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Global Gene Networks in Porcine Alveolar Macrophage Cells, 3D4/31, Stimulated with Antigenic Epitopes of Actinobacillus pleuropneumoniae ApxIA, IIA and IVA

ABSTRACT: Global Gene Networks in Porcine Alveolar Macrophage Cells, 3D4/31, Stimulated with Antigenic Epitopes of Actinobacillus pleuropneumoniae ApxIA, IIA and IVA

PROVIDER: PRJNA477927 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR7429150_1.fastq.gz	Fastqsanger.gz
	SRR7429150_2.fastq.gz	Fastqsanger.gz
	SRR7429151_1.fastq.gz	Fastqsanger.gz
	SRR7429151_2.fastq.gz	Fastqsanger.gz
	SRR7429152_1.fastq.gz	Fastqsanger.gz

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Global Gene Networks in Porcine Alveolar Macrophage Cells, 3D4/31, Stimulated with Antigenic Epitopes of Actinobacillus pleuropneumoniae ApxIA, IIA and IVA

Project description:Purpose: The goals of this study are to examine the host response with porcine alveolar macrophages (PAMs) cells, 3D4/31 by stimulation of four antigenic epitopes of App exotoxins, ApxIA, IIA and IVA. Methods: total RNA profiles of porcine alveolar macrophage cells stimulated with ApxIA Ct, ApxIIA Nt, ApxIVA C1, ApxIVA C2 and DPBS were generated by transcriptome sequencing, in duplicate, using HiSeq4000 platform.The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by Cufflinks. qRT–PCR validation was performed using SYBR Green assays Results: RNA sequencing yielded 617 million 101 bp paired-end clean reads, varying from 28 to 32 million for each sample. Among the clean reads, approximately 95.24% clean reads were uniquely mapped onto the version 11.1 of the sus scrofa. Gene expression was quantified through FPKM conversion of raw reads. The 15,269 genes (mean FPKM of the 10 samples > 0) were considered as expressed in PAMs over the 30,511 gene annotations. RNA-seq data confirmed stable expression of 1 known housekeeping genes, and 5 of these were validated with qRT–PCR. RNA-seq data had a linear relationship with qRT–PCR for more than four orders of magnitude and a goodness of fit (R2) of 0.906. Conclusions: Transcriptional responses of the porcine alveolar macrophages (PAMs) stimulated with the antigenic epitopes of ApxIA, ApxIIA, and ApxIVA were analyzed to identify the precious mechanism of Apx toxins in the host. This study will be foundational to understanding the host response by Apx toxins.

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Project description:Actinobacillus pleuropneumoniae (App) is the causative agent of porcine pleuropneumonia. Although App produces several virulence factors, Apx toxins, the primary App virulence factors, have been the focus of numerous studies. However, the host response against the Apx toxins has not been elucidated at the transcriptomic level. Therefore, in this study, we examined the response of an immortalized porcine alveolar macrophage cell line (IPAM 3D4/31) to four antigenic epitopes of the App exotoxins, ApxIA, IIA and IVA. The antigenic epitopes of the Apx toxins (ApxIA Ct, ApxIIA Nt, ApxIVA C1 and ApxIV C2) were determined by an in-silico antigenicity prediction analysis. Gene expression in IPAMs was analyzed by RNA-Seq after treatment with the four proteins for 24?h. A total of 15,269 DEGs were observed to be associated with cellular and metabolic processes in the GO category Biological Process and nuclear receptors and apoptosis signaling in IPA analyses. These DEGs were also related to M2 macrophage polarization and apoptosis in IPAMs. These host transcriptional analyses present novel global gene networks of the host response to treatment with Apx toxins.

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