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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: 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.

ORGANISM(S): Bos taurus

PROVIDER: GSE136176 | GEO | 2020/01/14

REPOSITORIES: GEO

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Project description:Purpose: Next-generation sequencing (NGS) was used to select genes potentially associated with fiber-type distribution and cell size in porcine muscle tissue. Methods: The histological profile of the longissimus lumborum muscle was establish by method involving detection of NADPH dehydrogenase (diaphorase) and immunohistochemically detection of myosin chains. The muscle transcriptome sequencing was performed for 11 pigs using Illumina HiScan SQ in 50 single-end cycles. The quantifying transcript abundances was made using the RSEM supported by STAR aligner. The raw reads were aligned to the Sus scrofa reference genome (assembly Sscrofa10.2). Differentially expressed genes were detected by edgeR, baySeq and DESeq2. The RNA-seq results were validated using by qPCR. Results: The RNA-seq approach allows to identify 397 differentially expressed genes (DEGs) indicated as significant (FDR<0.05) using three software: DESeq2, edgeR and baySeq. Detected genes and pathways deregulated in muscle depend on tissue microstructure were associated with metabolic processes â?? 158 genes; cellular processes â?? 122; biological regulation â?? 62; localization â?? 51 and 35 genes with developmental processes. The detected DEGs were included in such pathways as: PI3K-Akt; FoxO and MAPK signaling pathways, regulation of actin cytoskeleton, lysine degradation and insulin signaling pathway as well as in mTOR and Hippo signaling. Conclusions: This results highlight the mainly metabolic pathways related with glucose metabolism and contraction processes of muscle cells. The comparison of whole gene expression profiles between muscles characterized by different fiber-type distribution showed that processes of growth and proliferation of different fiber types are determined by diverse molecular mechanism, which conditioned the unique histological structure of muscle tissue. The muscle (longissimus lumborum) transcriptome sequencing was performed for 11 pigs using Illumina HiScan SQ in 50 single-end cycles and in five technical repetitions.

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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

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