Single-cell transcriptomic and chromatin accessibility analyses of dairy cattle peripheral blood mononuclear cells and their responses to lipopolysaccharide View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2022-04-30

AUTHORS

Yahui Gao, Jianbin Li, Gaozhan Cai, Yujiao Wang, Wenjing Yang, Yanqin Li, Xiuxin Zhao, Rongling Li, Yundong Gao, Wenbin Tuo, Ransom L. Baldwin, Cong-jun Li, Lingzhao Fang, George E. Liu

ABSTRACT

BackgroundGram-negative bacteria are important pathogens in cattle, causing severe infectious diseases, including mastitis. Lipopolysaccharides (LPS) are components of the outer membrane of Gram-negative bacteria and crucial mediators of chronic inflammation in cattle. LPS modulations of bovine immune responses have been studied before. However, the single-cell transcriptomic and chromatin accessibility analyses of bovine peripheral blood mononuclear cells (PBMCs) and their responses to LPS stimulation were never reported.ResultsWe performed single-cell RNA sequencing (scRNA-seq) and single-cell sequencing assay for transposase-accessible chromatin (scATAC-seq) in bovine PBMCs before and after LPS treatment and demonstrated that seven major cell types, which included CD4 T cells, CD8 T cells, and B cells, monocytes, natural killer cells, innate lymphoid cells, and dendritic cells. Bioinformatic analyses indicated that LPS could increase PBMC cell cycle progression, cellular differentiation, and chromatin accessibility. Gene analyses further showed significant changes in differential expression, transcription factor binding site, gene ontology, and regulatory interactions during the PBMC responses to LPS. Consistent with the findings of previous studies, LPS induced activation of monocytes and dendritic cells, likely through their upregulated TLR4 receptor. NF-κB was observed to be activated by LPS and an increased transcription of an array of pro-inflammatory cytokines, in agreement that NF-κB is an LPS-responsive regulator of innate immune responses. In addition, by integrating LPS-induced differentially expressed genes (DEGs) with large-scale GWAS of 45 complex traits in Holstein, we detected trait-relevant cell types. We found that selected DEGs were significantly associated with immune-relevant health, milk production, and body conformation traits.ConclusionThis study provided the first scRNAseq and scATAC-seq data for cattle PBMCs and their responses to the LPS stimulation to the best of our knowledge. These results should also serve as valuable resources for the future study of the bovine immune system and open the door for discoveries about immune cell roles in complex traits like mastitis at single-cell resolution. More... »

PAGES

338

References to SciGraph publications

  • 2020-07-03. Epigenomics and genotype-phenotype association analyses reveal conserved genetic architecture of complex traits in cattle and human in BMC BIOLOGY
  • 2004-09-28. Toll-like receptor control of the adaptive immune responses in NATURE IMMUNOLOGY
  • 2014-06-11. Single-cell RNA-seq reveals dynamic paracrine control of cellular variation in NATURE
  • 2017-08-21. Reversed graph embedding resolves complex single-cell trajectories in NATURE METHODS
  • 2017-10-09. SCENIC: single-cell regulatory network inference and clustering in NATURE METHODS
  • 2008-12-29. WGCNA: an R package for weighted correlation network analysis in BMC BIOINFORMATICS
  • 2019-01-14. Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage in NATURE IMMUNOLOGY
  • 2017-01-16. Massively parallel digital transcriptional profiling of single cells in NATURE COMMUNICATIONS
  • 2017-05-25. Multiple Trait Covariance Association Test Identifies Gene Ontology Categories Associated with Chill Coma Recovery Time in Drosophila melanogaster in SCIENTIFIC REPORTS
  • 2017-05-12. Exploring the genetic architecture and improving genomic prediction accuracy for mastitis and milk production traits in dairy cattle by mapping variants to hepatic transcriptomic regions responsive to intra-mammary infection in GENETICS SELECTION EVOLUTION
  • 2013-05-19. Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells in NATURE
  • 1995-12. Molecular mechanisms of endotoxin activity in ARCHIVES OF MICROBIOLOGY
  • 2021-11-01. Single-cell chromatin state analysis with Signac in NATURE METHODS
  • 2017-07-31. Simultaneous epitope and transcriptome measurement in single cells in NATURE METHODS
  • 2016-01-05. Increased prediction accuracy using a genomic feature model including prior information on quantitative trait locus regions in purebred Danish Duroc pigs in BMC GENOMIC DATA
  • 2012-09-05. An integrated encyclopedia of DNA elements in the human genome in NATURE
  • 2019-06-18. Functional annotation and Bayesian fine-mapping reveals candidate genes for important agronomic traits in Holstein bulls in COMMUNICATIONS BIOLOGY
  • 2020-03-25. Construction of a human cell landscape at single-cell level in NATURE
  • 2020-01-13. GWAS and fine-mapping of livability and six disease traits in Holstein cattle in BMC GENOMICS
  • 2019-12-23. Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression in GENOME BIOLOGY
  • 2017-03-30. Integrating Sequence-based GWAS and RNA-Seq Provides Novel Insights into the Genetic Basis of Mastitis and Milk Production in Dairy Cattle in SCIENTIFIC REPORTS
  • 2009-03-05. Lipopolysaccharide-induced early response genes in bovine peripheral blood mononuclear cells implicate GLG1/E-selectin as a key ligand–receptor interaction in FUNCTIONAL & INTEGRATIVE GENOMICS
  • 2017-12-11. Multiplexed droplet single-cell RNA-sequencing using natural genetic variation in NATURE BIOTECHNOLOGY
  • 2008-05-30. Divergence of canonical danger signals: The genome-level expression patterns of human mononuclear cells subjected to heat shock or lipopolysaccharide in BMC IMMUNOLOGY
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1186/s12864-022-08562-0

    DOI

    http://dx.doi.org/10.1186/s12864-022-08562-0

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1147539637

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/35501711


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