LPS-induced modules of co-expressed genes in equine peripheral blood mononuclear cells

Pacholewska, Alicja; Marti, Eliane Isabelle; Leeb, Tosso; Jagannathan, Vidhya; Gerber, Vinzenz (2017). LPS-induced modules of co-expressed genes in equine peripheral blood mononuclear cells. BMC Genomics, 18(1), p. 34. BioMed Central 10.1186/s12864-016-3390-y

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Background Lipopolysaccharide (endotoxin, LPS) is a strong inducer of the innate immune response. It is widespread in our environment, e.g. in house dust and contributes to asthma. Compared to humans, horses are even more sensitive to LPS. However, data on LPS effects on the equine transcriptome are very limited. Using RNA-seq we analysed LPS-induced differences in the gene expression in equine peripheral blood mononuclear cells at the gene and gene-network level in two half-sib families and one group of unrelated horses. Results 24 h-LPS challenge of equine immune cells resulted in substantial changes in the transcriptomic profile (1,265 differentially expressed genes) showing partial overlap with human data. One of the half-sib families showed a specific response different from the other two groups of horses. We also identified co-expressed gene modules that clearly differentiated 24 h-LPS- from non-stimulated samples. These modules consisted of 934 highly interconnected genes and included genes involved in the immune response (e.g. IL6, CCL22, CXCL6, CXCL2), however, none of the top ten hub genes of the modules have been annotated as responsive to LPS in gene ontology. Conclusions Using weighted gene co-expression network analysis we identified ten co-expressed gene modules significantly regulated by in vitro stimulation with LPS. Apart from 47 genes (5%) all other genes highly interconnected within the most up- and down-regulated modules were also significantly differentially expressed (FDR < 0.05). The LPS-regulated module hub genes have not yet been described as having a role in the immune response to LPS (e.g. VAT1 and TTC25).

Item Type:

Journal Article (Original Article)

Division/Institute:

05 Veterinary Medicine > Department of Clinical Veterinary Medicine (DKV) > Equine Clinic
05 Veterinary Medicine > Department of Clinical Veterinary Medicine (DKV)
05 Veterinary Medicine > Department of Clinical Research and Veterinary Public Health (DCR-VPH) > Experimental Clinical Research
05 Veterinary Medicine > Department of Clinical Research and Veterinary Public Health (DCR-VPH) > Institute of Genetics
05 Veterinary Medicine > Department of Clinical Research and Veterinary Public Health (DCR-VPH)

UniBE Contributor:

Pacholewska, Alicja Elzbieta; Marti, Eliane Isabelle; Leeb, Tosso; Jagannathan, Vidya and Gerber, Vinzenz

Subjects:

500 Science > 570 Life sciences; biology
500 Science > 590 Animals (Zoology)
600 Technology > 610 Medicine & health

ISSN:

1471-2164

Publisher:

BioMed Central

Funders:

[4] Swiss National Science Foundation
[107] Swiss Institute of Equine Medicine Research

Projects:

[751] Immunology and genetics of equine recurrent airway obstruction and defence against nematodes
[752] Pathogenetic and immunological aspects of equine allergic diseases in relationship to their genetic basis

Language:

English

Submitter:

Alicja Elzbieta Pacholewska

Date Deposited:

20 Mar 2017 09:09

Last Modified:

20 Mar 2017 09:09

Publisher DOI:

10.1186/s12864-016-3390-y

PubMed ID:

28056766

Uncontrolled Keywords:

Lipopolysaccharides; LPS; Differential expression; Gene modules; WGCNA; Horse; RNA-seq

BORIS DOI:

10.7892/boris.92598

URI:

https://boris.unibe.ch/id/eprint/92598

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