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Relationships between immune gene expression and circulating cytokine levels in wild house mice

Citation

Young, Stuart et al. (2021), Relationships between immune gene expression and circulating cytokine levels in wild house mice, Dryad, Dataset, https://doi.org/10.5061/dryad.n8pk0p2t8

Abstract

1. Quantitative PCR (qPCR) has been commonly used to measure gene expression in a number of research contexts, but the measured RNA concentrations do not always represent the concentrations of active proteins which they encode. This can be due to transcriptional regulation or post-translational modifications, or localisation of immune environments, as can occur during infection. However, in studies using free-living non-model species, such as in ecoimmunological research, qPCR may be the only available option to measure a parameter of interest, and so understanding the quantitative link between gene expression and associated effector protein levels is vital.

2. Here we use qPCR to measure concentrations of RNA from mesenteric lymph node (MLN) and spleen tissue, and multiplex ELISA of blood serum to measure circulating cytokine concentrations in a wild population of a model species, Mus musculus domesticus.

3. Few significant correlations were found between gene expression levels and circulating cytokines of the same immune genes or proteins, or related functional groups. Where significant correlations were observed, these were most frequently within the measured tissue (i.e. the expression levels of genes measured from spleen tissue were more likely to correlate with each other rather than with genes measured from MLN tissue, or with cytokine concentrations measured from blood).

4. Potential reasons for discrepancies between measures, including differences in decay rates and transcriptional regulation networks are discussed. We highlight the relative usefulness of different measures under different research questions, and consider what might be inferred from immune assays.

Methods

Gene expression levels were obtained by qPCR from spleen and mesenteric lymph node tissue. Concentrations of circulating cytokines were measured by multiplex ELISA of blood serum. Groupings by functional arm of the immune system and inflammation type were done by PCA. All samples were from wild Mus musculus domesticus trapped on the Isle of May, Scotland between August 2014 and October 2016. For full details of methodology, please refer to: Young et al. 2020, "Relationships between immune gene expression and circulating cytokine levels in wild house mice", Ecology and Evolution.

Usage Notes

Raw gene expression and circulating cytokine data

all_genes_cytokines.csv contains gene expression data and circulating cytokine concentrations for all immue genes/cytokines measured. The "Cyt" prefix refers to circulating cytokines, "MLN" refers to gene expression data from mesenteric lymph node tissue, and "Spleen" refers to gene expression data from spleen tissue. Gene expression data is measured as ΔΔCT, circulating cytokines are measured as pg ml-1. "id" refers to the individual mouse from which samples came. 

Inflammation type

Immune genes and circulating cytokines were grouped by inflammation type (pro-inflammatory or anti-inflammatory) by PCA. inflamation_type.csv contains the PC1 scores of these groupings. Here, "Cyt.pro" refers to pro-inflammatory circulating cytokines, for example. For full details of these groupings, see Young et al. 2020, "Relationships between immune gene expression and circulating cytokine levels in wild house mice", Ecology and Evolution.

Response type

The genes and cytokines were further grouped according to the functional arms of the immune system. response_type.csv contains the PC1 scores of these groupings. Young et al. 2020, "Relationships between immune gene expression and circulating cytokine levels in wild house mice", Ecology and Evolution.

Funding

Biotechnology and Biological Sciences Research Council, Award: BB/J014508/1