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Whole blood transcriptomic analysis of beef cattle at arrival identifies potential predictive molecules and mechanisms that indicate animals that naturally resist bovine respiratory disease

ABSTRACT: Whole blood transcriptomic analysis of beef cattle at arrival identifies potential predictive molecules and mechanisms that indicate animals that naturally resist bovine respiratory disease

PROVIDER: PRJNA561508 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10027332_1.fastq.gz	Fastqsanger.gz
	SRR10027332_2.fastq.gz	Fastqsanger.gz
	SRR10027333_1.fastq.gz	Fastqsanger.gz
	SRR10027333_2.fastq.gz	Fastqsanger.gz
	SRR10027334_1.fastq.gz	Fastqsanger.gz

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Whole blood transcriptomic analysis of beef cattle at arrival identifies potential predictive molecules and mechanisms that indicate animals that naturally resist bovine respiratory disease

Project description:Objectives: Identify gene products that characterize the biological status of typical calves which have been recently weaned, transported, and co-mingled prior to arrival at stocker facilities in order to identify gene products associated with BRD resistance. Methods: Whole blood RNA profiles were generated via NGS approach, using an Illumina HiSeq 3000. Individual samples were processed using an adaptation of the Revised Tuxedo Suite protocol (Tuxedo 2), then analyzed in R using edgeR and DESeq2 with likelihood-ratio testing. Genes were considered differentially expressed with an FDR cutoff of 0.10. qRT-PCR validation was performed using a SYBR green assay. Results: 135 differentially expressed genes were identified between healthy and BRD animals; 36 were shared between edgeR and DESeq2. Biological processes, using the 36 DEGs, were identified to be involved with inflammation, defense response, macrophage function, and lipoxin metabolism/biosynthesis. Enriched pathways of the 36 DEGs were involving SPM synthesis and angiotensinogen metabolism to angiotensins. Genes increased in diseased animals had known function towards anitmicrobial activity. Conlusions: Our analysis has provided, for the first time, a list of whole blood molecular biomarkers that may predict disease risk in the first 28 days of stocker cattle arrival. We identified pathways related to immune response, inflammatory mediation, metabolic processes, and stress regulation. Using whole blood transcriptomic analysis, this study provides an insight to host immunity in response to BRD.

2020-01-14 | GSE136176 | GEO

Whole blood transcriptomic analysis of beef cattle at arrival identifies potential predictive molecules and mechanisms that indicate animals that naturally resist bovine respiratory disease.

Project description:Bovine respiratory disease (BRD) is a multifactorial disease complex and the leading infectious disease in post-weaned beef cattle. Clinical manifestations of BRD are recognized in beef calves within a high-risk setting, commonly associated with weaning, shipping, and novel feeding and housing environments. However, the understanding of complex host immune interactions and genomic mechanisms involved in BRD susceptibility remain elusive. Utilizing high-throughput RNA-sequencing, we contrasted the at-arrival blood transcriptomes of 6 beef cattle that ultimately developed BRD against 5 beef cattle that remained healthy within the same herd, differentiating BRD diagnosis from production metadata and treatment records. We identified 135 differentially expressed genes (DEGs) using the differential gene expression tools edgeR and DESeq2. Thirty-six of the DEGs shared between these two analysis platforms were prioritized for investigation of their relevance to infectious disease resistance using WebGestalt, STRING, and Reactome. Biological processes related to inflammatory response, immunological defense, lipoxin metabolism, and macrophage function were identified. Production of specialized pro-resolvin mediators (SPMs) and endogenous metabolism of angiotensinogen were increased in animals that resisted BRD. Protein-protein interaction modeling of gene products with significantly higher expression in cattle that naturally acquire BRD identified molecular processes involving microbial killing. Accordingly, identification of DEGs in whole blood at arrival revealed a clear distinction between calves that went on to develop BRD and those that resisted BRD. These results provide novel insight into host immune factors that are present at the time of arrival that confer protection from BRD.

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Multipopulational transcriptome analysis of beef cattle at arrival to identify and further validate candidate biomarkers for predicting clinical bovine respiratory disease

Project description:Objective: Classify and further validate BRD-associated genes and mechanisms found to be differentially expressed at facility arrival in post-weaned beef cattle from multiple independent populations. Our approach was to profile and compare at-arrival whole blood transcriptomes of post-weaned beef cattle that failed to develop symptoms associated with clinical BRD and cattle that ultimately were diagnosed and treated for clinical BRD within the first 28 days of facility arrival, further stratifying diseased animals into severity cohorts. Methods: Whole blood RNA profiles were generated via NGS approach, using an Illumina Novaseq 6000. Individual samples were processed using an adaptation of the Revised Tuxedo Suite protocol (Tuxedo 2), then analyzed in R using edgeR with likelihood-ratio testing. Genes were considered differentially expressed with an FDR cutoff of 0.05. Downstream analysis involved PCA, gene ontology term enrichment, pathway analysis, protein-protein interaction networking, and IPA. Results: 132 differentially expressed genes were identified between all three cohorts. Biological processes and pathways primarily involved neutrophilic activity, antimicrobial killing, cell cornification, and inflammatory signaling/regulation. Conlusions: This study corroborated genes and pathways identified in our previous work, while providing novel genes and pathways for future analysis.

2021-12-13 | GSE161396 | GEO

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2020-12-31 | GSE150706 | GEO

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Xenopus Piwi protein associated transcripts indicate regulation beyond transposons

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Blood-Derived CD4 T Cells Naturally Resist Pyroptosis during Abortive HIV-1 Infection.

Project description:Progression to AIDS is driven by CD4 T cell depletion, mostly involving pyroptosis elicited by abortive HIV infection of CD4 T cells in lymphoid tissues. Inefficient reverse transcription in these cells leads to cytoplasmic accumulation of viral DNAs that are detected by the DNA sensor IFI16, resulting in inflammasome assembly, caspase-1 activation, and pyroptosis. Unexpectedly, we found that peripheral blood-derived CD4 T cells naturally resist pyroptosis. This resistance is partly due to their deeper resting state, resulting in fewer HIV-1 reverse transcripts and lower IFI16 expression. However, when co-cultured with lymphoid-derived cells, blood-derived CD4 T cells become sensitized to pyroptosis, likely recapitulating interactions occurring within lymphoid tissues. Sensitization correlates with higher levels of activated NF-?B, IFI16 expression, and reverse transcription. Blood-derived lymphocytes purified from co-cultures lose sensitivity to pyroptosis. These differences highlight how the lymphoid tissue microenvironment encountered by trafficking CD4 T lymphocytes dynamically shapes their biological response to HIV.

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