched and were acquired from farms outside of our facility, where the cows were naturally infected with MAP. However, despite all the animals coming from different outside sources at different stages of disease, the samples differentiated according to their disease status (Fig 2B).

Bottom Line: The ICV is known to be a primary site of MAP colonization and provides an ideal location to identify genes that are relevant to the progression of this disease.Interpretation of the gene expression data was performed using pathway analysis and gene ontology categories containing multiple differentially expressed genes.The results from the comparison between clinical and subclinical animals indicate recruitment of neutrophils, up regulation of lysosomal peptidases, increase in immune cell transendothelial migration, and modifications of the extracelluar matrix.

View Article: PubMed Central - PubMed

Affiliation: USDA-Agricultural Research Service (ARS), National Animal Disease Center, Ames, Iowa, United States of America.

ABSTRACT
Johne's disease is a chronic infection of the small intestine caused by Mycobacterium avium subspecies paratuberculosis (MAP), an intracellular bacterium. The events of pathogen survival within the host cell(s), chronic inflammation and the progression from asymptomatic subclinical stage to an advanced clinical stage of infection, are poorly understood. This study examines gene expression in the ileocecal valve (ICV) of Holstein dairy cows at different stages of MAP infection. The ICV is known to be a primary site of MAP colonization and provides an ideal location to identify genes that are relevant to the progression of this disease. RNA was prepared from ICV tissues and RNA-Seq was used to compare gene transcription between clinical, subclinical, and uninfected control animals. Interpretation of the gene expression data was performed using pathway analysis and gene ontology categories containing multiple differentially expressed genes. Results demonstrated that many of the pathways that had strong differential gene expression between uninfected control and clinical cows were related to the immune system, such as the T- and B-cell receptor signaling, apoptosis, NOD-like receptor signaling, and leukocyte transendothelial migration pathways. In contrast, the comparison of gene transcription between control and subclinical cows identified pathways that were primarily involved in metabolism. The results from the comparison between clinical and subclinical animals indicate recruitment of neutrophils, up regulation of lysosomal peptidases, increase in immune cell transendothelial migration, and modifications of the extracelluar matrix. This study provides important insight into how cattle respond to a natural MAP infection at the gene transcription level within a key target tissue for infection.

No MeSH data available.


Related in: MedlinePlus